Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold198

Parameters: 2 7 7 80 10 50 500

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500

Length: 1589021
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.28

Warning! 220217 characters in sequence are not A, C, G, or T


File 5 of 5

Found at i:1067786 original size:17 final size:17

Alignment explanation

Indices: 1067732--1067789 Score: 50 Period size: 17 Copynumber: 3.4 Consensus size: 17 1067722 CTGTAAACTT 1067732 GTTTGAAGCAGTGTGAC 1 GTTTGAAGCAGTGTGAC * * 1067749 ATTTGAA-C--TGTAAAC 1 GTTTGAAGCAGTGT-GAC 1067764 TTGTTTGAAGCAGTGTGAC 1 --GTTTGAAGCAGTGTGAC 1067783 GTTTGAA 1 GTTTGAA 1067790 CTGTAAACTG Statistics Matches: 31, Mismatches: 4, Indels: 12 0.66 0.09 0.26 Matches are distributed among these distances: 14 3 0.10 15 2 0.06 16 1 0.03 17 19 0.61 18 1 0.03 19 2 0.06 20 3 0.10 ACGTcount: A:0.28, C:0.10, G:0.28, T:0.34 Consensus pattern (17 bp): GTTTGAAGCAGTGTGAC Found at i:1067788 original size:34 final size:34 Alignment explanation

Indices: 1067574--1067798 Score: 181 Period size: 34 Copynumber: 6.3 Consensus size: 34 1067564 TAAAATCCTA 1067574 AACTGTAAACTTGTTTGAAGCAGTGTGACATTTG 1 AACTGTAAACTTGTTTGAAGCAGTGTGACATTTG * * ** ** 1067608 AATTGTAAACTTTTCTTTCTA-CTAGATGTG-TGTTATG 1 AACTGTAAAC--TTGTTTGAAGC-AG-TGTGACATT-TG 1067645 CAAACTGTAAACTTGTTTGAAGCAGTGTGACATTTG 1 --AACTGTAAACTTGTTTGAAGCAGTGTGACATTTG * * ** 1067681 AACTGTAAACTT-TTCT--ACCTACTAGATTTCTATTATG 1 AACTGTAAACTTGTT-TGAAGC-AGT-G-TGAC-ATT-TG 1067718 CAAACTGTAAACTTGTTTGAAGCAGTGTGACATTTG 1 --AACTGTAAACTTGTTTGAAGCAGTGTGACATTTG * 1067754 AACTGTAAACTTGTTTGAAGCAGTGTGACGTTTG 1 AACTGTAAACTTGTTTGAAGCAGTGTGACATTTG 1067788 AACTGTAAACT 1 AACTGTAAACT 1067799 GTTCTACTTT Statistics Matches: 150, Mismatches: 21, Indels: 40 0.71 0.10 0.19 Matches are distributed among these distances: 32 2 0.01 33 4 0.03 34 67 0.45 35 3 0.02 36 21 0.14 37 21 0.14 38 3 0.02 39 23 0.15 40 4 0.03 41 2 0.01 ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38 Consensus pattern (34 bp): AACTGTAAACTTGTTTGAAGCAGTGTGACATTTG Found at i:1068004 original size:23 final size:24 Alignment explanation

Indices: 1067978--1068035 Score: 68 Period size: 23 Copynumber: 2.5 Consensus size: 24 1067968 TAGTGGTTCC 1067978 AGGTCAAGGTCAAAT-ACATAT-A 1 AGGTCAAGGTCAAATAACATATCA * 1068000 TAGGTCAAGG-CCAATAACATATCA 1 -AGGTCAAGGTCAAATAACATATCA * 1068024 AGCTCAAGGTCA 1 AGGTCAAGGTCA 1068036 TATGCATGAA Statistics Matches: 29, Mismatches: 3, Indels: 5 0.78 0.08 0.14 Matches are distributed among these distances: 22 4 0.14 23 23 0.79 24 2 0.07 ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21 Consensus pattern (24 bp): AGGTCAAGGTCAAATAACATATCA Found at i:1075445 original size:21 final size:21 Alignment explanation

Indices: 1075421--1075509 Score: 108 Period size: 21 Copynumber: 4.2 Consensus size: 21 1075411 GTGTTTTATG * * 1075421 TATATGCAATAGTAATATCAT 1 TATATGCAGTAGTAACATCAT * 1075442 TATATGCAGTGGTAACATCAT 1 TATATGCAGTAGTAACATCAT * 1075463 TACATGCAGT-GCTAACATCAT 1 TATATGCAGTAG-TAACATCAT * * 1075484 TATATGCAGTACTAAAATCAT 1 TATATGCAGTAGTAACATCAT 1075505 TATAT 1 TATAT 1075510 ACTATTATTT Statistics Matches: 59, Mismatches: 7, Indels: 4 0.84 0.10 0.06 Matches are distributed among these distances: 20 1 0.02 21 58 0.98 ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35 Consensus pattern (21 bp): TATATGCAGTAGTAACATCAT Found at i:1077528 original size:21 final size:21 Alignment explanation

Indices: 1077502--1077541 Score: 80 Period size: 21 Copynumber: 1.9 Consensus size: 21 1077492 AATGATGTAC 1077502 GTTAGCACTGCATATAATGAT 1 GTTAGCACTGCATATAATGAT 1077523 GTTAGCACTGCATATAATG 1 GTTAGCACTGCATATAATG 1077542 CTATTACTAT Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 19 1.00 ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33 Consensus pattern (21 bp): GTTAGCACTGCATATAATGAT Found at i:1081301 original size:68 final size:68 Alignment explanation

Indices: 1081218--1081351 Score: 214 Period size: 68 Copynumber: 2.0 Consensus size: 68 1081208 GATCATCTCC * * * * 1081218 TTGTACATGATGCTCTCTTACCATTGTATTAAGATAATCCATTCTCTCTGTATGACTGATCACCT 1 TTGTACATGATGCTCTCTTACCATTATATTAAGACAATCCATTCTCTCTGTAGGACTGATAACCT 1081283 CAT 66 CAT * * 1081286 TTGTACATGATGCTCTGTTACCATTATATTAAGACAATCCATTCTTTCTGTAGGACTGATAACCT 1 TTGTACATGATGCTCTCTTACCATTATATTAAGACAATCCATTCTCTCTGTAGGACTGATAACCT 1081351 C 66 C 1081352 CTTCGCTGTC Statistics Matches: 60, Mismatches: 6, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 68 60 1.00 ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39 Consensus pattern (68 bp): TTGTACATGATGCTCTCTTACCATTATATTAAGACAATCCATTCTCTCTGTAGGACTGATAACCT CAT Found at i:1081477 original size:21 final size:21 Alignment explanation

Indices: 1081453--1081527 Score: 82 Period size: 21 Copynumber: 3.6 Consensus size: 21 1081443 AACTCTATTG * 1081453 TACACCCCACAGGTAAATTTT 1 TACACCCCACAGGTAAATTTA * 1081474 TACACCCCTA-AAGTAACA-TTA 1 TACACCCC-ACAGGTAA-ATTTA * 1081495 TACACCCCACAGGTAAATTTC 1 TACACCCCACAGGTAAATTTA * 1081516 TACACCCAACAG 1 TACACCCCACAG 1081528 CATCATTGTA Statistics Matches: 45, Mismatches: 5, Indels: 8 0.78 0.09 0.14 Matches are distributed among these distances: 20 2 0.04 21 41 0.91 22 2 0.04 ACGTcount: A:0.37, C:0.32, G:0.08, T:0.23 Consensus pattern (21 bp): TACACCCCACAGGTAAATTTA Found at i:1081512 original size:42 final size:41 Alignment explanation

Indices: 1081449--1081744 Score: 286 Period size: 42 Copynumber: 7.2 Consensus size: 41 1081439 CATCAACTCT * 1081449 ATTGTACACCCCACAGGTAAATTTTTACACCCCTAA-AGTAAC 1 ATTGTACACCCCACAGGTAAA-TTGTACACCCC-AACAGTAAC * * * * 1081491 ATTATACACCCCACAGGTAAATTTCTACA-CCCAACAGCATC 1 ATTGTACACCCCACAGGTAAA-TTGTACACCCCAACAGTAAC * * 1081532 ATTGTACACCCCAC------ATTGTACACCCCAACAGCAAT 1 ATTGTACACCCCACAGGTAAATTGTACACCCCAACAGTAAC * * * 1081567 ATTGTACATCTCACAGGTAATATTGTACACCCCAAAAGTAAC 1 ATTGTACACCCCACAGGTAA-ATTGTACACCCCAACAGTAAC ** 1081609 ATTGTACATTCCACAGGTAACATTGTACACCCCAACAGTAAC 1 ATTGTACACCCCACAGGTAA-ATTGTACACCCCAACAGTAAC * * 1081651 ATTGTACACCCCACAGGTAACATTGTACACCCCAACAGCAAT 1 ATTGTACACCCCACAGGTAA-ATTGTACACCCCAACAGTAAC * * * * * 1081693 ATTGTACATCTCACAGGTAACATTGTAC-TCCCTACAGTTAAA 1 ATTGTACACCCCACAGGTAA-ATTGTACACCCCAACAG-TAAC 1081735 ATTGTACACC 1 ATTGTACACC 1081745 TCAACAGTAA Statistics Matches: 216, Mismatches: 28, Indels: 20 0.82 0.11 0.08 Matches are distributed among these distances: 34 6 0.03 35 23 0.11 40 2 0.01 41 27 0.12 42 158 0.73 ACGTcount: A:0.35, C:0.30, G:0.10, T:0.24 Consensus pattern (41 bp): ATTGTACACCCCACAGGTAAATTGTACACCCCAACAGTAAC Found at i:1081550 original size:14 final size:14 Alignment explanation

Indices: 1081531--1081558 Score: 56 Period size: 14 Copynumber: 2.0 Consensus size: 14 1081521 CCAACAGCAT 1081531 CATTGTACACCCCA 1 CATTGTACACCCCA 1081545 CATTGTACACCCCA 1 CATTGTACACCCCA 1081559 ACAGCAATAT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 14 1.00 ACGTcount: A:0.29, C:0.43, G:0.07, T:0.21 Consensus pattern (14 bp): CATTGTACACCCCA Found at i:1081907 original size:21 final size:21 Alignment explanation

Indices: 1081544--1081938 Score: 268 Period size: 21 Copynumber: 18.6 Consensus size: 21 1081534 TGTACACCCC * 1081544 ACATTGTACACCCCAACA-GCA 1 ACATTGTACACCCC-ACAGGTA * * * 1081565 ATATTGTACATCTCACAGGTA 1 ACATTGTACACCCCACAGGTA * * * 1081586 ATATTGTACACCCCAAAAGTA 1 ACATTGTACACCCCACAGGTA ** 1081607 ACATTGTACATTCCACAGGTA 1 ACATTGTACACCCCACAGGTA 1081628 ACATTGTACACCCCAACA-GTA 1 ACATTGTACACCCC-ACAGGTA 1081649 ACATTGTACACCCCACAGGTA 1 ACATTGTACACCCCACAGGTA * 1081670 ACATTGTACACCCCAACA-GCA 1 ACATTGTACACCCC-ACAGGTA * * * 1081691 ATATTGTACATCTCACAGGTA 1 ACATTGTACACCCCACAGGTA * * * 1081712 ACATTGTACTCCCTACAGTTA 1 ACATTGTACACCCCACAGGTA * * 1081733 AAATTGTACACCTCAACA-GTA 1 ACATTGTACACC-CCACAGGTA * *** 1081754 ACGTTGTACACCTGGCAGGTA 1 ACATTGTACACCCCACAGGTA * * 1081775 ATATTGTACTGTACACCCAACA-ATA 1 ACATTGTAC---AC-CCC-ACAGGTA ** 1081800 ACATTAAACACCCCACAGGTA 1 ACATTGTACACCCCACAGGTA * 1081821 AAATTGTACACCCCAACA-GTA 1 ACATTGTACACCCC-ACAGGTA * * * 1081842 ATATTATACATCCCACAGGTA 1 ACATTGTACACCCCACAGGTA * * * 1081863 ACATTGTACGCCCTAACA-GCA 1 ACATTGTACACCC-CACAGGTA * * 1081884 ATATTGTACATCCCACAGGTA 1 ACATTGTACACCCCACAGGTA * * * 1081905 ATATTATACA-CCCAGTAGGTGA 1 ACATTGTACACCCCA-CAGGT-A 1081927 A-ATTGTACACCC 1 ACATTGTACACCC 1081939 TTCAGAGTGA Statistics Matches: 289, Mismatches: 65, Indels: 39 0.74 0.17 0.10 Matches are distributed among these distances: 20 24 0.08 21 230 0.80 22 22 0.08 24 2 0.01 25 9 0.03 26 2 0.01 ACGTcount: A:0.36, C:0.27, G:0.12, T:0.24 Consensus pattern (21 bp): ACATTGTACACCCCACAGGTA Found at i:1081915 original size:151 final size:152 Alignment explanation

Indices: 1081632--1081916 Score: 398 Period size: 151 Copynumber: 1.9 Consensus size: 152 1081622 CAGGTAACAT * ** * * 1081632 TGTACACCCCAACAGTAACATTGTACACCCCACAGGTAACATTGTACACCCCAACAGCAATATTG 1 TGTACACCCCAACAATAACATTAAACACCCCACAGGTAAAATTGTACACCCCAACAGCAATATTA * * * * * 1081697 TACATCTCACAGGTAACATTGTACTCCCTACAGTTAAAATTGTACACCTCAACAGTAACGTTGTA 66 TACATCCCACAGGTAACATTGTACGCCCTACAGTCAAAATTGTACACCTCAACAGTAACATTATA 1081762 CACCTGGCAGGTAATATTGTAC 131 CACCTGGCAGGTAATATTGTAC * 1081784 TGTACA-CCCAACAATAACATTAAACACCCCACAGGTAAAATTGTACACCCCAACAGTAATATTA 1 TGTACACCCCAACAATAACATTAAACACCCCACAGGTAAAATTGTACACCCCAACAGCAATATTA * * 1081848 TACATCCCACAGGTAACATTGTACGCCCTAACAG-CAATATTGTACATCC-C-ACAGGTAATATT 66 TACATCCCACAGGTAACATTGTACGCCCT-ACAGTCAAAATTGTACA-CCTCAACA-GTAACATT 1081910 ATACACC 128 ATACACC 1081917 CAGTAGGTGA Statistics Matches: 117, Mismatches: 13, Indels: 7 0.85 0.09 0.05 Matches are distributed among these distances: 150 3 0.03 151 102 0.87 152 12 0.10 ACGTcount: A:0.36, C:0.28, G:0.12, T:0.24 Consensus pattern (152 bp): TGTACACCCCAACAATAACATTAAACACCCCACAGGTAAAATTGTACACCCCAACAGCAATATTA TACATCCCACAGGTAACATTGTACGCCCTACAGTCAAAATTGTACACCTCAACAGTAACATTATA CACCTGGCAGGTAATATTGTAC Found at i:1082203 original size:30 final size:32 Alignment explanation

Indices: 1082167--1082228 Score: 94 Period size: 30 Copynumber: 2.0 Consensus size: 32 1082157 CTCAGTCTGA 1082167 ATCAGGTAATGTC-AGTGGGAC-A-ATTAATGC 1 ATCAGGTAATGTCAAG-GGGACAACATTAATGC 1082197 ATCAGGTAATGTCAAGGGGACAACATTAATGC 1 ATCAGGTAATGTCAAGGGGACAACATTAATGC 1082229 CCCTCATTTA Statistics Matches: 29, Mismatches: 0, Indels: 4 0.88 0.00 0.12 Matches are distributed among these distances: 30 18 0.62 31 3 0.10 32 8 0.28 ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24 Consensus pattern (32 bp): ATCAGGTAATGTCAAGGGGACAACATTAATGC Found at i:1083957 original size:31 final size:28 Alignment explanation

Indices: 1083919--1083994 Score: 91 Period size: 28 Copynumber: 2.6 Consensus size: 28 1083909 TCAGTCAGAA 1083919 CAAACAATTAGTCCAATGGATAACAACCATT 1 CAAACAATTAGTCCAATGG---ACAACCATT * 1083950 CAAACAATTAGTCCATTGGACAACCATT 1 CAAACAATTAGTCCAATGGACAACCATT * 1083978 CAGAA-ATTTAGTCCAAT 1 CA-AACAATTAGTCCAAT 1083995 TAACTGTGAT Statistics Matches: 41, Mismatches: 3, Indels: 5 0.84 0.06 0.10 Matches are distributed among these distances: 28 21 0.51 29 2 0.05 31 18 0.44 ACGTcount: A:0.42, C:0.22, G:0.11, T:0.25 Consensus pattern (28 bp): CAAACAATTAGTCCAATGGACAACCATT Found at i:1084780 original size:38 final size:38 Alignment explanation

Indices: 1084710--1084784 Score: 98 Period size: 38 Copynumber: 2.0 Consensus size: 38 1084700 CAGGAGTCAA * * ** 1084710 AGTGTATAAGTACCTTAAACTGAGACGTTTCTTCTCCT 1 AGTGAATAAATACCTTAAACTGAGACAATTCTTCTCCT 1084748 AGTGAATAAATACCTTAAACTCG-GACAATTCTTCTCC 1 AGTGAATAAATACCTTAAACT-GAGACAATTCTTCTCC 1084785 ATTCGTAGAT Statistics Matches: 32, Mismatches: 4, Indels: 2 0.84 0.11 0.05 Matches are distributed among these distances: 38 31 0.97 39 1 0.03 ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33 Consensus pattern (38 bp): AGTGAATAAATACCTTAAACTGAGACAATTCTTCTCCT Found at i:1087421 original size:28 final size:28 Alignment explanation

Indices: 1087396--1088324 Score: 1615 Period size: 28 Copynumber: 33.2 Consensus size: 28 1087386 ACCTACAGGA * 1087396 AGTGTACTATAGTTTGGTACTGACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG * 1087424 AGTGTATTATAGTTTGGTACTTACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG 1087452 AGTGTATTATAGTTTGGTACTGACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG * * 1087480 AGTGTACTATAGTTTGGTACTTACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG 1087508 AGTGTATTATAGTTTGGTACTGACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG * * * 1087536 AGTTTACTATAGTTTGGTACTTACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG 1087564 AGTGTATTATAGTTTGGTACTGACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG * 1087592 AGTGTAATATAGTTTGGTACTGACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG 1087620 AGTGTATTATAGTTTGGTACTGACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG * 1087648 AGTGTATTATAGTTTGGTACTTACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG 1087676 AGTGTATTATAGTTTGGTACTGACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG 1087704 AGTGTATTATAGTTTGGTACTGACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG * 1087732 AGTGTATTATAGTTTGGTACTTACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG * * 1087760 AGTGTATTGTAGTTTGGTACTTACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG * 1087788 AGTGTATTATAGTTTGGTACTTACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG * 1087816 AGTGTATTATAGTTTGTTACTGACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG * 1087844 AGTGTATTATAGTTTGGTACTTACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG 1087872 AGTGTATTATAGTTTGGTACTGACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG 1087900 AGTGTATTATAGTTTGGTACTGACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG * 1087928 AGTGTATTATAGTTTGGTACTTACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG * 1087956 AGTGTAATATAGTTTGGTACTGACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG * 1087984 AGTGTATTATAGTTTGGTACTTACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG 1088012 AGTGTATTATAGTTTGGTACTGACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG * 1088040 AGTGCATTATAGTTTGGTACTGACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG * 1088068 AGTGTAATATAGTTTGGTACTGACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG 1088096 AGTGTATTATAGTTTGGTACTGACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG * 1088124 AGTGTATTATACTTTGGTACTGACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG 1088152 AGTGTATTATAGTTTGGTACTGACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG * 1088180 AGTGTATTATAGTTTGTTACTGACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG * 1088208 AGTGTACTATAGTTTGGTACTGACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG * 1088236 AGTGTATTATAGTTTGGTACTTACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG 1088264 AGTGTATTATAGTTTGGTACTGACAGTG 1 AGTGTATTATAGTTTGGTACTGACAGTG * * * 1088292 AGTGTAGTATAGTTTGGTACTTACAGTA 1 AGTGTATTATAGTTTGGTACTGACAGTG 1088320 AGTGT 1 AGTGT 1088325 GTTGTAGACC Statistics Matches: 855, Mismatches: 46, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 28 855 1.00 ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40 Consensus pattern (28 bp): AGTGTATTATAGTTTGGTACTGACAGTG Found at i:1089260 original size:80 final size:80 Alignment explanation

Indices: 1089120--1089858 Score: 815 Period size: 80 Copynumber: 9.2 Consensus size: 80 1089110 GTTATGAAAA * * * * * * 1089120 ACTTTTGTACAATGCATGTCCTCACAAGCTT-AGACGACTTACTTTTGTACAATGCGTGTCATCA 1 ACTTTTGTACAATGCGTGTCCTCACGAG-TTGGGAGGACTTACTTTTGTACGATGCCTGTCATCA * 1089184 TTTGTTTGGAGGACTT 65 TTGGTTTGGAGGACTT * * * * 1089200 ACTTTCGTACAATGCGTGTCCTCACAAGTTGGGAGGACTTGCTTTTGTATGATGCCTGTCATCAT 1 ACTTTTGTACAATGCGTGTCCTCACGAGTTGGGAGGACTTACTTTTGTACGATGCCTGTCATCAT * * 1089265 TGGTTGGGTGGACTT 66 TGGTTTGGAGGACTT * * * * 1089280 ACTTTTGTACAATACATGTCCTCATGAGTTGGGAGGACTTACTTTTGTATGATGCCTGTCATCAT 1 ACTTTTGTACAATGCGTGTCCTCACGAGTTGGGAGGACTTACTTTTGTACGATGCCTGTCATCAT 1089345 TGGTTTGGAGGACTT 66 TGGTTTGGAGGACTT * ** * * 1089360 ACTTTCGTACAATGCAAGTCCTCACGAGTTGGGAGGACTTACTTTTGTATGATGCCTGTCATCAA 1 ACTTTTGTACAATGCGTGTCCTCACGAGTTGGGAGGACTTACTTTTGTACGATGCCTGTCATCAT 1089425 TGGTTTGGAGGACTT 66 TGGTTTGGAGGACTT ** * * 1089440 ACTTTCATACAATGCGTGTCCTCACGAGTTTGGAGGACTTACTTTTGTATGATGCCTGTCATCAT 1 ACTTTTGTACAATGCGTGTCCTCACGAGTTGGGAGGACTTACTTTTGTACGATGCCTGTCATCAT 1089505 TGG-TTGGAAGGACTT 66 TGGTTTGG-AGGACTT * * * * * * * ** * ** 1089520 ACTTTTGTACGATGTGTGTCATCATTG-GTTTGGAGGACTTACATTTGTACAATGTGTCTCCGCA 1 ACTTTTGTACAATGCGTGTCCTCA-CGAGTTGGGAGGACTTACTTTTGTACGATGCCTGTCATCA *** * * 1089584 AAAGTTGGGAGGACCT 65 TTGGTTTGGAGGACTT * * 1089600 ACTTTCGTACAATGCGTGTCCTCACGAGTTGGGAGGACTTACTTTTGTACGATGCATGTCATCAT 1 ACTTTTGTACAATGCGTGTCCTCACGAGTTGGGAGGACTTACTTTTGTACGATGCCTGTCATCAT 1089665 TGGTTTGGAGGACTT 66 TGGTTTGGAGGACTT * * * * ** * * * 1089680 ACTTTTGTACGATGTGTCTCCTCAAGAGTTGGGAGGACTTACTTTCATACAATGCATGTCCTCA- 1 ACTTTTGTACAATGCGTGTCCTCACGAGTTGGGAGGACTTACTTTTGTACGATGCCTGTCATCAT * * 1089744 CGAATTTGGAGGACTT 66 TG-GTTTGGAGGACTT * * * * * * 1089760 ACTTTTGTACAATGTGTGTCATCATTG-GTTTGGAGGACTTACTTTTTTA-GATGCGTGTCATCA 1 ACTTTTGTACAATGCGTGTCCTCA-CGAGTTGGGAGGACTTACTTTTGTACGATGCCTGTCATCA * 1089823 TTGATTTGGAGGACTT 65 TTGGTTTGGAGGACTT * 1089839 ACTTTTGTACGATGCGTGTC 1 ACTTTTGTACAATGCGTGTC 1089859 ATCATTGGCT Statistics Matches: 561, Mismatches: 90, Indels: 17 0.84 0.13 0.03 Matches are distributed among these distances: 79 50 0.09 80 506 0.90 81 5 0.01 ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37 Consensus pattern (80 bp): ACTTTTGTACAATGCGTGTCCTCACGAGTTGGGAGGACTTACTTTTGTACGATGCCTGTCATCAT TGGTTTGGAGGACTT Found at i:1089359 original size:120 final size:119 Alignment explanation

Indices: 1089120--1089862 Score: 731 Period size: 120 Copynumber: 6.2 Consensus size: 119 1089110 GTTATGAAAA * * * * * 1089120 ACTTTTGTACAATGCATGTCCTCACAAGCTT-AGACGACTTACTTTTGTACAATGCGTGTCATCA 1 ACTTTCGTACAATGCATGTCATCACGAG-TTGGGAGGACTTACTTTTGTACAATGCGTGTCATCA * * * 1089184 TTTGTTTGGAGGACTTACTTTCGTACAATGCGTGTCCTCACAAGTTGGGAGGACTT 65 TTGGTTTGGAGGACTTACTTTTGTACAATGCGTGTCCTCA-AGGTTGGGAGGACTT * * ** * * * * * * 1089240 GCTTTTGTATGATGCCTGTCATCATTG-GTTGGGTGGACTTACTTTTGTACAATACATGTCCTCA 1 ACTTTCGTACAATGCATGTCATCA-CGAGTTGGGAGGACTTACTTTTGTACAATGCGTGTCATCA * ** * * * * 1089304 -TGAGTTGGGAGGACTTACTTTTGTATGATGCCTGTCATCATTGGTTTGGAGGACTT 65 TTG-GTTTGGAGGACTTACTTTTGTACAATGCGTGTCCTCA-AGGTTGGGAGGACTT * * ** * * 1089360 ACTTTCGTACAATGCAAGTCCTCACGAGTTGGGAGGACTTACTTTTGTATGATGCCTGTCATCAA 1 ACTTTCGTACAATGCATGTCATCACGAGTTGGGAGGACTTACTTTTGTACAATGCGTGTCATCAT ** * * 1089425 TGGTTTGGAGGACTTACTTTCATACAATGCGTGTCCTCACGAGTTTGGAGGACTT 66 TGGTTTGGAGGACTTACTTTTGTACAATGCGTGTCCTCAAG-GTTGGGAGGACTT * ** * * * * * 1089480 ACTTTTGTATGATGCCTGTCATCATTG-GTTGGAAGGACTTACTTTTGTACGATGTGTGTCATCA 1 ACTTTCGTACAATGCATGTCATCA-CGAGTTGGGAGGACTTACTTTTGTACAATGCGTGTCATCA * * * * * * 1089544 TTGGTTTGGAGGACTTACATTTGTACAATGTGTCTCCGCAAAAGTTGGGAGGACCT 65 TTGGTTTGGAGGACTTACTTTTGTACAATGCGTGTCCTC-AAGGTTGGGAGGACTT * * * * 1089600 ACTTTCGTACAATGCGTGTCCTCACGAGTTGGGAGGACTTACTTTTGTACGATGCATGTCATCAT 1 ACTTTCGTACAATGCATGTCATCACGAGTTGGGAGGACTTACTTTTGTACAATGCGTGTCATCAT * * * 1089665 TGGTTTGGAGGACTTACTTTTGTACGATGTGTCTCCTCAAGAGTTGGGAGGACTT 66 TGGTTTGGAGGACTTACTTTTGTACAATGCGTGTCCTCAAG-GTTGGGAGGACTT * * * * * 1089720 ACTTTCATACAATGCATGTCCTCACGAATTTGGAGGACTTACTTTTGTACAATGTGTGTCATCAT 1 ACTTTCGTACAATGCATGTCATCACGAGTTGGGAGGACTTACTTTTGTACAATGCGTGTCATCAT * * * * * * 1089785 TGGTTTGGAGGACTTACTTTTTTA-GATGCGTGTCATCATTGATTTGGAGGACTT 66 TGGTTTGGAGGACTTACTTTTGTACAATGCGTGTCCTCA-AGGTTGGGAGGACTT * * * 1089839 ACTTTTGTACGATGCGTGTCATCA 1 ACTTTCGTACAATGCATGTCATCA 1089863 TTGGCTTTGA Statistics Matches: 511, Mismatches: 101, Indels: 23 0.80 0.16 0.04 Matches are distributed among these distances: 119 49 0.10 120 458 0.90 121 4 0.01 ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37 Consensus pattern (119 bp): ACTTTCGTACAATGCATGTCATCACGAGTTGGGAGGACTTACTTTTGTACAATGCGTGTCATCAT TGGTTTGGAGGACTTACTTTTGTACAATGCGTGTCCTCAAGGTTGGGAGGACTT Found at i:1089864 original size:40 final size:40 Alignment explanation

Indices: 1089155--1089878 Score: 590 Period size: 40 Copynumber: 18.1 Consensus size: 40 1089145 AAGCTTAGAC 1089155 GACTTACTTTTGTACAATGCGTGTCATCATTTG-TTTGGAG 1 GACTTACTTTTGTACAATGCGTGTCATCA-TTGATTTGGAG * * ** * 1089195 GACTTACTTTCGTACAATGCGTGTCCTCA-CAAGTTGGGAG 1 GACTTACTTTTGTACAATGCGTGTCATCATTGA-TTTGGAG * ** * * * * 1089235 GACTTGCTTTTGTATGATGCCTGTCATCATTGGTTGGGTG 1 GACTTACTTTTGTACAATGCGTGTCATCATTGATTTGGAG * * * * 1089275 GACTTACTTTTGTACAATACATGTCCTCA-TGAGTTGGGAG 1 GACTTACTTTTGTACAATGCGTGTCATCATTGA-TTTGGAG ** * * 1089315 GACTTACTTTTGTATGATGCCTGTCATCATTGGTTTGGAG 1 GACTTACTTTTGTACAATGCGTGTCATCATTGATTTGGAG * ** * * * 1089355 GACTTACTTTCGTACAATGCAAGTCCTCA-CGAGTTGGGAG 1 GACTTACTTTTGTACAATGCGTGTCATCATTGA-TTTGGAG ** * * * 1089395 GACTTACTTTTGTATGATGCCTGTCATCAATGGTTTGGAG 1 GACTTACTTTTGTACAATGCGTGTCATCATTGATTTGGAG ** * * 1089435 GACTTACTTTCATACAATGCGTGTCCTCA-CGAGTTTGGAG 1 GACTTACTTTTGTACAATGCGTGTCATCATTGA-TTTGGAG ** * * 1089475 GACTTACTTTTGTATGATGCCTGTCATCATTG-GTTGGAAG 1 GACTTACTTTTGTACAATGCGTGTCATCATTGATTTGG-AG * * * 1089515 GACTTACTTTTGTACGATGTGTGTCATCATTGGTTTGGAG 1 GACTTACTTTTGTACAATGCGTGTCATCATTGATTTGGAG * * * ** ** * 1089555 GACTTACATTTGTACAATGTGTCTCCGCA-AAAGTTGGGAG 1 GACTTACTTTTGTACAATGCGTGTCATCATTGA-TTTGGAG * * * * * 1089595 GACCTACTTTCGTACAATGCGTGTCCTCA-CGAGTTGGGAG 1 GACTTACTTTTGTACAATGCGTGTCATCATTGA-TTTGGAG * * * 1089635 GACTTACTTTTGTACGATGCATGTCATCATTGGTTTGGAG 1 GACTTACTTTTGTACAATGCGTGTCATCATTGATTTGGAG * * * * * * 1089675 GACTTACTTTTGTACGATGTGTCTCCTCA-AGAGTTGGGAG 1 GACTTACTTTTGTACAATGCGTGTCATCATTGA-TTTGGAG ** * * * 1089715 GACTTACTTTCATACAATGCATGTCCTCA-CGAATTTGGAG 1 GACTTACTTTTGTACAATGCGTGTCATCATTG-ATTTGGAG * * 1089755 GACTTACTTTTGTACAATGTGTGTCATCATTGGTTTGGAG 1 GACTTACTTTTGTACAATGCGTGTCATCATTGATTTGGAG * * 1089795 GACTTACTTTTTTA-GATGCGTGTCATCATTGATTTGGAG 1 GACTTACTTTTGTACAATGCGTGTCATCATTGATTTGGAG * * 1089834 GACTTACTTTTGTACGATGCGTGTCATCATTGGCTTT-GAG 1 GACTTACTTTTGTACAATGCGTGTCATCATT-GATTTGGAG 1089874 GACTT 1 GACTT 1089879 GGCTAACTGT Statistics Matches: 545, Mismatches: 121, Indels: 36 0.78 0.17 0.05 Matches are distributed among these distances: 39 44 0.08 40 486 0.89 41 15 0.03 ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37 Consensus pattern (40 bp): GACTTACTTTTGTACAATGCGTGTCATCATTGATTTGGAG Found at i:1091964 original size:34 final size:34 Alignment explanation

Indices: 1091902--1092057 Score: 249 Period size: 34 Copynumber: 4.6 Consensus size: 34 1091892 ACCCTGGCTG * * 1091902 TTTATGTGTGGCAGCCTCACTATATAACCTCGCTA 1 TTTATGTGTGGCAACC-CTCTATATAACCTCGCTA 1091937 TTTATGTGTGGCAACCCTCTATATAACCTCGCTA 1 TTTATGTGTGGCAACCCTCTATATAACCTCGCTA * 1091971 TTTATGTGTGGCAACCCTCTATATAACCTTGCTA 1 TTTATGTGTGGCAACCCTCTATATAACCTCGCTA * * * 1092005 TTTATGTGTGGCAACCCTCAAAATAACCTCGCTT 1 TTTATGTGTGGCAACCCTCTATATAACCTCGCTA 1092039 TTTATGTGTGGCAACCCTC 1 TTTATGTGTGGCAACCCTC 1092058 AAAATAACTA Statistics Matches: 114, Mismatches: 7, Indels: 1 0.93 0.06 0.01 Matches are distributed among these distances: 34 99 0.87 35 15 0.13 ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35 Consensus pattern (34 bp): TTTATGTGTGGCAACCCTCTATATAACCTCGCTA Found at i:1092536 original size:42 final size:42 Alignment explanation

Indices: 1092473--1093030 Score: 753 Period size: 42 Copynumber: 13.0 Consensus size: 42 1092463 CAACCGTTTT * 1092473 CTAACATTG-CTGTACAGTTGCCCACACTAACAGGCCCACTTC 1 CTAACATTGACT-TACAGTTGCCCACACTAACAGGCCCACTCC * * * 1092515 CTAACACTGACTTACATTTGCCCACACTAACAGACCCACTCC 1 CTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCC * * 1092557 CTAACATTGACTTACAGTTGCCAACACTAACAGGCTCACTCC 1 CTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCC 1092599 CTAACATTGACTTACAGTTG-CCACCACTAACAGGCCCACTCC 1 CTAACATTGACTTACAGTTGCCCA-CACTAACAGGCCCACTCC 1092641 CTAACATTGACTTACAGTTG-CCACCACTAACAGGCCCACTCC 1 CTAACATTGACTTACAGTTGCCCA-CACTAACAGGCCCACTCC * ** 1092683 CTAACACTGACTTACAGTTGCCTGCACTAACAGGCCCACTTCCCACTCC 1 CTAACATTGACTTACAGTTGCCCACACTAACAGG-------CCCACTCC * * * 1092732 CTTACACTGACTTACAGTTGCCAACACTAACAGGCCCACTCC 1 CTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCC * 1092774 CTAACATTGACTTACAGTTGCCCACACTAACAGACCCACTCC 1 CTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCC 1092816 CTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCC 1 CTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCC * ** 1092858 CTAACACTGACTTACAGTTGCCTGCACTAACAGGCCCACTTCCCACTCC 1 CTAACATTGACTTACAGTTGCCCACACTAACAGG-------CCCACTCC * * * 1092907 CTTACACTGACTTACAGTTGCCAACACTAACAGGCCCACTCC 1 CTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCC * 1092949 CTAACATTGACTTACAGTTGCCCACACTAACAGACCCACTCC 1 CTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCC * 1092991 CTAACATTGACTTACAGTTGCCCACACTAAAAGGCCCACT 1 CTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACT 1093031 TACAATGACA Statistics Matches: 465, Mismatches: 34, Indels: 34 0.87 0.06 0.06 Matches are distributed among these distances: 41 2 0.00 42 382 0.82 43 3 0.01 49 78 0.17 ACGTcount: A:0.29, C:0.38, G:0.11, T:0.22 Consensus pattern (42 bp): CTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCC Found at i:1092790 original size:175 final size:175 Alignment explanation

Indices: 1092473--1093030 Score: 938 Period size: 175 Copynumber: 3.2 Consensus size: 175 1092463 CAACCGTTTT * * 1092473 CTAACATTG-CTGTACAGTTGCCCACACTAACAGGCCCACTTCCTAACACTGACTTACATTTGCC 1 CTAACATTGACT-TACAGTTGCCCACACTAACAGGCCCACTCCCTAACACTGACTTACAGTTGCC ** * * * 1092537 CACACTAACA-G---A---CCCACTCCCTAACATTGACTTACAGTTGCCAACACTAACAGGCTCA 65 TGCACTAACAGGCCCACTTCCCACTCCCTTACACTGACTTACAGTTGCCAACACTAACAGGCCCA * 1092595 CTCCCTAACATTGACTTACAGTTG-CCACCACTAACAGGCCCACTCC 130 CTCCCTAACATTGACTTACAGTTGCCCA-CACTAACAGACCCACTCC 1092641 CTAACATTGACTTACAGTTG-CCACCACTAACAGGCCCACTCCCTAACACTGACTTACAGTTGCC 1 CTAACATTGACTTACAGTTGCCCA-CACTAACAGGCCCACTCCCTAACACTGACTTACAGTTGCC 1092705 TGCACTAACAGGCCCACTTCCCACTCCCTTACACTGACTTACAGTTGCCAACACTAACAGGCCCA 65 TGCACTAACAGGCCCACTTCCCACTCCCTTACACTGACTTACAGTTGCCAACACTAACAGGCCCA 1092770 CTCCCTAACATTGACTTACAGTTGCCCACACTAACAGACCCACTCC 130 CTCCCTAACATTGACTTACAGTTGCCCACACTAACAGACCCACTCC 1092816 CTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCCCTAACACTGACTTACAGTTGCCT 1 CTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCCCTAACACTGACTTACAGTTGCCT 1092881 GCACTAACAGGCCCACTTCCCACTCCCTTACACTGACTTACAGTTGCCAACACTAACAGGCCCAC 66 GCACTAACAGGCCCACTTCCCACTCCCTTACACTGACTTACAGTTGCCAACACTAACAGGCCCAC 1092946 TCCCTAACATTGACTTACAGTTGCCCACACTAACAGACCCACTCC 131 TCCCTAACATTGACTTACAGTTGCCCACACTAACAGACCCACTCC * 1092991 CTAACATTGACTTACAGTTGCCCACACTAAAAGGCCCACT 1 CTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACT 1093031 TACAATGACA Statistics Matches: 370, Mismatches: 9, Indels: 15 0.94 0.02 0.04 Matches are distributed among these distances: 167 3 0.01 168 63 0.17 169 3 0.01 172 1 0.00 175 294 0.79 176 6 0.02 ACGTcount: A:0.29, C:0.38, G:0.11, T:0.22 Consensus pattern (175 bp): CTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCCCTAACACTGACTTACAGTTGCCT GCACTAACAGGCCCACTTCCCACTCCCTTACACTGACTTACAGTTGCCAACACTAACAGGCCCAC TCCCTAACATTGACTTACAGTTGCCCACACTAACAGACCCACTCC Found at i:1092853 original size:217 final size:211 Alignment explanation

Indices: 1092485--1093030 Score: 799 Period size: 217 Copynumber: 2.5 Consensus size: 211 1092475 AACATTGCTG * * * 1092485 TACAGTTGCCCACACTAACAGGCCCACTTCCTAACACTGACTTACATTTGCCCACACTAACAGAC 1 TACAGTTGCCAACACTAACAGGCCCACTCCCTAACACTGACTTACAGTTGCCCACACTAACAGAC * * 1092550 CCACTCCCTAACATTGACTTACAGTTGCCAACACTAACAGGCTCACTCCCTAACATTGACTTACA 66 CCACTCCCTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCCCTAACATTGACTTACA * 1092615 GTTGCCACCACTAACAGGCCCACTCCCTAACATTGACTTACAGTTGCCACCACTAACAGG-CCCA 131 GTTGCCACCACTAACAGGCCCACTCCCTAACACTGACTTACAGTTGCCACCACTAACAGGCCCCA 1092679 CTCCCTAACACTGACT 196 CTCCCTAACACTGACT ** * * 1092695 TACAGTTGCCTGCACTAACAGGCCCACTTCCCACTCCCTTACACTGACTTACAGTTGCCAACACT 1 TACAGTTGCCAACACTAACAGG-------CCCACTCCCTAACACTGACTTACAGTTGCCCACACT * * 1092760 AACAGGCCCACTCCCTAACATTGACTTACAGTTGCCCACACTAACAGACCCACTCCCTAACATTG 59 AACAGACCCACTCCCTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCCCTAACATTG ** 1092825 ACTTACAGTTGCC-CACACTAACAGGCCCACTCCCTAACACTGACTTACAGTTGCCTGCACTAAC 124 ACTTACAGTTGCCAC-CACTAACAGGCCCACTCCCTAACACTGACTTACAGTTGCCACCACTAAC * 1092889 AGGCCCACTTCCCACTCCCTTACACTGACT 188 AGG----C--CCCACTCCCTAACACTGACT * 1092919 TACAGTTGCCAACACTAACAGGCCCACTCCCTAACATTGACTTACAGTTGCCCACACTAACAGAC 1 TACAGTTGCCAACACTAACAGGCCCACTCCCTAACACTGACTTACAGTTGCCCACACTAACAGAC * 1092984 CCACTCCCTAACATTGACTTACAGTTGCCCACACTAAAAGGCCCACT 66 CCACTCCCTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACT 1093031 TACAATGACA Statistics Matches: 299, Mismatches: 22, Indels: 23 0.87 0.06 0.07 Matches are distributed among these distances: 210 20 0.07 216 1 0.00 217 239 0.80 224 39 0.13 ACGTcount: A:0.29, C:0.38, G:0.11, T:0.22 Consensus pattern (211 bp): TACAGTTGCCAACACTAACAGGCCCACTCCCTAACACTGACTTACAGTTGCCCACACTAACAGAC CCACTCCCTAACATTGACTTACAGTTGCCCACACTAACAGGCCCACTCCCTAACATTGACTTACA GTTGCCACCACTAACAGGCCCACTCCCTAACACTGACTTACAGTTGCCACCACTAACAGGCCCCA CTCCCTAACACTGACT Found at i:1098088 original size:27 final size:27 Alignment explanation

Indices: 1098058--1098327 Score: 163 Period size: 27 Copynumber: 10.3 Consensus size: 27 1098048 CCAATTACAC 1098058 TGTCATATA-ATGCTGTCACTGACACAG 1 TGTCATA-ACATGCTGTCACTGACACAG * ** * 1098085 TGTCACAATGTGTTGTCACTGACACAG 1 TGTCATAACATGCTGTCACTGACACAG * ** * 1098112 TGTCACAATGTGCTGTCACTGACACAT 1 TGTCATAACATGCTGTCACTGACACAG * * 1098139 TGTCA-CACTGTGCTGTCACTG--ACAG 1 TGTCATAAC-ATGCTGTCACTGACACAG * * * 1098164 TATCATAACCTGCGGT-ATCTG--ACAG 1 TGTCATAACATGCTGTCA-CTGACACAG * 1098189 TTTCATAA-ACTGCTGTCACTGACA-A- 1 TGTCATAACA-TGCTGTCACTGACACAG * * 1098214 TGTCACAATC-TGCTGTTACTGACACCA- 1 TGTCATAA-CATGCTGTCACTGACA-CAG * ** 1098241 TGTCAGAACATGCTGTCACTGACATGG 1 TGTCATAACATGCTGTCACTGACACAG * * 1098268 TGTCAGAACATGTTGTCACTG--ACAG 1 TGTCATAACATGCTGTCACTGACACAG * * * * 1098293 TGTAATAACTTGCTGTCACTGAAACAA 1 TGTCATAACATGCTGTCACTGACACAG 1098320 TGTCATAA 1 TGTCATAA 1098328 ATTGAAAGTG Statistics Matches: 196, Mismatches: 31, Indels: 32 0.76 0.12 0.12 Matches are distributed among these distances: 24 1 0.01 25 72 0.37 26 7 0.04 27 116 0.59 ACGTcount: A:0.28, C:0.23, G:0.19, T:0.29 Consensus pattern (27 bp): TGTCATAACATGCTGTCACTGACACAG Found at i:1102336 original size:9 final size:9 Alignment explanation

Indices: 1102322--1102346 Score: 50 Period size: 9 Copynumber: 2.8 Consensus size: 9 1102312 AGAATTCTGG 1102322 ATATTTAGA 1 ATATTTAGA 1102331 ATATTTAGA 1 ATATTTAGA 1102340 ATATTTA 1 ATATTTA 1102347 AATCTTTAAG Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 9 16 1.00 ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48 Consensus pattern (9 bp): ATATTTAGA Found at i:1103052 original size:22 final size:21 Alignment explanation

Indices: 1103012--1103052 Score: 55 Period size: 21 Copynumber: 1.9 Consensus size: 21 1103002 TTTGTAACAA * 1103012 GTAAAAATAAACAGTAAACTT 1 GTAAAAATAAACAGCAAACTT * 1103033 GTAAAAATATACATGCAAAC 1 GTAAAAATAAACA-GCAAAC 1103053 CTTTTTTTAA Statistics Matches: 17, Mismatches: 2, Indels: 1 0.85 0.10 0.05 Matches are distributed among these distances: 21 12 0.71 22 5 0.29 ACGTcount: A:0.56, C:0.12, G:0.10, T:0.22 Consensus pattern (21 bp): GTAAAAATAAACAGCAAACTT Found at i:1106741 original size:38 final size:38 Alignment explanation

Indices: 1106723--1107513 Score: 1564 Period size: 38 Copynumber: 20.8 Consensus size: 38 1106713 AAGCATACCT * 1106723 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCT 1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1106761 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1106799 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1106837 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1106875 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1106913 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1106951 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1106989 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1107027 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1107065 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1107103 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1107141 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1107179 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1107217 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1107255 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1107293 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1107331 CAACAATAGAGTGTACAGTTATTTATCAAGACTACATCC 1 CAACAATAGAG-GTACAGTTATTTATCAAGACTACATCC 1107370 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1107408 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1107446 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1 CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC 1107484 CAACAATAGAGGTACAGTTATTTATCAAGA 1 CAACAATAGAGGTACAGTTATTTATCAAGA 1107514 TGTTGTGTAC Statistics Matches: 751, Mismatches: 1, Indels: 2 1.00 0.00 0.00 Matches are distributed among these distances: 38 713 0.95 39 38 0.05 ACGTcount: A:0.40, C:0.21, G:0.13, T:0.27 Consensus pattern (38 bp): CAACAATAGAGGTACAGTTATTTATCAAGACTACATCC Found at i:1114887 original size:44 final size:44 Alignment explanation

Indices: 1114824--1114914 Score: 173 Period size: 44 Copynumber: 2.1 Consensus size: 44 1114814 AAAATCAATG 1114824 TATTTTTATGGCTCACCCTACCAAAACATCATCAATACTGTGAT 1 TATTTTTATGGCTCACCCTACCAAAACATCATCAATACTGTGAT * 1114868 TATTTTTATGGCTCACCCTACCAAAATATCATCAATACTGTGAT 1 TATTTTTATGGCTCACCCTACCAAAACATCATCAATACTGTGAT 1114912 TAT 1 TAT 1114915 CAAATATTAA Statistics Matches: 46, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 44 46 1.00 ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36 Consensus pattern (44 bp): TATTTTTATGGCTCACCCTACCAAAACATCATCAATACTGTGAT Found at i:1118824 original size:35 final size:35 Alignment explanation

Indices: 1118778--1118884 Score: 187 Period size: 35 Copynumber: 3.1 Consensus size: 35 1118768 AAATCTTATA * 1118778 GTGAATCACAATCAGTACTGTACATATATTTGTTT 1 GTGAATCACAATCAGTACTGTACATACATTTGTTT * 1118813 GTGAATCACAATCAGTACTGTACATACATTTGTTA 1 GTGAATCACAATCAGTACTGTACATACATTTGTTT * 1118848 GTGAATCAAAATCAGTACTGTACATACATTTGTTT 1 GTGAATCACAATCAGTACTGTACATACATTTGTTT 1118883 GT 1 GT 1118885 TTCAAGCCCA Statistics Matches: 68, Mismatches: 4, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 35 68 1.00 ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37 Consensus pattern (35 bp): GTGAATCACAATCAGTACTGTACATACATTTGTTT Found at i:1127094 original size:61 final size:61 Alignment explanation

Indices: 1127025--1127599 Score: 745 Period size: 61 Copynumber: 9.4 Consensus size: 61 1127015 GTCTGTGTGT * * 1127025 GGGTTGGATGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTGTACGGA-TGTTTGTGAGC 1 GGGTTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGT-TAAGGAGTGTTTGTGAGC * * * * 1127086 GGGTTGGATACGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTGTACGGA-TGTTTGTAAGC 1 GGGTTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGT-TAAGGAGTGTTTGTGAGC * * * 1127147 GGGTTGGATGCGTCACAGTTTGTTTGTGTATTTGTTTGGTTGTCT--GTGAATGTTTGTGAGC 1 GGGTTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGT-TAAG-GAGTGTTTGTGAGC * * * * 1127208 GGGTTGGATACGTCACGGTTTGTTTGTGTGTTTGTTTGATTGTCT--GTGAGTGTTTATGAGT 1 GGGTTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGT-TAAG-GAGTGTTTGTGAGC * * * * 1127269 GGATTGGATGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTCAATGAGTGTTTGTGAGC 1 GGGTTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTTAAGGAGTGTTTGTGAGC * * * 1127330 GGGTTGGATACGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTCAATGAGTGTTTGTGAGC 1 GGGTTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTTAAGGAGTGTTTGTGAGC * * * 1127391 GGGTTGGATACGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTCAATGAGTGTTTGTGAGC 1 GGGTTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTTAAGGAGTGTTTGTGAGC * * * 1127452 GGGTTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGATTGTCT--GTGAGTGTTTATGAGT 1 GGGTTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGT-TAAG-GAGTGTTTGTGAGC * * * 1127513 GGATTGGATGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTGTACGGA-TGTTTGTGAGC 1 GGGTTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGT-TAAGGAGTGTTTGTGAGC 1127574 GGGTTGGATGCGTCACGGTTTGTTTG 1 GGGTTGGATGCGTCACGGTTTGTTTG 1127600 GTTGTCTGTG Statistics Matches: 466, Mismatches: 40, Indels: 16 0.89 0.08 0.03 Matches are distributed among these distances: 59 1 0.00 60 2 0.00 61 460 0.99 62 2 0.00 63 1 0.00 ACGTcount: A:0.11, C:0.09, G:0.37, T:0.44 Consensus pattern (61 bp): GGGTTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTTAAGGAGTGTTTGTGAGC Found at i:1127333 original size:183 final size:183 Alignment explanation

Indices: 1127025--1127599 Score: 823 Period size: 183 Copynumber: 3.1 Consensus size: 183 1127015 GTCTGTGTGT * * * 1127025 GGGTTGGATGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTGTACG-GA-TGTTTGTGAGCGG 1 GGGTTGGATACGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTCT--GTGAGTGTTTGTGAGCGG * * * * 1127088 GTTGGATACGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTGTACG-GATGTTTGTAAGCGGGTT 64 GTTGGATGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTCTATGAG-TGTTTGTGAGCGGGTT * * * 1127152 GGATGCGTCACAGTTTGTTTGTGTATTTGTTTGGTTGTCTGTGAATGTTTGTGAGC 128 GGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTCTATGAATGTTTGTGAGC * * * * 1127208 GGGTTGGATACGTCACGGTTTGTTTGTGTGTTTGTTTGATTGTCTGTGAGTGTTTATGAGTGGAT 1 GGGTTGGATACGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTCTGTGAGTGTTTGTGAGCGGGT * 1127273 TGGATGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTCAATGAGTGTTTGTGAGCGGGTTGGA 66 TGGATGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTCTATGAGTGTTTGTGAGCGGGTTGGA * * * 1127338 TACGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTCAATGAGTGTTTGTGAGC 131 TGCGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTCTATGAATGTTTGTGAGC ** 1127391 GGGTTGGATACGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTCAATGAGTGTTTGTGAGCGGGT 1 GGGTTGGATACGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTCTGTGAGTGTTTGTGAGCGGGT * * * * * * 1127456 TGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGATTGTCTGTGAGTGTTTATGAGTGGATTGGA 66 TGGATGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTCTATGAGTGTTTGTGAGCGGGTTGGA * * * * 1127521 TGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTGTACGGATGTTTGTGAGC 131 TGCGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTCTATGAATGTTTGTGAGC * 1127574 GGGTTGGATGCGTCACGGTTTGTTTG 1 GGGTTGGATACGTCACGGTTTGTTTG 1127600 GTTGTCTGTG Statistics Matches: 350, Mismatches: 39, Indels: 6 0.89 0.10 0.02 Matches are distributed among these distances: 181 1 0.00 182 2 0.01 183 346 0.99 184 1 0.00 ACGTcount: A:0.11, C:0.09, G:0.37, T:0.44 Consensus pattern (183 bp): GGGTTGGATACGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTCTGTGAGTGTTTGTGAGCGGGT TGGATGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTCTATGAGTGTTTGTGAGCGGGTTGGA TGCGTCACGGTTTGTTTGTGTGTTTGTTTGGTTGTCTATGAATGTTTGTGAGC Found at i:1127622 original size:161 final size:153 Alignment explanation

Indices: 1127445--1127741 Score: 416 Period size: 161 Copynumber: 1.9 Consensus size: 153 1127435 AATGAGTGTT * 1127445 TGTGAGCGGGTTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGATTGTCTGT-GAGTGTTTAT 1 TGTGAGCGGATTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGATTGTCTGTGGA-TGTTTAT * * 1127509 GAGTGGATTGGATGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTGTACGGATGTTTGTGAGC 65 GAGCGGATTGGATGCGTCAC-G---G--T-T-TGTTTGTTTGGTTGTCTACGGATGTTTGTGAGC 1127574 GGGTTGGATGCGTCACGGTTTGTTTGGTTGTC 122 GGGTTGGATGCGTCACGGTTTGTTTGGTTGTC * * * * 1127606 TGTGAGTGGATTGGATGCGTCATGGTTTGTTTGTGTGTTTGTTTGGTTGTCTGTGGATGTTTGTG 1 TGTGAGCGGATTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGATTGTCTGTGGATGTTTATG * * * 1127671 AGCGGGTTGGATGCGTCACGGTTTGTTTGTTTGGTTGTCTATGGATTTTTGTGAGCGGGTTGGAT 66 AGCGGATTGGATGCGTCACGGTTTGTTTGTTTGGTTGTCTACGGATGTTTGTGAGCGGGTTGGAT 1127736 GCGTCA 131 GCGTCA 1127742 GAACGCCTAC Statistics Matches: 125, Mismatches: 10, Indels: 10 0.86 0.07 0.07 Matches are distributed among these distances: 153 45 0.36 154 1 0.01 155 1 0.01 157 1 0.01 160 1 0.01 161 74 0.59 162 2 0.02 ACGTcount: A:0.09, C:0.09, G:0.38, T:0.44 Consensus pattern (153 bp): TGTGAGCGGATTGGATGCGTCACGGTTTGTTTGTGTGTTTGTTTGATTGTCTGTGGATGTTTATG AGCGGATTGGATGCGTCACGGTTTGTTTGTTTGGTTGTCTACGGATGTTTGTGAGCGGGTTGGAT GCGTCACGGTTTGTTTGGTTGTC Found at i:1127717 original size:100 final size:100 Alignment explanation

Indices: 1127508--1127699 Score: 339 Period size: 100 Copynumber: 1.9 Consensus size: 100 1127498 TGAGTGTTTA * 1127508 TGAGTGGATTGGATGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTGTACGGATGTTTGTGAG 1 TGAGTGGATTGGATGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTCTACGGATGTTTGTGAG 1127573 CGGGTTGGATGCGTCACGGTTTGTTTGGTTGTCTG 66 CGGGTTGGATGCGTCACGGTTTGTTTGGTTGTCTG * * ** 1127608 TGAGTGGATTGGATGCGTCATGGTTTGTTTGTGTGTTTGTTTGGTTGTCTGTGGATGTTTGTGAG 1 TGAGTGGATTGGATGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTCTACGGATGTTTGTGAG 1127673 CGGGTTGGATGCGTCACGGTTTGTTTG 66 CGGGTTGGATGCGTCACGGTTTGTTTG 1127700 TTTGGTTGTC Statistics Matches: 87, Mismatches: 5, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 100 87 1.00 ACGTcount: A:0.09, C:0.09, G:0.39, T:0.43 Consensus pattern (100 bp): TGAGTGGATTGGATGCGTCACGGTCTGTTTGTGTGTTTGTTTGGTTGTCTACGGATGTTTGTGAG CGGGTTGGATGCGTCACGGTTTGTTTGGTTGTCTG Found at i:1127722 original size:53 final size:53 Alignment explanation

Indices: 1127541--1127741 Score: 186 Period size: 53 Copynumber: 3.9 Consensus size: 53 1127531 TCTGTTTGTG * * 1127541 TGTTTGTTTGGTTGTGTACGGATGTTTGTGAGCGGGTTGGATGCGTCAC-G-- 1 TGTTTGTTTGGTTGTCTATGGATGTTTGTGAGCGGGTTGGATGCGTCACGGTT * * *** ** ** * 1127591 -GTTTGTTTGGTTGTCTGT-GAGTGGATTG-GATGCGTCATGG-TTTGT--TTGTG 1 TGTTTGTTTGGTTGTCTATGGA-T-GTTTGTGA-GCGGGTTGGATGCGTCACGGTT * 1127641 TGTTTGTTTGGTTGTCTGTGGATGTTTGTGAGCGGGTTGGATGCGTCACGGTT 1 TGTTTGTTTGGTTGTCTATGGATGTTTGTGAGCGGGTTGGATGCGTCACGGTT * 1127694 TGTTTGTTTGGTTGTCTATGGATTTTTGTGAGCGGGTTGGATGCGTCA 1 TGTTTGTTTGGTTGTCTATGGATGTTTGTGAGCGGGTTGGATGCGTCA 1127742 GAACGCCTAC Statistics Matches: 118, Mismatches: 21, Indels: 21 0.74 0.13 0.13 Matches are distributed among these distances: 48 3 0.03 49 21 0.18 50 20 0.17 51 24 0.20 52 2 0.02 53 48 0.41 ACGTcount: A:0.09, C:0.08, G:0.38, T:0.44 Consensus pattern (53 bp): TGTTTGTTTGGTTGTCTATGGATGTTTGTGAGCGGGTTGGATGCGTCACGGTT Found at i:1132089 original size:21 final size:21 Alignment explanation

Indices: 1131923--1132076 Score: 263 Period size: 21 Copynumber: 7.3 Consensus size: 21 1131913 GAATAAACTA 1131923 TAAAGTACCATCATGTAATGT 1 TAAAGTACCATCATGTAATGT * 1131944 TAAAGTACCATCATGCAATGT 1 TAAAGTACCATCATGTAATGT * 1131965 TGAAGTACCATCATGTAATGT 1 TAAAGTACCATCATGTAATGT * 1131986 TAAAGTACCATCACGTAATGT 1 TAAAGTACCATCATGTAATGT * 1132007 TGAAGTACCATCATGTAATGT 1 TAAAGTACCATCATGTAATGT 1132028 TAAAGTACCATCATGTAATGT 1 TAAAGTACCATCATGTAATGT * 1132049 TGAAGTACCATCATGTAATGT 1 TAAAGTACCATCATGTAATGT 1132070 TAAAGTA 1 TAAAGTA 1132077 TAATCATATA Statistics Matches: 123, Mismatches: 10, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 21 123 1.00 ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32 Consensus pattern (21 bp): TAAAGTACCATCATGTAATGT Found at i:1140039 original size:20 final size:20 Alignment explanation

Indices: 1139993--1140063 Score: 67 Period size: 20 Copynumber: 3.6 Consensus size: 20 1139983 ATTGTATTTG * 1139993 ATCACATAATACAATATCAT 1 ATCATATAATACAATATCAT ** 1140013 AAAATATAATACAATAT-AGT 1 ATCATATAATACAATATCA-T 1140033 ATCATAT--TACAATATCAT 1 ATCATATAATACAATATCAT * * 1140051 ATTACATAATACA 1 ATCATATAATACA 1140064 TCATAACACT Statistics Matches: 40, Mismatches: 7, Indels: 8 0.73 0.13 0.15 Matches are distributed among these distances: 18 14 0.35 19 2 0.05 20 24 0.60 ACGTcount: A:0.52, C:0.14, G:0.01, T:0.32 Consensus pattern (20 bp): ATCATATAATACAATATCAT Found at i:1140050 original size:13 final size:13 Alignment explanation

Indices: 1140032--1140056 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 1140022 TACAATATAG 1140032 TATCATATTACAA 1 TATCATATTACAA 1140045 TATCATATTACA 1 TATCATATTACA 1140057 TAATACATCA Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40 Consensus pattern (13 bp): TATCATATTACAA Found at i:1140310 original size:15 final size:15 Alignment explanation

Indices: 1140292--1140415 Score: 83 Period size: 15 Copynumber: 7.7 Consensus size: 15 1140282 TAAAATGAAT 1140292 TACAATATCATATAA 1 TACAATATCATATAA * 1140307 TACAATTTCATTTGATATGA 1 TACAATATCA--T-ATA--A 1140327 TA-ATATATCATATAA 1 TACA-ATATCATATAA 1140342 -ACCAATATCATATCAA 1 TA-CAATATCATAT-AA * * 1140358 -ACAATATCGTATGA 1 TACAATATCATATAA * 1140372 TACAATATTATATAATA 1 TACAATATCATAT-A-A 1140389 TTACAATATCATATAA 1 -TACAATATCATATAA * 1140405 TACAATTTCAT 1 TACAATATCAT 1140416 GTGATATAAT Statistics Matches: 87, Mismatches: 9, Indels: 26 0.71 0.07 0.21 Matches are distributed among these distances: 14 2 0.02 15 49 0.56 16 5 0.06 17 6 0.07 18 16 0.18 19 1 0.01 20 8 0.09 ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37 Consensus pattern (15 bp): TACAATATCATATAA Found at i:1140348 original size:50 final size:49 Alignment explanation

Indices: 1140294--1140494 Score: 164 Period size: 50 Copynumber: 4.1 Consensus size: 49 1140284 AAATGAATTA * * 1140294 CAATATCATATAATACAATTTCATTTGATATGATAATATATCATATAAAC 1 CAATATCATATAATACAATTTCATATGATATAATAATATAT-ATATAAAC * * * * * 1140344 CAATATCATATCAA-ACAATATCGTATGATACAATATTATATA-ATATTA- 1 CAATATCATAT-AATACAATTTCATATGATATAATAATATATATATA-AAC * ** 1140392 CAATATCATATAATACAATTTCATGTGATATAATTCTATATA-ACTGAAAC 1 CAATATCATATAATACAATTTCATATGATATAATAATATATATA-T-AAAC * * * * * 1140442 CAATATCATATTATACAATATT-GTATGATACAATATTATAGA-ATAAA- 1 CAATATCATATAATACAAT-TTCATATGATATAATAATATATATATAAAC 1140489 CAATAT 1 CAATAT 1140495 TGTATCATAG Statistics Matches: 123, Mismatches: 21, Indels: 17 0.76 0.13 0.11 Matches are distributed among these distances: 47 8 0.07 48 40 0.33 49 5 0.04 50 66 0.54 51 4 0.03 ACGTcount: A:0.47, C:0.12, G:0.05, T:0.36 Consensus pattern (49 bp): CAATATCATATAATACAATTTCATATGATATAATAATATATATATAAAC Found at i:1140395 original size:18 final size:18 Alignment explanation

Indices: 1140372--1140406 Score: 61 Period size: 18 Copynumber: 1.9 Consensus size: 18 1140362 TATCGTATGA * 1140372 TACAATATTATATAATAT 1 TACAATATCATATAATAT 1140390 TACAATATCATATAATA 1 TACAATATCATATAATA 1140407 CAATTTCATG Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 16 1.00 ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40 Consensus pattern (18 bp): TACAATATCATATAATAT Found at i:1140401 original size:98 final size:98 Alignment explanation

Indices: 1140290--1140494 Score: 290 Period size: 98 Copynumber: 2.1 Consensus size: 98 1140280 AATAAAATGA * * 1140290 ATTACAATATCATATAATACAATTTCATTTGATATGATAATATATCATA-T-AAACCAATATCAT 1 ATTACAATATCATATAATACAATTTCATGTGATATAATAATATAT-A-ACTGAAACCAATATCAT * 1140353 ATCAAACAATATCGTATGATACAATATTATATAAT 64 ATCAAACAATATCGTATGATACAATATTATAGAAT ** 1140388 ATTACAATATCATATAATACAATTTCATGTGATATAATTCTATATAACTGAAACCAATATCATAT 1 ATTACAATATCATATAATACAATTTCATGTGATATAATAATATATAACTGAAACCAATATCATAT * * * 1140453 TATACAATATTGTATGATACAATATTATAGAAT 66 CAAACAATATCGTATGATACAATATTATAGAAT * 1140486 A-AACAATAT 1 ATTACAATAT 1140495 TGTATCATAG Statistics Matches: 96, Mismatches: 9, Indels: 5 0.87 0.08 0.05 Matches are distributed among these distances: 96 1 0.01 97 9 0.09 98 86 0.90 ACGTcount: A:0.47, C:0.12, G:0.05, T:0.37 Consensus pattern (98 bp): ATTACAATATCATATAATACAATTTCATGTGATATAATAATATATAACTGAAACCAATATCATAT CAAACAATATCGTATGATACAATATTATAGAAT Found at i:1140638 original size:18 final size:18 Alignment explanation

Indices: 1140615--1140649 Score: 54 Period size: 18 Copynumber: 1.9 Consensus size: 18 1140605 ATACAATACT 1140615 ATACATAA-CAATATCATG 1 ATACATAATC-ATATCATG 1140633 ATACATAATCATATCAT 1 ATACATAATCATATCAT 1140650 AAAATATCAA Statistics Matches: 16, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 18 15 0.94 19 1 0.06 ACGTcount: A:0.49, C:0.17, G:0.03, T:0.31 Consensus pattern (18 bp): ATACATAATCATATCATG Found at i:1140740 original size:20 final size:20 Alignment explanation

Indices: 1140715--1140767 Score: 72 Period size: 20 Copynumber: 2.6 Consensus size: 20 1140705 ACATGATATC 1140715 ATATTGTATCATATCAAACA 1 ATATTGTATCATATCAAACA * * 1140735 ATATTGTTTCATATCATACA 1 ATATTGTATCATATCAAACA 1140755 ATACTT-TATCATA 1 ATA-TTGTATCATA 1140768 GGAATCATGT Statistics Matches: 29, Mismatches: 3, Indels: 2 0.85 0.09 0.06 Matches are distributed among these distances: 20 27 0.93 21 2 0.07 ACGTcount: A:0.40, C:0.15, G:0.04, T:0.42 Consensus pattern (20 bp): ATATTGTATCATATCAAACA Found at i:1141794 original size:176 final size:177 Alignment explanation

Indices: 1141424--1142221 Score: 941 Period size: 177 Copynumber: 4.5 Consensus size: 177 1141414 ACCAGACTAT * * * * * 1141424 GCATTCAAGCCTGTCAGGTGCATCAGTATCATAAGACACACCATCCATGGAAGTCTGGTGAAGTA 1 GCATTCAAGCTTGTCAGGTGCATCAGTATCATAAGACGCACCATCCATGCAAGTTTGGTGAAGTT * *** 1141489 AGGACAAGTAATAACTAAGAT-AT-CATCATCAGAGGGCACCTGTTTCAAAAACTTTATCTAACC 66 AGGACCAGTAATAACTAAGATAATGC-T-ATCAGAGGGCACCTGCAACAAAAAC--T-T-TAACC ** 1141552 AGCTCTTAAAACCTTAACCTCCTCCAGCATCCGAAACCTATTGCTCAGATTCA 125 AGCTCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATTGCTCAGATTCA * 1141605 GCATTCAAGCTTGTCAGGTGCATCAGTATCATAAGACGCACCATCCATACAAGTTTGGTGAAGTT 1 GCATTCAAGCTTGTCAGGTGCATCAGTATCATAAGACGCACCATCCATGCAAGTTTGGTGAAGTT 1141670 AGGACCAGTAATAACTAAGATTAAT-C-ATCAGAGGGCACCTGCAACAAAAACTTTAACCAGCTC 66 AGGACCAGTAATAACTAAGA-TAATGCTATCAGAGGGCACCTGCAACAAAAACTTTAACCAGCTC * * 1141733 TAAAAACCTTAACCTCTTCCAGCATCCGAAACCTATTGCTCAGATTCA 130 CAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATTGCTCAGATTCA * * 1141781 GCATTCAAGCTTGTCAGGTGCATCAGTATCATAAGACGCATCATCCATACAAGTTTGGTGAAGTT 1 GCATTCAAGCTTGTCAGGTGCATCAGTATCATAAGACGCACCATCCATGCAAGTTTGGTGAAGTT * * * * * 1141846 AGGACCAGTAGTAACTTAGATATTGCTATCA-ATGGGCACCCGCAACAAAAACTTTAACCTGCTC 66 AGGACCAGTAATAACTAAGATAATGCTATCAGA-GGGCACCTGCAACAAAAACTTTAACCAGCTC * 1141910 CAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCTCAGATTCA 130 CAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATTGCTCAGATTCA * * * * * * 1141958 GCACTCAAGCCTGTCTGGTGCATCAGTATCATAAGGCACACCATCCATGCAAGTTAGGTGAAG-T 1 GCATTCAAGCTTGTCAGGTGCATCAGTATCATAAGACGCACCATCCATGCAAGTTTGGTGAAGTT * * * * * * * 1142022 ACAGACCAGCAGTAACTAAGATACTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCTGGTC 66 A-GGACCAGTAATAACTAAGATAATGCTATCAGAGGGCACCTGCAACAAAAACTTTAACCAGCTC * * ** * * 1142087 CAACAACCTTAACCTCCTCCAGCATCTGAAATTTA-GGACCCAGATTCA 130 CAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATTG-CTCAGATTCA * * * * * * * 1142135 GCATCCAAGTCTT-TCAAGTCCATAAGTAGGTC--CAGATGCATCATCCATGCAAGTTTGGTGAA 1 GCATTCAAG-CTTGTCAGGTGCATCAGTA--TCATAAGACGCACCATCCATGCAAGTTTGGTGAA * * * * 1142197 GATAGGACAAGTAATAGCTTAGATA 63 GTTAGGACCAGTAATAACTAAGATA 1142222 CAGGACCTGC Statistics Matches: 545, Mismatches: 60, Indels: 28 0.86 0.09 0.04 Matches are distributed among these distances: 175 3 0.01 176 143 0.26 177 287 0.53 178 6 0.01 179 2 0.00 180 22 0.04 181 78 0.14 182 1 0.00 183 3 0.01 ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24 Consensus pattern (177 bp): GCATTCAAGCTTGTCAGGTGCATCAGTATCATAAGACGCACCATCCATGCAAGTTTGGTGAAGTT AGGACCAGTAATAACTAAGATAATGCTATCAGAGGGCACCTGCAACAAAAACTTTAACCAGCTCC AAAAACCTTAACCTCCTCCAGCATCCGAAACCTATTGCTCAGATTCA Found at i:1141915 original size:19 final size:19 Alignment explanation

Indices: 1141891--1141930 Score: 62 Period size: 19 Copynumber: 2.1 Consensus size: 19 1141881 GCACCCGCAA * * 1141891 CAAAAACTTTAACCTGCTC 1 CAAAAACCTTAACCTCCTC 1141910 CAAAAACCTTAACCTCCTC 1 CAAAAACCTTAACCTCCTC 1141929 CA 1 CA 1141931 GCATCCGAAA Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 19 19 1.00 ACGTcount: A:0.38, C:0.38, G:0.03, T:0.23 Consensus pattern (19 bp): CAAAAACCTTAACCTCCTC Found at i:1146538 original size:21 final size:21 Alignment explanation

Indices: 1146513--1146563 Score: 68 Period size: 21 Copynumber: 2.4 Consensus size: 21 1146503 ATTTTCCTGA * 1146513 TACACGCACGATC-CCGCACGT 1 TACACGAACGATCACC-CACGT 1146534 TACACGAACGATCACCCACGT 1 TACACGAACGATCACCCACGT * 1146555 AACACGAAC 1 TACACGAAC 1146564 TATTTAACAC Statistics Matches: 27, Mismatches: 2, Indels: 2 0.87 0.06 0.06 Matches are distributed among these distances: 21 25 0.93 22 2 0.07 ACGTcount: A:0.33, C:0.39, G:0.16, T:0.12 Consensus pattern (21 bp): TACACGAACGATCACCCACGT Found at i:1146860 original size:21 final size:21 Alignment explanation

Indices: 1146805--1146863 Score: 66 Period size: 21 Copynumber: 2.8 Consensus size: 21 1146795 TTTGCACGTC * * 1146805 CTCTCGCATACATTGCACAAG 1 CTCTCGCATTCGTTGCACAAG * * 1146826 CCCTCGC-TTACGTTGCACGAG 1 CTCTCGCATT-CGTTGCACAAG 1146847 CTCTCGCATTCGTTGCA 1 CTCTCGCATTCGTTGCA 1146864 TACGTTTTAC Statistics Matches: 31, Mismatches: 5, Indels: 4 0.77 0.12 0.10 Matches are distributed among these distances: 20 1 0.03 21 28 0.90 22 2 0.06 ACGTcount: A:0.19, C:0.36, G:0.19, T:0.27 Consensus pattern (21 bp): CTCTCGCATTCGTTGCACAAG Found at i:1147641 original size:18 final size:18 Alignment explanation

Indices: 1147587--1147646 Score: 59 Period size: 18 Copynumber: 3.3 Consensus size: 18 1147577 TGTATTGTGT 1147587 TAATACAATATCATAATATA 1 TAATACAATATCAT-AT-TA * ** 1147607 TAAAACAATATGGTATTA 1 TAATACAATATCATATTA * 1147625 TATTACAATATCATATTA 1 TAATACAATATCATATTA 1147643 -AATA 1 TAATA 1147647 ATACATCATA Statistics Matches: 32, Mismatches: 8, Indels: 3 0.74 0.19 0.07 Matches are distributed among these distances: 17 3 0.09 18 16 0.50 19 2 0.06 20 11 0.34 ACGTcount: A:0.52, C:0.08, G:0.03, T:0.37 Consensus pattern (18 bp): TAATACAATATCATATTA Found at i:1147941 original size:15 final size:15 Alignment explanation

Indices: 1147807--1147992 Score: 65 Period size: 15 Copynumber: 11.5 Consensus size: 15 1147797 GATAAAGTAA * * 1147807 AATATAATATAATAC 1 AATATCATATTATAC * 1147822 AATATTATATTATAC 1 AATATCATATTATAC 1147837 ATATTGTATCATA--ATAC 1 A-A---TATCATATTATAC * 1147854 AATAAT-ATATTTTAC 1 AAT-ATCATATTATAC ** 1147869 AATATCATACAATAC 1 AATATCATATTATAC * 1147884 AATTTCATGTGATGTGATA- 1 AATATCA--T-AT-T-ATAC 1147903 ATATATCATATTATAAACC 1 A-ATATCATATTAT--A-C * 1147922 AATATTATATTATAC 1 AATATCATATTATAC * * 1147937 AATATCGTATGATAC 1 AATATCATATTATAC * * 1147952 TATATTATATAATATAAC 1 AATATCATAT--TAT-AC * 1147970 AGTATCATATTATAC 1 AATATCATATTATAC * 1147985 AATTTCAT 1 AATATCAT 1147993 GTGATATAAT Statistics Matches: 126, Mismatches: 24, Indels: 42 0.66 0.12 0.22 Matches are distributed among these distances: 13 4 0.03 14 4 0.03 15 62 0.49 16 7 0.06 17 11 0.09 18 22 0.17 19 8 0.06 20 8 0.06 ACGTcount: A:0.45, C:0.10, G:0.04, T:0.40 Consensus pattern (15 bp): AATATCATATTATAC Found at i:1147998 original size:48 final size:48 Alignment explanation

Indices: 1147895--1147998 Score: 120 Period size: 48 Copynumber: 2.2 Consensus size: 48 1147885 ATTTCATGTG * * 1147895 ATGTGATAATATATCATATTATAAACCAATATTATATTATACAATATC 1 ATGTGATAATATATCATATAATAAACCAATATCATATTATACAATATC * * * * * * 1147943 GTATGATACTATATTATATAATATAA-CAGTATCATATTATACAATTTC 1 ATGTGATAATATATCATATAATA-AACCAATATCATATTATACAATATC 1147991 ATGTGATA 1 ATGTGATA 1147999 TAATTCTTTT Statistics Matches: 45, Mismatches: 10, Indels: 2 0.79 0.18 0.04 Matches are distributed among these distances: 48 43 0.96 49 2 0.04 ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40 Consensus pattern (48 bp): ATGTGATAATATATCATATAATAAACCAATATCATATTATACAATATC Found at i:1149271 original size:177 final size:178 Alignment explanation

Indices: 1148966--1149882 Score: 1244 Period size: 177 Copynumber: 5.2 Consensus size: 178 1148956 TGTGACCTGT * * * * * * ** 1148966 TCCAAAAAACTTAACCAT-ATCCAGCATCTGAAACCTATGGCTCAGACTCAGCATTCAAAACTGT 1 TCCAAAAACCTTAACC-TCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGT * * * * * * * * * 1149030 CAGGTGCATCAGTATCATAAGACGCACCATTCATGGAAGTCTGGTGAAGTTA-GAACAAGTAATA 65 CTGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAG-TACGGACCAGCAGTA * * *** * 1149094 ACTAAGATATAAT-C-ATCAGAGGGCACCTGTTTCAAACACTTTAACCAGC 129 ACTTAGATAT-ATGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC * * * * 1149143 TCTAAAAACCTTAACCTCCTTCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTC 1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC * * * * * * * 1149208 TGGTGCATCAGTATCATAAGACGCACCATCCATGGAAGTCTGGTGAAGTTA-GAACAAGTAATAA 66 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAG-TACGGACCAGCAGTAA * * 1149272 CTAAGATATAAT-C-ATCAGAGGGCACCTGCAACAAAAACTTTAACCAGC 130 CTTAGATAT-ATGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC * * * * 1149320 T-CTAAAACCTTAACCTCCTCCAGCATCCGAAACCCATAGCTCAGATTCAGCACCCAAGCCTGCC 1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC * * 1149384 TGGTTCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAAC 66 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCAGCAGTAAC * * * 1149449 TTAGTTAT-TGCTATCAATGGGCACCTGCAACAAAAACTTTAACCTGC 131 TTAGATATATGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC * 1149496 TCCAAAAACCTTAACCTCCTCCAGCATCCAAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC 1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC 1149561 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCAGCAGTAAC 66 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCAGCAGTAAC 1149626 TTAGATAT-TGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC 131 TTAGATATATGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC * 1149673 TCCAAAAACCTTAACCTCCTCCAGCATCCAAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC 1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC * 1149738 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAAC 66 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCAGCAGTAAC * * 1149803 TTAGATAT-TGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCTGG 131 TTAGATATATGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC * * 1149850 TCCAACAACCTTAACCTCCTCCAGCATCTGAAA 1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAA 1149883 TTTAGGACTC Statistics Matches: 683, Mismatches: 52, Indels: 10 0.92 0.07 0.01 Matches are distributed among these distances: 174 1 0.00 175 3 0.00 176 148 0.22 177 531 0.78 ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23 Consensus pattern (178 bp): TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCAGCAGTAAC TTAGATATATGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC Found at i:1149495 original size:19 final size:19 Alignment explanation

Indices: 1149471--1149512 Score: 57 Period size: 19 Copynumber: 2.2 Consensus size: 19 1149461 ATCAATGGGC * 1149471 ACCTGCAACAAAAACTTTA 1 ACCTGCAACAAAAACCTTA ** 1149490 ACCTGCTCCAAAAACCTTA 1 ACCTGCAACAAAAACCTTA 1149509 ACCT 1 ACCT 1149513 CCTCCAGCAT Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 19 20 1.00 ACGTcount: A:0.40, C:0.33, G:0.05, T:0.21 Consensus pattern (19 bp): ACCTGCAACAAAAACCTTA Found at i:1149517 original size:19 final size:19 Alignment explanation

Indices: 1149479--1149518 Score: 62 Period size: 19 Copynumber: 2.1 Consensus size: 19 1149469 GCACCTGCAA * * 1149479 CAAAAACTTTAACCTGCTC 1 CAAAAACCTTAACCTCCTC 1149498 CAAAAACCTTAACCTCCTC 1 CAAAAACCTTAACCTCCTC 1149517 CA 1 CA 1149519 GCATCCAAAA Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 19 19 1.00 ACGTcount: A:0.38, C:0.38, G:0.03, T:0.23 Consensus pattern (19 bp): CAAAAACCTTAACCTCCTC Found at i:1149694 original size:19 final size:19 Alignment explanation

Indices: 1149656--1149695 Score: 53 Period size: 19 Copynumber: 2.1 Consensus size: 19 1149646 GCACCTGCAA * * 1149656 CAAAAACTTTAACCAGCTC 1 CAAAAACCTTAACCACCTC * 1149675 CAAAAACCTTAACCTCCTC 1 CAAAAACCTTAACCACCTC 1149694 CA 1 CA 1149696 GCATCCAAAA Statistics Matches: 18, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 19 18 1.00 ACGTcount: A:0.40, C:0.38, G:0.03, T:0.20 Consensus pattern (19 bp): CAAAAACCTTAACCACCTC Found at i:1149834 original size:354 final size:353 Alignment explanation

Indices: 1148966--1149877 Score: 1262 Period size: 353 Copynumber: 2.6 Consensus size: 353 1148956 TGTGACCTGT * * * * * * ** 1148966 TCCAAAAAACTTAACCAT-ATCCAGCATCTGAAACCTATGGCTCAGACTCAGCATTCAAAACTGT 1 TCCAAAAACCTTAACC-TCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGT * * * * * * ** * * 1149030 CAGGTGCATCAGTATCATAAGACGCACCATTCATGGAAGTCTGGTGAAGTTA-GAACAAGTAATA 65 CTGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAG-TACGGACCTGCAGTA * * *** * * * 1149094 ACTAAGATATAAT-C-ATCAGAGGGCACCTGTTTCAAACACTTTAACCAGCTCTAAAAACCTTAA 129 ACTTAGATAT--TGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAA * * * * 1149157 CCTCCTTCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCTGGTGCATCAGTAT 192 CCTCCTCCAGCATCCAAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTCTGGTGCATCAGTAT * * * 1149222 CATAAGACGCACCATCCATGGAAGTCTGGTGAAGTTAGAACAAGTAATAACTAAGATATAATCAT 257 CATAAGACACACCATCCATGCAAGTCTGGTGAAGTTAGAACAAGCAATAACTAAGATAT-ATCAT * 1149287 CAGAGGGCACCTGCAACAAAAACTTTAACCAGC 321 CAAAGGGCACCTGCAACAAAAACTTTAACCAGC * * * * 1149320 T-CTAAAACCTTAACCTCCTCCAGCATCCGAAACCCATAGCTCAGATTCAGCACCCAAGCCTGCC 1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC * 1149384 TGGTTCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAAC 66 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAAC * * 1149449 TTAGTTATTGCTATCAATGGGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTC 131 TTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTC 1149514 CTCCAGCATCCAAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTCTGGTGCATCAGTATCATA 196 CTCCAGCATCCAAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTCTGGTGCATCAGTATCATA * * * * * 1149579 AGACACACCATCCATGCAAGTTTGGTGAAG-TACGGACCAGCAGTAACTTAGATAT-TGCTATCA 261 AGACACACCATCCATGCAAGTCTGGTGAAGTTA-GAACAAGCAATAACTAAGATATAT-C-ATCA 1149642 AAGGGCACCTGCAACAAAAACTTTAACCAGC 323 AAGGGCACCTGCAACAAAAACTTTAACCAGC * 1149673 TCCAAAAACCTTAACCTCCTCCAGCATCCAAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC 1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC 1149738 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAAC 66 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAAC * * 1149803 TTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCTGGTCCAACAACCTTAACCTC 131 TTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTC 1149868 CTCCAGCATC 196 CTCCAGCATC 1149878 TGAAATTTAG Statistics Matches: 494, Mismatches: 56, Indels: 16 0.87 0.10 0.03 Matches are distributed among these distances: 351 2 0.00 352 7 0.01 353 291 0.59 354 194 0.39 ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23 Consensus pattern (353 bp): TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAAC TTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTC CTCCAGCATCCAAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTCTGGTGCATCAGTATCATA AGACACACCATCCATGCAAGTCTGGTGAAGTTAGAACAAGCAATAACTAAGATATATCATCAAAG GGCACCTGCAACAAAAACTTTAACCAGC Found at i:1149947 original size:354 final size:351 Alignment explanation

Indices: 1148966--1149986 Score: 1227 Period size: 353 Copynumber: 2.9 Consensus size: 351 1148956 TGTGACCTGT * * * * * * ** 1148966 TCCAAAAAACTTAACCAT-ATCCAGCATCTGAAACCTATGGCTCAGACTCAGCATTCAAAACTGT 1 TCCAAAAACCTTAACC-TCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGT * * * * * * ** * * 1149030 CAGGTGCATCAGTATCATAAGACGCACCATTCATGGAAGTCTGGTGAAGTTA-GAACAAGTAATA 65 CTGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAG-TACGGACCTGCAGTA * * *** * * * 1149094 ACTAAGATATAAT-C-ATCAGAGGGCACCTGTTTCAAACACTTTAACCAGCTCTAAAAACCTTAA 129 ACTTAGATAT--TGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAA * * 1149157 CCTCCTTCAGCATCCGAAACCTAT-GGCTCAGATTCAGCATTCAAGCCTGTCTGGTGCATCAGTA 192 CCTCCTCCAGCATCCGAAA--TATAGGCTCAGATTCAGCATCCAAGCCTGTCTGGTGCATCAGTA * * * 1149221 TCATAAGACGCACCATCCATGGAAGTCTGGTGAAGTTAGAACAAGTAATAACTAAGATATAATCA 255 TCA-AAGACGCACCATCCATGCAAGTTTGGTGAAGTTAGAACAAGCAATAACTAAGATAT-ATCA * 1149286 TCAGAGGGCACCTGCAACAAAAACTTTAACCAGC 318 TCAAAGGGCACCTGCAACAAAAACTTTAACCAGC * * * * 1149320 T-CTAAAACCTTAACCTCCTCCAGCATCCGAAACCCATAGCTCAGATTCAGCACCCAAGCCTGCC 1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC * 1149384 TGGTTCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAAC 66 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAAC * * 1149449 TTAGTTATTGCTATCAATGGGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTC 131 TTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTC * 1149514 CTCCAGCATCCAAAACCTATA-GCTCAGATTCAGCA-CTCAAGCCTGTCTGGTGCATCAGTATCA 196 CTCCAGCATCCGAAA--TATAGGCTCAGATTCAGCATC-CAAGCCTGTCTGGTGCATCAGTATCA * * * * * 1149577 TAAGACACACCATCCATGCAAGTTTGGTGAAG-TACGGACCAGCAGTAACTTAGATAT-TGCTAT 258 -AAGACGCACCATCCATGCAAGTTTGGTGAAGTTA-GAACAAGCAATAACTAAGATATAT-C-AT 1149640 CAAAGGGCACCTGCAACAAAAACTTTAACCAGC 319 CAAAGGGCACCTGCAACAAAAACTTTAACCAGC * 1149673 TCCAAAAACCTTAACCTCCTCCAGCATCCAAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC 1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC 1149738 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAAC 66 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAAC * * 1149803 TTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCTGGTCCAACAACCTTAACCTC 131 TTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTC * * * * ** * * 1149868 CTCCAGCATCTGAAATTTAGGACTCAGATTCAGCATCCAAGTCTTTCAAGTCCATAAGTAGGTC- 196 CTCCAGCATCCGAAATATAGG-CTCAGATTCAGCATCCAAGCCTGTCTGGTGCATCAGTA--TCA * * * * * * * * 1149932 CAGATGCATCATCCATGCAAGTTTGGTGAAGATAGGACAAGTAATAGCTTAGATA 258 AAGACGCACCATCCATGCAAGTTTGGTGAAGTTAGAACAAGCAATAACTAAGATA 1149987 CAGGACCTGC Statistics Matches: 579, Mismatches: 72, Indels: 32 0.85 0.11 0.05 Matches are distributed among these distances: 351 2 0.00 352 10 0.02 353 291 0.50 354 271 0.47 355 3 0.01 356 2 0.00 ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24 Consensus pattern (351 bp): TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAAC TTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCTGCTCCAAAAACCTTAACCTC CTCCAGCATCCGAAATATAGGCTCAGATTCAGCATCCAAGCCTGTCTGGTGCATCAGTATCAAAG ACGCACCATCCATGCAAGTTTGGTGAAGTTAGAACAAGCAATAACTAAGATATATCATCAAAGGG CACCTGCAACAAAAACTTTAACCAGC Found at i:1149985 original size:177 final size:174 Alignment explanation

Indices: 1148966--1149986 Score: 1119 Period size: 177 Copynumber: 5.8 Consensus size: 174 1148956 TGTGACCTGT * * * * * * ** 1148966 TCCAAAAAACTTAACCAT-ATCCAGCATCTGAAACCTATGGCTCAGACTCAGCATTCAAAACTGT 1 TCCAAAAACCTTAACC-TCCTCCAGCATCCGAAA-CTATAGCTCAGATTCAGCA-CCAAGCCTGT * * * * * * * 1149030 CAGGTGCATCAGTATCATAAGACGCACCATTCATGGAAGTCTGGTGAAGTTA-GAACAAGTAATA 63 CTGGTGCATCAGTATCA-AAGACACACCATCCATGCAAGTTTGGTGAAG-TACGGACAAGCAATA * * *** * 1149094 ACTAAGATATAAT-C-ATCAGAGGGCACCTGTTTCAAACACTTTAACCAGC 126 ACTTAGATAT--TGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC * * * * 1149143 TCTAAAAACCTTAACCTCCTTCAGCATCCGAAACCTATGGCTCAGATTCAGCATTCAAGCCTGTC 1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAA-CTATAGCTCAGATTCAGCA-CCAAGCCTGTC * * * * * 1149208 TGGTGCATCAGTATCATAAGACGCACCATCCATGGAAGTCTGGTGAAGTTA-GAACAAGTAATAA 64 TGGTGCATCAGTATCA-AAGACACACCATCCATGCAAGTTTGGTGAAG-TACGGACAAGCAATAA * * 1149272 CTAAGATATAAT-C-ATCAGAGGGCACCTGCAACAAAAACTTTAACCAGC 127 CTTAGATAT--TGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC * * * 1149320 T-CTAAAACCTTAACCTCCTCCAGCATCCGAAACCCATAGCTCAGATTCAGCACCCAAGCCTGCC 1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAA-CTATAGCTCAGATTCAGCA-CCAAGCCTGTC * ** * 1149384 TGGTTCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAAC 64 TGGTGCATCAGTATCA-AAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACAAGCAATAAC * * * 1149449 TTAGTTATTGCTATCAATGGGCACCTGCAACAAAAACTTTAACCTGC 128 TTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC * 1149496 TCCAAAAACCTTAACCTCCTCCAGCATCCAAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC 1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAA-CTATAGCTCAGATTCAGCAC-CAAGCCTGTC * * 1149561 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCAGCAGTAAC 64 TGGTGCATCAGTATCA-AAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACAAGCAATAAC 1149626 TTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC 128 TTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC * 1149673 TCCAAAAACCTTAACCTCCTCCAGCATCCAAAACCTATAGCTCAGATTCAGCACTCAAGCCTGTC 1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAA-CTATAGCTCAGATTCAGCAC-CAAGCCTGTC ** * 1149738 TGGTGCATCAGTATCATAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACCTGCAGTAAC 64 TGGTGCATCAGTATCA-AAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACAAGCAATAAC * * 1149803 TTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCTGG 128 TTAGATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC * * * * * 1149850 TCCAACAACCTTAACCTCCTCCAGCATCTGAAA-TTTAGGACTCAGATTCAGCATCCAAGTCTTT 1 TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACTATA-G-CTCAGATTCAGCA-CCAAGCCTGT ** * * * ** * * 1149914 CAAGTCCATAAGTAGGTC-CAGATGCATCATCCATGCAAGTTTGGTGAAGATA-GGACAAGTAAT 63 CTGGTGCATCAGTA--TCAAAGACACACCATCCATGCAAGTTTGGTGAAG-TACGGACAAGCAAT * 1149977 AGCTTAGATA 125 AACTTAGATA 1149987 CAGGACCTGC Statistics Matches: 765, Mismatches: 67, Indels: 24 0.89 0.08 0.03 Matches are distributed among these distances: 174 1 0.00 175 6 0.01 176 150 0.20 177 603 0.79 178 3 0.00 179 2 0.00 ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24 Consensus pattern (174 bp): TCCAAAAACCTTAACCTCCTCCAGCATCCGAAACTATAGCTCAGATTCAGCACCAAGCCTGTCTG GTGCATCAGTATCAAAGACACACCATCCATGCAAGTTTGGTGAAGTACGGACAAGCAATAACTTA GATATTGCTATCAAAGGGCACCTGCAACAAAAACTTTAACCAGC Found at i:1152888 original size:2 final size:2 Alignment explanation

Indices: 1152881--1152907 Score: 54 Period size: 2 Copynumber: 13.5 Consensus size: 2 1152871 TGATCGTCAT 1152881 GA GA GA GA GA GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA GA GA GA GA G 1152908 TACTGGTATG Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 25 1.00 ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00 Consensus pattern (2 bp): GA Found at i:1154712 original size:3 final size:3 Alignment explanation

Indices: 1154698--1154733 Score: 54 Period size: 3 Copynumber: 12.0 Consensus size: 3 1154688 TTTGTCGACT * * 1154698 TTC TTT TTC TTC TTC TTC TTC TTC TTA TTC TTC TTC 1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC 1154734 ATCCAAATTT Statistics Matches: 29, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 3 29 1.00 ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69 Consensus pattern (3 bp): TTC Found at i:1157752 original size:21 final size:22 Alignment explanation

Indices: 1157717--1157758 Score: 59 Period size: 21 Copynumber: 2.0 Consensus size: 22 1157707 ACTGTATAGC * * 1157717 TGTCCGATGCTTGGT-AAATAT 1 TGTCCGATCCATGGTGAAATAT 1157738 TGTCCGATCCATGGTGAAATA 1 TGTCCGATCCATGGTGAAATA 1157759 GTTCAACACT Statistics Matches: 18, Mismatches: 2, Indels: 1 0.86 0.10 0.05 Matches are distributed among these distances: 21 13 0.72 22 5 0.28 ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33 Consensus pattern (22 bp): TGTCCGATCCATGGTGAAATAT Found at i:1162395 original size:166 final size:166 Alignment explanation

Indices: 1162220--1162538 Score: 437 Period size: 166 Copynumber: 1.9 Consensus size: 166 1162210 CAGGTTAAAG * * 1162220 TTTTTGTTGCAGGTGTCCTCTGATAGCA-ATATCTAACTTACTGCTGGTCCAAACTTCACCAAAC 1 TTTTTGTTGCAGGTGCCCTCTGAT-G-ATATATCTAACTTACTACTGGTCCAAACTTCACCAAAC * * * 1162284 TTGCATGGATGGT-GTCTTATGATACTGATGCACCAGACAGGCTTAAATGCTGAATCTGAGCTAT 64 TTGCATGGATGGTCGTCTCATGATACTGATGCACCAGACAGACTTAAATGCTGAATCTGAGCCAT 1162348 AGG-CTTCGGATGCTGGATGAGGTTAAGGTTTTTTGAGC 129 AGGTCTTCGGA-GCTGGATGAGGTTAAGGTTTTTTGAGC * * ** * 1162386 TTTTTGTTGCAGGTGCCCTCTGATGATTATATCTTAGTTACTACTGGTCCTTACTTCATCAAACT 1 TTTTTGTTGCAGGTGCCCTCTGATGA-TATATCTAACTTACTACTGGTCCAAACTTCACCAAACT * * * 1162451 TGCATGGATGGTGCGTCTCATGATAGTGATGCACCATACAGACTTGAATGCTGAATCTGAGCCAT 65 TGCATGGATGGT-CGTCTCATGATACTGATGCACCAGACAGACTTAAATGCTGAATCTGAGCCAT * * 1162516 AGGTTTTTGGAGCTGGATGAGGT 129 AGGTCTTCGGAGCTGGATGAGGT 1162539 GAAGATTAAA Statistics Matches: 133, Mismatches: 15, Indels: 8 0.85 0.10 0.05 Matches are distributed among these distances: 164 1 0.01 165 1 0.01 166 66 0.50 168 60 0.45 169 5 0.04 ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34 Consensus pattern (166 bp): TTTTTGTTGCAGGTGCCCTCTGATGATATATCTAACTTACTACTGGTCCAAACTTCACCAAACTT GCATGGATGGTCGTCTCATGATACTGATGCACCAGACAGACTTAAATGCTGAATCTGAGCCATAG GTCTTCGGAGCTGGATGAGGTTAAGGTTTTTTGAGC Found at i:1165118 original size:171 final size:172 Alignment explanation

Indices: 1164700--1165151 Score: 773 Period size: 172 Copynumber: 2.6 Consensus size: 172 1164690 TCACACTTTT 1164700 TTGTAAGCGCTCTCATGCCTA-ATAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTAT 1 TTGTAAGCGCTCTCATGCCTACA-AATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTAT ** * * 1164764 ACCACTTTTACCTTGGTCAAGTTTGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGG 65 ACCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTAATGGG 1164829 ACTTTGACCACAATAATGACTCCATTTTATCCAAAAATTGACC 130 ACTTTGACCACAATAATGACTCCATTTTATCCAAAAATTGACC * 1164872 TTGTAAGCGCTCTCATGCCAACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA 1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA * * 1164937 CCATTAATACCTTGGTCAAGTTCGAAAATCAGCGTTGGTCGATACTTTTTGTTGGAGTAATGGGA 66 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTAATGGGA ** 1165002 CTTTGACCACAATAATGACT-TGTTTTATCCAAAAATTGACC 131 CTTTGACCACAATAATGACTCCATTTTATCCAAAAATTGACC 1165043 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA 1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA ** * 1165108 CCACTAATACCTTGGTCAAGTTCCTAAATCAGCCTTGGTCGATA 66 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATA 1165152 GACTCGATAC Statistics Matches: 265, Mismatches: 14, Indels: 3 0.94 0.05 0.01 Matches are distributed among these distances: 171 123 0.46 172 141 0.53 173 1 0.00 ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37 Consensus pattern (172 bp): TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTAATGGGA CTTTGACCACAATAATGACTCCATTTTATCCAAAAATTGACC Found at i:1166627 original size:19 final size:20 Alignment explanation

Indices: 1166593--1166637 Score: 65 Period size: 19 Copynumber: 2.3 Consensus size: 20 1166583 CCGTGTCGCA * 1166593 CCGTGGCCGCCTGTGTAACT 1 CCGTGGCCGACTGTGTAACT * 1166613 CCGTGGCC-ACTGTGTTACT 1 CCGTGGCCGACTGTGTAACT 1166632 CCGTGG 1 CCGTGG 1166638 ATATCGTTAC Statistics Matches: 23, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 19 15 0.65 20 8 0.35 ACGTcount: A:0.09, C:0.33, G:0.31, T:0.27 Consensus pattern (20 bp): CCGTGGCCGACTGTGTAACT Found at i:1168109 original size:2 final size:2 Alignment explanation

Indices: 1168104--1168148 Score: 90 Period size: 2 Copynumber: 22.5 Consensus size: 2 1168094 ACACTTTCAC 1168104 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1168146 AG A 1 AG A 1168149 TTTTACAACG Statistics Matches: 43, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 43 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:1168480 original size:2 final size:2 Alignment explanation

Indices: 1168473--1168524 Score: 104 Period size: 2 Copynumber: 26.0 Consensus size: 2 1168463 ATACTGGTTT 1168473 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1168515 TC TC TC TC TC 1 TC TC TC TC TC 1168525 ATATGACGAT Statistics Matches: 50, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 50 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:1170144 original size:180 final size:180 Alignment explanation

Indices: 1169838--1170208 Score: 600 Period size: 180 Copynumber: 2.1 Consensus size: 180 1169828 TGGCGGCTGC * 1169838 CATA-AGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTT 1 CATATAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTT * * * 1169902 TCGCAGATCAATTGTACATATATCAGAGGTGTGCATATTGCAAGGATTTTGATTTCTGATAATTT 66 TCGCAGATCAAATGTACATATATCAGAGGTGTGCATAATGCAAGGATCTTGATTTCTGATAATTT * 1169967 ATCAAAAAAATACCAGGTTTTGAACTTAGTCATTTTTTGGCAAAATATTG 131 ATCAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTG * 1170017 CATATAGGGTACCCTCATTGTGCGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTT 1 CATATAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTT * * * 1170082 TTGCAGATCAAATGTACTTATATCAGAGGTGTGCATAATGCTAGGATCTTGATTTCTGATAATTT 66 TCGCAGATCAAATGTACATATATCAGAGGTGTGCATAATGCAAGGATCTTGATTTCTGATAATTT * * * * * 1170147 ATGAAAAAAATACTAGCTTTTGAACTTGGTCATTTTTTTGCAAAATGTTG 131 ATCAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTG * 1170197 CATGTAGGGTAC 1 CATATAGGGTAC 1170209 TCCATTTCAC Statistics Matches: 176, Mismatches: 15, Indels: 1 0.92 0.08 0.01 Matches are distributed among these distances: 179 4 0.02 180 172 0.98 ACGTcount: A:0.30, C:0.16, G:0.19, T:0.36 Consensus pattern (180 bp): CATATAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTT TCGCAGATCAAATGTACATATATCAGAGGTGTGCATAATGCAAGGATCTTGATTTCTGATAATTT ATCAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTG Found at i:1173880 original size:38 final size:38 Alignment explanation

Indices: 1173822--1174639 Score: 1317 Period size: 38 Copynumber: 21.6 Consensus size: 38 1173812 TGAATGACTA * * 1173822 AGCCCCATCCATCTCTTAAAACAGTTCCTGTAACACTG 1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG 1173860 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG 1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG * 1173898 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAGCACTG 1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG * * * 1173936 AGCCCCATCCAACACTTAAAGCAGTTCCTGTAACACTG 1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG * 1173974 AGCCCCATCCAAC-CCTTAAAACAATTCCTGTAACACTG 1 AGCCCCATCCAACTCC-TAAAACAGTTCCTGTAACACTG 1174012 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG 1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG 1174050 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG 1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG * 1174088 AGCCTCATCCAAC-CCTTAAAACAAG-TCCTGTAACACTG 1 AGCCCCATCCAACTCC-TAAAAC-AGTTCCTGTAACACTG * 1174126 AGCCCCATCCAAC-CCTTAAAACAGTTACTGTAACACTG 1 AGCCCCATCCAACTCC-TAAAACAGTTCCTGTAACACTG 1174164 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG 1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG 1174202 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG 1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG * * * 1174240 AGCCCAATCCAACTCCTAAAAAAGTTCCTGTAGCACTG 1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG 1174278 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG 1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG ** 1174316 AGCCTTATCCAAC-CCTTAAAACAGTTCCTGTAACACTG 1 AGCCCCATCCAACTCC-TAAAACAGTTCCTGTAACACTG * * * 1174354 AGCCCCATCCAACACTTAAAACAGTTCCTGTAACACTA 1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG 1174392 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG 1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG * * * 1174430 AGCCCCATCCAAC-ACTTAAGCAGTTCCTGTAACACTG 1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG * 1174467 AGCCCCATCCAACTCCTAAAGCAGTTCCTGTAACACTG 1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG 1174505 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG 1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG * * 1174543 AGCTCCATCCAACTCTTAAAACAGTTCCTGTAACACTG 1 AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG 1174581 AGCCCCATCCAAC-CCTCAAAACAGTTCCTGTAACACTG 1 AGCCCCATCCAACTCCT-AAAACAGTTCCTGTAACACTG * 1174619 AGCCCCATCCAACTCTTAAAA 1 AGCCCCATCCAACTCCTAAAA 1174640 TAGCTCTGTT Statistics Matches: 728, Mismatches: 41, Indels: 22 0.92 0.05 0.03 Matches are distributed among these distances: 37 43 0.06 38 676 0.93 39 9 0.01 ACGTcount: A:0.32, C:0.36, G:0.11, T:0.22 Consensus pattern (38 bp): AGCCCCATCCAACTCCTAAAACAGTTCCTGTAACACTG Found at i:1181047 original size:17 final size:17 Alignment explanation

Indices: 1181025--1181057 Score: 57 Period size: 17 Copynumber: 1.9 Consensus size: 17 1181015 TTTAAATTTT * 1181025 TAATTTTAATTTAATAG 1 TAATTTTAATTGAATAG 1181042 TAATTTTAATTGAATA 1 TAATTTTAATTGAATA 1181058 AATTAAAGAA Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 17 15 1.00 ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52 Consensus pattern (17 bp): TAATTTTAATTGAATAG Found at i:1190605 original size:2 final size:2 Alignment explanation

Indices: 1190598--1190639 Score: 84 Period size: 2 Copynumber: 21.0 Consensus size: 2 1190588 CCCCCTACCC 1190598 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1190640 CCCGGTACCT Statistics Matches: 40, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 40 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): AG Found at i:1195121 original size:12 final size:12 Alignment explanation

Indices: 1195106--1195131 Score: 52 Period size: 12 Copynumber: 2.2 Consensus size: 12 1195096 ATATATACAC 1195106 ATATATATTGCA 1 ATATATATTGCA 1195118 ATATATATTGCA 1 ATATATATTGCA 1195130 AT 1 AT 1195132 TAAGAATTAA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 14 1.00 ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42 Consensus pattern (12 bp): ATATATATTGCA Found at i:1195683 original size:11 final size:11 Alignment explanation

Indices: 1195669--1195697 Score: 51 Period size: 11 Copynumber: 2.7 Consensus size: 11 1195659 AATTTTTTAA 1195669 TTTTTTA-TTT 1 TTTTTTATTTT 1195679 TTTTTTATTTT 1 TTTTTTATTTT 1195690 TTTTTTAT 1 TTTTTTAT 1195698 AAAAAGTAGA Statistics Matches: 18, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 10 7 0.39 11 11 0.61 ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90 Consensus pattern (11 bp): TTTTTTATTTT Found at i:1195683 original size:17 final size:16 Alignment explanation

Indices: 1195661--1195695 Score: 52 Period size: 17 Copynumber: 2.1 Consensus size: 16 1195651 TTTTATATAA 1195661 TTTTTTAATTTTTTATT 1 TTTTTTAATTTTTT-TT * 1195678 TTTTTTTATTTTTTTT 1 TTTTTTAATTTTTTTT 1195694 TT 1 TT 1195696 ATAAAAAGTA Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 16 4 0.24 17 13 0.76 ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89 Consensus pattern (16 bp): TTTTTTAATTTTTTTT Found at i:1195694 original size:10 final size:10 Alignment explanation

Indices: 1195669--1195694 Score: 52 Period size: 10 Copynumber: 2.6 Consensus size: 10 1195659 AATTTTTTAA 1195669 TTTTTTATTT 1 TTTTTTATTT 1195679 TTTTTTATTT 1 TTTTTTATTT 1195689 TTTTTT 1 TTTTTT 1195695 TATAAAAAGT Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 16 1.00 ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92 Consensus pattern (10 bp): TTTTTTATTT Found at i:1196916 original size:22 final size:22 Alignment explanation

Indices: 1196891--1197059 Score: 194 Period size: 22 Copynumber: 7.5 Consensus size: 22 1196881 TAGAATGTTT * 1196891 ATTAAAGGACGGCTAGTATGTC 1 ATTAATGGACGGCTAGTATGTC 1196913 ATTAATGGACGGCTAGTATGTC 1 ATTAATGGACGGCTAGTATGTC * * * * 1196935 ATTGATGGACGGCTAGAAAGTTT 1 ATTAATGGACGGCTAGTATG-TC 1196958 ATTAATGGACGGCTAGTATGTC 1 ATTAATGGACGGCTAGTATGTC * * * 1196980 ATTGATGGACGGCTAGAAAGTC 1 ATTAATGGACGGCTAGTATGTC 1197002 TATTAATGGACGGCTAGTATGTC 1 -ATTAATGGACGGCTAGTATGTC * * * * 1197025 ATTGATGGACAGCTAGAAAGTC 1 ATTAATGGACGGCTAGTATGTC * 1197047 TATTAAAGGACGG 1 -ATTAATGGACGG 1197060 TTTTTTTTTT Statistics Matches: 122, Mismatches: 22, Indels: 5 0.82 0.15 0.03 Matches are distributed among these distances: 22 76 0.62 23 46 0.38 ACGTcount: A:0.31, C:0.12, G:0.28, T:0.28 Consensus pattern (22 bp): ATTAATGGACGGCTAGTATGTC Found at i:1196967 original size:45 final size:45 Alignment explanation

Indices: 1196897--1197059 Score: 274 Period size: 45 Copynumber: 3.6 Consensus size: 45 1196887 GTTTATTAAA * * 1196897 GGACGGCTAGTATGTC-ATTAATGGACGGCTAGTATGTCATTGAT 1 GGACGGCTAGAAAGTCTATTAATGGACGGCTAGTATGTCATTGAT * 1196941 GGACGGCTAGAAAGTTTATTAATGGACGGCTAGTATGTCATTGAT 1 GGACGGCTAGAAAGTCTATTAATGGACGGCTAGTATGTCATTGAT 1196986 GGACGGCTAGAAAGTCTATTAATGGACGGCTAGTATGTCATTGAT 1 GGACGGCTAGAAAGTCTATTAATGGACGGCTAGTATGTCATTGAT * * 1197031 GGACAGCTAGAAAGTCTATTAAAGGACGG 1 GGACGGCTAGAAAGTCTATTAATGGACGG 1197060 TTTTTTTTTT Statistics Matches: 112, Mismatches: 6, Indels: 1 0.94 0.05 0.01 Matches are distributed among these distances: 44 13 0.12 45 99 0.88 ACGTcount: A:0.29, C:0.13, G:0.29, T:0.28 Consensus pattern (45 bp): GGACGGCTAGAAAGTCTATTAATGGACGGCTAGTATGTCATTGAT Found at i:1196989 original size:67 final size:68 Alignment explanation

Indices: 1196881--1197018 Score: 215 Period size: 67 Copynumber: 2.0 Consensus size: 68 1196871 AGTATGTCGT * * * * 1196881 TAGAATGTTTATTAAAGGACGGCTAGTATGTCATTAATGGACGGCTAGTATGTC-ATTGATGGAC 1 TAGAAAGTTTATTAAAGGACGGCTAGTATGTCATTAATGGACGGCTAGAAAGTCTATTAATGGAC 1196945 GGC 66 GGC * * 1196948 TAGAAAGTTTATTAATGGACGGCTAGTATGTCATTGATGGACGGCTAGAAAGTCTATTAATGGAC 1 TAGAAAGTTTATTAAAGGACGGCTAGTATGTCATTAATGGACGGCTAGAAAGTCTATTAATGGAC 1197013 GGC 66 GGC 1197016 TAG 1 TAG 1197019 TATGTCATTG Statistics Matches: 64, Mismatches: 6, Indels: 1 0.90 0.08 0.01 Matches are distributed among these distances: 67 49 0.77 68 15 0.23 ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30 Consensus pattern (68 bp): TAGAAAGTTTATTAAAGGACGGCTAGTATGTCATTAATGGACGGCTAGAAAGTCTATTAATGGAC GGC Found at i:1197033 original size:67 final size:67 Alignment explanation

Indices: 1196881--1197059 Score: 198 Period size: 67 Copynumber: 2.7 Consensus size: 67 1196871 AGTATGTCGT * * * * * * 1196881 TAGAATGTTTATTAAAGGACGGCTAGTATGTCATTAATGGACGGCTAGTATGTCATTGATGGACG 1 TAGAAAGTTCATTAATGGACGGCTAGTATGTCATTAATGGACGGCTAGAAAGTCATTAATGGACG 1196946 GC 66 GC * * 1196948 TAGAAAGTTTATTAATGGACGGCTAGTATGTCATTGATGGACGGCTAGAAAGTCTATTAATGGAC 1 TAGAAAGTTCATTAATGGACGGCTAGTATGTCATTAATGGACGGCTAGAAAGTC-ATTAATGGAC 1197013 GGC 65 GGC * * * * * * * 1197016 TAGTATG-TCATTGATGGACAGCTAGAAAGTCTATTAAAGGACGG 1 TAGAAAGTTCATTAATGGACGGCTAGTATGTC-ATTAATGGACGG 1197060 TTTTTTTTTT Statistics Matches: 95, Mismatches: 15, Indels: 3 0.84 0.13 0.03 Matches are distributed among these distances: 67 68 0.72 68 27 0.28 ACGTcount: A:0.31, C:0.12, G:0.28, T:0.30 Consensus pattern (67 bp): TAGAAAGTTCATTAATGGACGGCTAGTATGTCATTAATGGACGGCTAGAAAGTCATTAATGGACG GC Found at i:1197248 original size:17 final size:17 Alignment explanation

Indices: 1197223--1197265 Score: 68 Period size: 17 Copynumber: 2.5 Consensus size: 17 1197213 TACTTTGCTT 1197223 CCAAAAAAAGAGAAAAAA 1 CCAAAAAAA-AGAAAAAA * 1197241 CCAAAAAAAATAAAAAA 1 CCAAAAAAAAGAAAAAA 1197258 CCAAAAAA 1 CCAAAAAA 1197266 TAAATAACAA Statistics Matches: 24, Mismatches: 1, Indels: 1 0.92 0.04 0.04 Matches are distributed among these distances: 17 15 0.62 18 9 0.38 ACGTcount: A:0.79, C:0.14, G:0.05, T:0.02 Consensus pattern (17 bp): CCAAAAAAAAGAAAAAA Found at i:1197276 original size:14 final size:15 Alignment explanation

Indices: 1197235--1197282 Score: 53 Period size: 15 Copynumber: 3.1 Consensus size: 15 1197225 AAAAAAAGAG 1197235 AAAAAACCAAAAAAAAT 1 AAAAAACC--AAAAAAT 1197252 AAAAAACCAAAAAAT 1 AAAAAACCAAAAAAT * * 1197267 AAATAA-CAAATAAT 1 AAAAAACCAAAAAAT 1197281 AA 1 AA 1197283 TACGAATAGT Statistics Matches: 29, Mismatches: 2, Indels: 3 0.85 0.06 0.09 Matches are distributed among these distances: 14 9 0.31 15 12 0.41 17 8 0.28 ACGTcount: A:0.79, C:0.10, G:0.00, T:0.10 Consensus pattern (15 bp): AAAAAACCAAAAAAT Found at i:1220405 original size:1 final size:1 Alignment explanation

Indices: 1220399--1220434 Score: 72 Period size: 1 Copynumber: 36.0 Consensus size: 1 1220389 NNNNNNNNNN 1220399 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1220435 TTAAAGTAAT Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 35 1.00 ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00 Consensus pattern (1 bp): A Found at i:1224008 original size:23 final size:18 Alignment explanation

Indices: 1223962--1223997 Score: 72 Period size: 18 Copynumber: 2.0 Consensus size: 18 1223952 TAAAGTGAAA 1223962 TACAAATACAAATATTTT 1 TACAAATACAAATATTTT 1223980 TACAAATACAAATATTTT 1 TACAAATACAAATATTTT 1223998 ATTGGCACAA Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 18 1.00 ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39 Consensus pattern (18 bp): TACAAATACAAATATTTT Found at i:1226300 original size:40 final size:39 Alignment explanation

Indices: 1226256--1226341 Score: 100 Period size: 39 Copynumber: 2.2 Consensus size: 39 1226246 TACGGATCGA * * * 1226256 AAACTGTAGTCAACGACGTTAATCTATATTTCACGTCTGT 1 AAACTATAGTCAACG-CGATAATCTATATTTCACATCTGT * * * 1226296 AAACTATAGTTAACGTGATAATCTATGTTTCACATCTGT 1 AAACTATAGTCAACGCGATAATCTATATTTCACATCTGT * 1226335 TAACTAT 1 AAACTAT 1226342 TATTGGTAAA Statistics Matches: 39, Mismatches: 7, Indels: 1 0.83 0.15 0.02 Matches are distributed among these distances: 39 26 0.67 40 13 0.33 ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37 Consensus pattern (39 bp): AAACTATAGTCAACGCGATAATCTATATTTCACATCTGT Found at i:1227213 original size:2 final size:2 Alignment explanation

Indices: 1227206--1227257 Score: 95 Period size: 2 Copynumber: 26.0 Consensus size: 2 1227196 TTTGCCACCA * 1227206 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1227248 TC TC TC TC TC 1 TC TC TC TC TC 1227258 ACACACACAC Statistics Matches: 48, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 2 48 1.00 ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52 Consensus pattern (2 bp): TC Found at i:1227312 original size:2 final size:2 Alignment explanation

Indices: 1227257--1227298 Score: 84 Period size: 2 Copynumber: 21.0 Consensus size: 2 1227247 CTCTCTCTCT 1227257 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA 1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA 1227299 ACCTTAAAAC Statistics Matches: 40, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 40 1.00 ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00 Consensus pattern (2 bp): CA Found at i:1227679 original size:12 final size:12 Alignment explanation

Indices: 1227662--1227714 Score: 63 Period size: 12 Copynumber: 4.4 Consensus size: 12 1227652 CGCGTTCATC 1227662 TGTTGATGTTGT 1 TGTTGATGTTGT 1227674 TGTTGATGTTGT 1 TGTTGATGTTGT 1227686 TGTTGAT-TTGGT 1 TGTTGATGTT-GT * * * 1227698 TGCTGTTGCTGT 1 TGTTGATGTTGT 1227710 TGTTG 1 TGTTG 1227715 TCCTAATTTA Statistics Matches: 35, Mismatches: 4, Indels: 4 0.81 0.09 0.09 Matches are distributed among these distances: 11 2 0.06 12 32 0.91 13 1 0.03 ACGTcount: A:0.06, C:0.04, G:0.34, T:0.57 Consensus pattern (12 bp): TGTTGATGTTGT Found at i:1227824 original size:24 final size:24 Alignment explanation

Indices: 1227779--1227825 Score: 60 Period size: 24 Copynumber: 2.0 Consensus size: 24 1227769 CTGCGCCGCC * 1227779 TGCATCTGCATCATCTGCTGCTGT 1 TGCATCTGCATCACCTGCTGCTGT * 1227803 TGCAT-TGCATTCACCTGTTGCTG 1 TGCATCTGCA-TCACCTGCTGCTG 1227826 ATACTGCGCA Statistics Matches: 20, Mismatches: 2, Indels: 2 0.83 0.08 0.08 Matches are distributed among these distances: 23 4 0.20 24 16 0.80 ACGTcount: A:0.13, C:0.28, G:0.21, T:0.38 Consensus pattern (24 bp): TGCATCTGCATCACCTGCTGCTGT Found at i:1228313 original size:63 final size:63 Alignment explanation

Indices: 1228214--1228343 Score: 242 Period size: 63 Copynumber: 2.1 Consensus size: 63 1228204 GTCGTTGTTT * 1228214 GTGTCGTGTAACCTGGAAAAGGTGTTTATTATCGTACAGAACTGATCGTATTAATATCTTAAC 1 GTGTCGTGTAACCTGGAAAAGGTGTTTATTATCGTACAGAACTGATCGTATTAATATCATAAC * 1228277 GTGTCGTGTAACCTGGAAAAGGTGTTTATTATCGTACAGGACTGATCGTATTAATATCATAAC 1 GTGTCGTGTAACCTGGAAAAGGTGTTTATTATCGTACAGAACTGATCGTATTAATATCATAAC 1228340 GTGT 1 GTGT 1228344 GTTCGAATAG Statistics Matches: 65, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 63 65 1.00 ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35 Consensus pattern (63 bp): GTGTCGTGTAACCTGGAAAAGGTGTTTATTATCGTACAGAACTGATCGTATTAATATCATAAC Found at i:1229442 original size:13 final size:13 Alignment explanation

Indices: 1229424--1229471 Score: 69 Period size: 13 Copynumber: 3.7 Consensus size: 13 1229414 ATTTTGTTAC 1229424 ATAATTGAATATA 1 ATAATTGAATATA ** 1229437 ATAATTGAATGCA 1 ATAATTGAATATA * 1229450 ATAATTGAATATG 1 ATAATTGAATATA 1229463 ATAATTGAA 1 ATAATTGAA 1229472 ATCCATATTG Statistics Matches: 30, Mismatches: 5, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 13 30 1.00 ACGTcount: A:0.50, C:0.02, G:0.12, T:0.35 Consensus pattern (13 bp): ATAATTGAATATA Found at i:1230910 original size:2 final size:2 Alignment explanation

Indices: 1230892--1230948 Score: 98 Period size: 2 Copynumber: 29.0 Consensus size: 2 1230882 CATAAAATAA * 1230892 TC TC TC TA TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1230933 TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC 1230949 GATATATGAT Statistics Matches: 52, Mismatches: 2, Indels: 2 0.93 0.04 0.04 Matches are distributed among these distances: 1 1 0.02 2 51 0.98 ACGTcount: A:0.02, C:0.47, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:1231205 original size:36 final size:36 Alignment explanation

Indices: 1231159--1231338 Score: 360 Period size: 36 Copynumber: 5.0 Consensus size: 36 1231149 GGTCATCACC 1231159 CAGACAGACAAACAAACAGTAGAATGGTAACTTACA 1 CAGACAGACAAACAAACAGTAGAATGGTAACTTACA 1231195 CAGACAGACAAACAAACAGTAGAATGGTAACTTACA 1 CAGACAGACAAACAAACAGTAGAATGGTAACTTACA 1231231 CAGACAGACAAACAAACAGTAGAATGGTAACTTACA 1 CAGACAGACAAACAAACAGTAGAATGGTAACTTACA 1231267 CAGACAGACAAACAAACAGTAGAATGGTAACTTACA 1 CAGACAGACAAACAAACAGTAGAATGGTAACTTACA 1231303 CAGACAGACAAACAAACAGTAGAATGGTAACTTACA 1 CAGACAGACAAACAAACAGTAGAATGGTAACTTACA 1231339 GGATTGGTTT Statistics Matches: 144, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 36 144 1.00 ACGTcount: A:0.50, C:0.19, G:0.17, T:0.14 Consensus pattern (36 bp): CAGACAGACAAACAAACAGTAGAATGGTAACTTACA Found at i:1236392 original size:15 final size:16 Alignment explanation

Indices: 1236362--1236395 Score: 52 Period size: 15 Copynumber: 2.2 Consensus size: 16 1236352 AGATTTTTTA 1236362 ATTTCTATACCAGTAC 1 ATTTCTATACCAGTAC * 1236378 ATTTCTA-AGCAGTAC 1 ATTTCTATACCAGTAC 1236393 ATT 1 ATT 1236396 GAGCTATACT Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 15 10 0.59 16 7 0.41 ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38 Consensus pattern (16 bp): ATTTCTATACCAGTAC Found at i:1243429 original size:22 final size:21 Alignment explanation

Indices: 1243391--1243556 Score: 113 Period size: 21 Copynumber: 7.6 Consensus size: 21 1243381 TTTTTGAGGT * 1243391 ATTTTCTGATATCAGAAAATG 1 ATTTTTTGATATCAGAAAATG * * 1243412 ATTTTTTGGTATCA-AGAATTCG 1 ATTTTTTGATATCAGA-AAAT-G * * 1243434 AATTTCTGATATCAGAAAATG 1 ATTTTTTGATATCAGAAAATG * 1243455 ATTTTTTGATATCAG--ACTCG 1 ATTTTTTGATATCAGAAAAT-G * * * 1243475 AATTCTTGATATAAGAAAATACG 1 ATTTTTTGATATCAGAAAAT--G * 1243498 ATCCATTTTCTGATATCAGAAATTCG 1 AT---TTTT-TGATATCAGAAAAT-G * * 1243524 ATTTTTTTATCTCAGAAAATG 1 ATTTTTTGATATCAGAAAATG 1243545 ATTTTTTGATAT 1 ATTTTTTGATAT 1243557 TACAAATTCA Statistics Matches: 111, Mismatches: 23, Indels: 22 0.71 0.15 0.14 Matches are distributed among these distances: 19 2 0.02 20 14 0.13 21 40 0.36 22 28 0.25 23 8 0.07 26 7 0.06 27 12 0.11 ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42 Consensus pattern (21 bp): ATTTTTTGATATCAGAAAATG Found at i:1243454 original size:43 final size:42 Alignment explanation

Indices: 1243393--1243556 Score: 170 Period size: 43 Copynumber: 3.7 Consensus size: 42 1243383 TTTGAGGTAT * 1243393 TTTCTGATATCAGAAAATGATTTTTTGGTATCAAGAATTCGAA 1 TTTCTGATATCAGAAAATGATTTTTTGATATC-AGAATTCGAA * 1243436 TTTCTGATATCAGAAAATGATTTTTTGATATCAG-ACTCGAA 1 TTTCTGATATCAGAAAATGATTTTTTGATATCAGAATTCGAA * * 1243477 -TTCTTGATATAAGAAAATACGATCCATTTTCTGATATCAGAAATTCGAT 1 TTTC-TGATATCAGAAAAT--GAT---TTTT-TGATATCAG-AATTCGAA * * * 1243526 TTTTTTATCTCAGAAAATGATTTTTTGATAT 1 TTTCTGATATCAGAAAATGATTTTTTGATAT 1243557 TACAAATTCA Statistics Matches: 102, Mismatches: 9, Indels: 20 0.78 0.07 0.15 Matches are distributed among these distances: 40 3 0.03 41 19 0.19 42 2 0.02 43 40 0.39 44 4 0.04 46 4 0.04 47 12 0.12 49 16 0.16 50 2 0.02 ACGTcount: A:0.34, C:0.11, G:0.13, T:0.41 Consensus pattern (42 bp): TTTCTGATATCAGAAAATGATTTTTTGATATCAGAATTCGAA Found at i:1244085 original size:21 final size:22 Alignment explanation

Indices: 1244059--1244254 Score: 130 Period size: 22 Copynumber: 8.8 Consensus size: 22 1244049 TGTAGGTCTT 1244059 ATTTTCTGATATCAAAAAAT-G 1 ATTTTCTGATATCAAAAAATCG * * 1244080 ATTTTCTGATATCAAGAATTCG 1 ATTTTCTGATATCAAAAAATCG * 1244102 A-TTTCTTGATATCAAAAAATCA 1 ATTTTC-TGATATCAAAAAATCG * 1244124 ACTTTAACTCTTGATATCAAAAAATCT 1 A-TTT---TC-TGATATCAAAAAATCG * * * * 1244151 ATTTTGTAATATC-AGAAATCC 1 ATTTTCTGATATCAAAAAATCG * ** * * 1244172 ATTTTTTTTTATCAAGAATTCG 1 ATTTTCTGATATCAAAAAATCG * ** 1244194 AATTAGTGATATCAAAAAAT-G 1 ATTTTCTGATATCAAAAAATCG * * * 1244215 ATTTCCTGATATCACAAAATAG 1 ATTTTCTGATATCAAAAAATCG * 1244237 ATTTTTTGATATCAAAAA 1 ATTTTCTGATATCAAAAA 1244255 TTATTTTTTT Statistics Matches: 137, Mismatches: 29, Indels: 17 0.75 0.16 0.09 Matches are distributed among these distances: 21 55 0.40 22 57 0.42 23 1 0.01 24 2 0.01 26 3 0.02 27 19 0.14 ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39 Consensus pattern (22 bp): ATTTTCTGATATCAAAAAATCG Found at i:1244121 original size:43 final size:43 Alignment explanation

Indices: 1244061--1244294 Score: 145 Period size: 43 Copynumber: 5.3 Consensus size: 43 1244051 TAGGTCTTAT 1244061 TTTC-TGATATCAAAAAATGATTTTCTGATATCAAGAATTCGA 1 TTTCTTGATATCAAAAAATGATTTTCTGATATCAAGAATTCGA * * * * 1244103 TTTCTTGATATCAAAAAATCAACTTTAACTCTTGATATCAAAAAATCTA 1 TTTCTTGATATCAAAAAAT-GA-TTT---TC-TGATATCAAGAATTCGA * * * * ** 1244152 TTT-TGTAATATC-AGAAATCCATTTTTTTTTATCAAGAATTCGA 1 TTTCT-TGATATCAAAAAAT-GATTTTCTGATATCAAGAATTCGA * ** * * * 1244195 ATTAGTGATATCAAAAAATGATTTCCTGATATCACA-AAATAGA 1 TTTCTTGATATCAAAAAATGATTTTCTGATATCA-AGAATTCGA * * * ** 1244238 TTTTTTGATATC-AAAAATTATTTTTTTGATATCAAGAATTTTA 1 TTTCTTGATATCAAAAAATGA-TTTTCTGATATCAAGAATTCGA * 1244281 TTTTTTGATATCAA 1 TTTCTTGATATCAA 1244295 TTCGAATTAT Statistics Matches: 145, Mismatches: 33, Indels: 26 0.71 0.16 0.13 Matches are distributed among these distances: 42 12 0.08 43 85 0.59 44 9 0.06 45 3 0.02 47 3 0.02 48 10 0.07 49 23 0.16 ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42 Consensus pattern (43 bp): TTTCTTGATATCAAAAAATGATTTTCTGATATCAAGAATTCGA Found at i:1244255 original size:21 final size:21 Alignment explanation

Indices: 1244200--1244294 Score: 86 Period size: 22 Copynumber: 4.4 Consensus size: 21 1244190 TTCGAATTAG ** 1244200 TGATATCAAAAA-ATGATTTCC 1 TGATATCAAAAATA-GATTTTT 1244221 TGATATCACAAAATAGATTTTT 1 TGATATCA-AAAATAGATTTTT * 1244243 TGATATCAAAAATTA-TTTTTT 1 TGATATCAAAAA-TAGATTTTT * ** 1244264 TGATATCAAGAATTTTATTTTT 1 TGATATCAA-AAATAGATTTTT 1244286 TGATATCAA 1 TGATATCAA 1244295 TTCGAATTAT Statistics Matches: 63, Mismatches: 6, Indels: 9 0.81 0.08 0.12 Matches are distributed among these distances: 21 27 0.43 22 35 0.56 23 1 0.02 ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44 Consensus pattern (21 bp): TGATATCAAAAATAGATTTTT Found at i:1244263 original size:22 final size:21 Alignment explanation

Indices: 1244057--1244339 Score: 106 Period size: 21 Copynumber: 13.0 Consensus size: 21 1244047 TATGTAGGTC * * 1244057 TTATTTTCTGATATCAAAAAA 1 TTATTTTTTGATATCAAAAAT * * * 1244078 TGATTTTCTGATATCAAGAAT 1 TTATTTTTTGATATCAAAAAT * * 1244099 TCGATTTCTTGATATCAAAAAAT 1 T-TATTTTTTGATATC-AAAAAT ** 1244122 CAACTTTAACTCTTGATATCAAAAAAT 1 TTA-TTT---T-TTGATATC-AAAAAT * * * * 1244149 CTATTTTGTAATATCAGAAAT 1 TTATTTTTTGATATCAAAAAT ** ** * 1244170 CCATTTTTTTTTATCAAGAAT 1 TTATTTTTTGATATCAAAAAT * * ** * 1244191 TCGAATTAGTGATATCAAAAAA 1 T-TATTTTTTGATATCAAAAAT * ** 1244213 TGATTTCCTGATATCACAAAAT 1 TTATTTTTTGATATCA-AAAAT ** 1244235 AGATTTTTTGATATCAAAAA- 1 TTATTTTTTGATATCAAAAAT * 1244255 TTATTTTTTTGATATCAAGAATT 1 TTA-TTTTTTGATATCAA-AAAT 1244278 TTATTTTTTGATATC---AAT 1 TTATTTTTTGATATCAAAAAT * * * * 1244296 TCGAATTATTGATATCAAATAT 1 T-TATTTTTTGATATCAAAAAT * 1244318 TTATTTTTTTATATCAGAAAAT 1 TTATTTTTTGATATCA-AAAAT 1244340 ACCTCAAAAA Statistics Matches: 197, Mismatches: 48, Indels: 33 0.71 0.17 0.12 Matches are distributed among these distances: 18 3 0.02 19 11 0.06 20 1 0.01 21 80 0.41 22 70 0.36 23 12 0.06 26 3 0.02 27 17 0.09 ACGTcount: A:0.38, C:0.10, G:0.08, T:0.43 Consensus pattern (21 bp): TTATTTTTTGATATCAAAAAT Found at i:1249394 original size:169 final size:166 Alignment explanation

Indices: 1248411--1250128 Score: 2368 Period size: 169 Copynumber: 10.2 Consensus size: 166 1248401 ATAGAATCAT * 1248411 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTAAAAGATTTACTCTATATATTCCTATGTAAAACT 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAAC- * * * 1248476 TTAAC-ACCCCCCCCCCAATGTGGCCTCAACCTACCCCCAGGGATCATG-TTTTCACAACTTTGA 65 TT--CGA---CCCCCCCATTGTGGCCCCACCCTA-CCCCAGGGATCATGATTTTCACAACTTTGA * 1248539 ATCTACACTACCTGAGGATACTTCCACACAAGTTTCAGCTTTC 124 ATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC * 1248582 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAATATTTACTCTATATATTCCTATGTAAAACT 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT 1248647 TCGA-CCCCCCATTGT-GCCCCACCCTACCCTCAGGGATCATGATTTTCACAACTTTGAATCTAC 66 TCGACCCCCCCATTGTGGCCCCACCCTACCC-CAGGGATCATGATTTTCACAACTTTGAATCTAC * * 1248710 ACTGCCTGAGGATGCTTCCACACGAGTTTCAGCTTTC 130 ACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC * * 1248747 CTGGCTGATAAG-TT-TGAGAAGAAGATTTTCAAAGATTTACTCTATATATTCCTATGTAAAACT 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT * * 1248810 TCGACCCCCCCCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTT--C-AC----AA 66 TCGA-----CCCCCCCATTGTGGCCCCACCCTA-CCCCAGGGATCATGATTTTCACAACTTTGAA * * 1248868 TCTACACTGCCTGAGGATGCTTCCACACAAGTTTCAGCTCTC 125 TCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC * 1248910 CTTGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTC--TATATTCCTATGTAAAACT 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAAC- * * 1248973 TTAAC-ACCCCCCCCCCAATGTGGCCTCACCCTACCCCCAGGGATCATGATTTTCACAACTTTGA 65 TT--CGA---CCCCCCCATTGTGGCCCCACCCTA-CCCCAGGGATCATGATTTTCACAACTTTGA * * 1249037 ATCTACACTGCCTGAGGATACTTCCACACAAGTTTCAGCTTTC 124 ATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC * * 1249080 CTGGCTGATTAGTTTCTGAGAAGAAGAATTTTGAAGATTTACTCTATATATTCCTATGTAAAACT 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT * * * * 1249145 ACGA-CCCTCCATTGT-GCTCCACCCTACCCCAAGGGATCATGATTTTCACAACTTTGAATCTGC 66 TCGACCCCCCCATTGTGGCCCCACCCTACCCC-AGGGATCATGATTTTCACAACTTTGAATCTAC * 1249208 ACTACCTGAGGATGCTTCCACATAAGTTTCAGCTTTC 130 ACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC * 1249245 CTGGCTGATTAGTTTCTGAGAAGAAGA-TTTTAAAGATTTACTCTATATATAAATTCTTATGTAA 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTC--TATAT--ATTCCTATGTAA * * * * * * 1249309 AAATTTGA-CCACCCATTGTGGCCCCACCCTACCCCTGGGAGTCATGAATTTAACAACTTTGAAT 62 AACTTCGACCCCCCCATTGTGGCCCCACCCTACCCCAGGGA-TCATGATTTTCACAACTTTGAAT * * 1249373 CTACACTACCTGAGAATGCTTCCACACAAGTTTCAGTTTTC 126 CTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC * 1249414 CTGGCTGATAAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT ** * 1249479 TCGACCCCCCCCCCCATTGTGGCCTTACCCTACACCCAGGGATCATGAATTTCACAACTTTGAAT 66 TCGA----CCCCCCCATTGTGGCCCCACCCTAC-CCCAGGGATCATGATTTTCACAACTTTGAAT * * 1249544 CTACACTTCCTGAGGATGCTACCACACAAGTTTCAGCTTTC 126 CTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC 1249585 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT * * ** * 1249650 TTGACCCCCCCCCCTTGTGGCCCCACCCTACACCTGGGGGTCATGATTTTCACAACTTTGAATCT 66 TCGA--CCCCCCCATTGTGGCCCCACCCTAC-CCCAGGGATCATGATTTTCACAACTTTGAATCT 1249715 ACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC 128 ACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC 1249754 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT * * ** * 1249819 TTGACCCCCCCCCCTTGTGGCCCCACCCTACACCTGGGGGTCATGATTTTCACAACTTTGAATCT 66 TCGA--CCCCCCCATTGTGGCCCCACCCTAC-CCCAGGGATCATGATTTTCACAACTTTGAATCT 1249884 ACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC 128 ACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC * 1249923 CTGGCTGATTACTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT * * * * 1249988 TCCA-CCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGAATTTCACAACTTTGAATCTAC 66 TCGACCCCCCCATTGTGGCCCCACCCTA-CCCCAGGGATCATGATTTTCACAACTTTGAATCTAC 1250052 ACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC 130 ACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC * * 1250089 CTGGCT--TTCTGGTTCTGGAGAAGAAGATTTTTGAAA-ATTT 1 CTGGCTGATT-AGTTTCT-GAGAAGAAGATTTTT-AAAGATTT 1250129 CTCGAAATTT Statistics Matches: 1419, Mismatches: 84, Indels: 93 0.89 0.05 0.06 Matches are distributed among these distances: 163 167 0.12 164 47 0.03 165 210 0.15 166 151 0.11 167 6 0.00 168 36 0.03 169 437 0.31 170 127 0.09 171 213 0.15 172 25 0.02 ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32 Consensus pattern (166 bp): CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT TCGACCCCCCCATTGTGGCCCCACCCTACCCCAGGGATCATGATTTTCACAACTTTGAATCTACA CTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC Found at i:1249677 original size:340 final size:339 Alignment explanation

Indices: 1248411--1250128 Score: 2482 Period size: 340 Copynumber: 5.1 Consensus size: 339 1248401 ATAGAATCAT * 1248411 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTAAAAGATTTACTCTATATATTCCTATGTAAAACT 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT ** * * * 1248476 TTAACACCCCCCCCCCAATGTGGCCTCAACCTACCCCCAGGGATCATG-TTTTCACAACTTTGAA 66 TCGAC-CCCCCCCCCCATTGTGGCCTCACCCTACACCCAGGGATCATGATTTTCACAACTTTGAA * 1248540 TCTACACTACCTGAGGATACTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAG 130 TCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAG * * 1248605 AAGATTTTTAAATATTTACTCTATATATTCCTATGTAAAACTTCGA--CCCCCCATTGT-GCCCC 195 AAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTTGACCCCCCCCATTGTGGCCCC * 1248667 ACCCTACCCTCAGGGA-TCATGATTTTCACAACTTTGAATCTACACTGCCTGAGGATGCTTCCAC 260 ACCCTACCC-CAGGGAGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCAC * 1248731 ACGAGTTTCAGCTTTC 324 ACAAGTTTCAGCTTTC * * 1248747 CTGGCTGATAAG-TT-TGAGAAGAAGATTTTCAAAGATTTACTCTATATATTCCTATGTAAAACT 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT * * * * 1248810 TCGACCCCCCCCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTT--C-AC----AA 66 TCGA-CCCCCCCCCCCATTGTGGCCTCACCCTACACCCAGGGATCATGATTTTCACAACTTTGAA * * * 1248868 TCTACACTGCCTGAGGATGCTTCCACACAAGTTTCAGCTCTCCTTGCTGATTAGTTTCTGAGAAG 130 TCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAG * * 1248933 AAGATTTTTAAAGATTTACTC--TATATTCCTATGTAAAACTTTAACACCCCCCCCCCAATGTGG 195 AAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTT--GA--CCCCCCCCATTGTGG * * * 1248996 CCTCACCCTACCCCCAGGGA-TCATGATTTTCACAACTTTGAATCTACACTGCCTGAGGATACTT 256 CCCCACCCTA-CCCCAGGGAGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTT 1249060 CCACACAAGTTTCAGCTTTC 320 CCACACAAGTTTCAGCTTTC * * 1249080 CTGGCTGATTAGTTTCTGAGAAGAAGAATTTTGAAGATTTACTCTATATATTCCTATGTAAAACT 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT * * 1249145 ACGA-----CCCTCCATTGT-G-CTCCACCCTAC-CCCAAGGGATCATGATTTTCACAACTTTGA 66 TCGACCCCCCCCCCCATTGTGGCCT-CACCCTACACCC-AGGGATCATGATTTTCACAACTTTGA * * 1249202 ATCTGCACTACCTGAGGATGCTTCCACATAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAA 129 ATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAA * * * 1249267 GAAGA-TTTTAAAGATTTACTCTATATATAAATTCTTATGTAAAAATTTGA--CCACCCATTGTG 194 GAAGATTTTTAAAGATTTACTC--TATAT--ATTCCTATGTAAAACTTTGACCCCCCCCATTGTG * * * * 1249329 GCCCCACCCTACCCCTGGGAGTCATGAATTTAACAACTTTGAATCTACACTACCTGAGAATGCTT 255 GCCCCACCCTACCCCAGGGAGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTT * 1249394 CCACACAAGTTTCAGTTTTC 320 CCACACAAGTTTCAGCTTTC * 1249414 CTGGCTGATAAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT * * 1249479 TCGACCCCCCCCCCCATTGTGGCCTTACCCTACACCCAGGGATCATGAATTTCACAACTTTGAAT 66 TCGACCCCCCCCCCCATTGTGGCCTCACCCTACACCCAGGGATCATGATTTTCACAACTTTGAAT * * 1249544 CTACACTTCCTGAGGATGCTACCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGA 131 CTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGA * 1249609 AGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTTGACCCCCCCCCCTTGTGGCCCC 196 AGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTTGA-CCCCCCCCATTGTGGCCCC * * * 1249674 ACCCTACACCTGGGGGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACA 260 ACCCTACCCCAGGGAGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACA 1249739 CAAGTTTCAGCTTTC 325 CAAGTTTCAGCTTTC 1249754 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT 1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT * * ** * 1249819 TTGA-CCCCCCCCCC-TTGTGGCCCCACCCTACACCTGGGGGTCATGATTTTCACAACTTTGAAT 66 TCGACCCCCCCCCCCATTGTGGCCTCACCCTACACCCAGGGATCATGATTTTCACAACTTTGAAT * 1249882 CTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTACTTTCTGAGAAGA 131 CTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGA 1249947 AGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAAC-TT--CCACCCCCCATTGTGGCCCC 196 AGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTTGACC-CCCCCCATTGTGGCCCC * * * 1250009 ACCCTACCCCCGGGGGTCATGAATTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACA 260 ACCCTACCCCAGGGAGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACA 1250074 CAAGTTTCAGCTTTC 325 CAAGTTTCAGCTTTC * * 1250089 CTGGCT--TTCTGGTTCTGGAGAAGAAGATTTTTGAAA-ATTT 1 CTGGCTGATT-AGTTTCT-GAGAAGAAGATTTTT-AAAGATTT 1250129 CTCGAAATTT Statistics Matches: 1253, Mismatches: 85, Indels: 89 0.88 0.06 0.06 Matches are distributed among these distances: 326 20 0.02 327 4 0.00 328 106 0.08 329 10 0.01 330 1 0.00 331 2 0.00 332 12 0.01 333 100 0.08 334 258 0.21 335 240 0.19 336 14 0.01 337 20 0.02 338 149 0.12 339 25 0.02 340 271 0.22 341 21 0.02 ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32 Consensus pattern (339 bp): CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT TCGACCCCCCCCCCCATTGTGGCCTCACCCTACACCCAGGGATCATGATTTTCACAACTTTGAAT CTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGA AGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTTGACCCCCCCCATTGTGGCCCCA CCCTACCCCAGGGAGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACAC AAGTTTCAGCTTTC Found at i:1256061 original size:33 final size:32 Alignment explanation

Indices: 1255889--1256266 Score: 427 Period size: 32 Copynumber: 11.7 Consensus size: 32 1255879 ACACCATATA * * * * 1255889 TTTACCTGAAGCAACTGTTTCTACAGCTGGGT 1 TTTACCTGAAGTAACTGTTCCTACACCTGGTT * 1255921 TTTACCTGAAGTAACTGTTCCTACACCTGATT 1 TTTACCTGAAGTAACTGTTCCTACACCTGGTT * ** * * * 1255953 TTTACCTGAAGAAACCATTCCTGCAACTAGTT 1 TTTACCTGAAGTAACTGTTCCTACACCTGGTT * * *** 1255985 TTTACCCGAAGAAACTGTTCCTACACCAT-ACA 1 TTTACCTGAAGTAACTGTTCCTACACC-TGGTT * 1256017 TTTACCAGAAGTAACTGTTCCTACCACCTGGTT 1 TTTACCTGAAGTAACTGTTCCTA-CACCTGGTT 1256050 TTTACCTGAAGTAACTGTTCCTACCACCTGGTT 1 TTTACCTGAAGTAACTGTTCCTA-CACCTGGTT * * 1256083 TTTACCTGAAGTAACTGTTCCTGCACTTGGTT 1 TTTACCTGAAGTAACTGTTCCTACACCTGGTT * * ** * * 1256115 TTTACCTAAAGAAACCATTCCTGCAACTGGTT 1 TTTACCTGAAGTAACTGTTCCTACACCTGGTT * *** 1256147 TTTACCTGAAGAAACTGTTCCTACACCAT-ACA 1 TTTACCTGAAGTAACTGTTCCTACACC-TGGTT 1256179 TTTACCTGAAGTAACTGTTCCTACCACCTGGTT 1 TTTACCTGAAGTAACTGTTCCTA-CACCTGGTT 1256212 TTTACCTGAAGTAACTGTTCCTACCACCTGGTT 1 TTTACCTGAAGTAACTGTTCCTA-CACCTGGTT 1256245 TTTACCTGAAGTAACTGTTCCT 1 TTTACCTGAAGTAACTGTTCCT 1256267 NNNNNNNNNN Statistics Matches: 294, Mismatches: 46, Indels: 11 0.84 0.13 0.03 Matches are distributed among these distances: 32 175 0.60 33 119 0.40 ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34 Consensus pattern (32 bp): TTTACCTGAAGTAACTGTTCCTACACCTGGTT Found at i:1256160 original size:162 final size:162 Alignment explanation

Indices: 1255889--1256266 Score: 650 Period size: 162 Copynumber: 2.3 Consensus size: 162 1255879 ACACCATATA * * * * 1255889 TTTACCTGAAGCAACTGTTTCTA-CAGCTGGGTTTTACCTGAAGTAACTGTTCCTACACCTGATT 1 TTTACCTGAAGTAACTGTTCCTACCACCTGGTTTTTACCTGAAGTAACTGTTCCTACACCTGATT * 1255953 TTTACCTGAAGAAACCATTCCTGCAACTAGTTTTTACCCGAAGAAACTGTTCCTACACCATACAT 66 TTTACCTAAAGAAACCATTCCTGCAACTAGTTTTTACCCGAAGAAACTGTTCCTACACCATACAT 1256018 TTACCAGAAGTAACTGTTCCTACCACCTGGTT 131 TTACCAGAAGTAACTGTTCCTACCACCTGGTT * * * 1256050 TTTACCTGAAGTAACTGTTCCTACCACCTGGTTTTTACCTGAAGTAACTGTTCCTGCACTTGGTT 1 TTTACCTGAAGTAACTGTTCCTACCACCTGGTTTTTACCTGAAGTAACTGTTCCTACACCTGATT * * 1256115 TTTACCTAAAGAAACCATTCCTGCAACTGGTTTTTACCTGAAGAAACTGTTCCTACACCATACAT 66 TTTACCTAAAGAAACCATTCCTGCAACTAGTTTTTACCCGAAGAAACTGTTCCTACACCATACAT * 1256180 TTACCTGAAGTAACTGTTCCTACCACCTGGTT 131 TTACCAGAAGTAACTGTTCCTACCACCTGGTT 1256212 TTTACCTGAAGTAACTGTTCCTACCACCTGGTTTTTACCTGAAGTAACTGTTCCT 1 TTTACCTGAAGTAACTGTTCCTACCACCTGGTTTTTACCTGAAGTAACTGTTCCT 1256267 NNNNNNNNNN Statistics Matches: 205, Mismatches: 11, Indels: 1 0.94 0.05 0.00 Matches are distributed among these distances: 161 21 0.10 162 184 0.90 ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34 Consensus pattern (162 bp): TTTACCTGAAGTAACTGTTCCTACCACCTGGTTTTTACCTGAAGTAACTGTTCCTACACCTGATT TTTACCTAAAGAAACCATTCCTGCAACTAGTTTTTACCCGAAGAAACTGTTCCTACACCATACAT TTACCAGAAGTAACTGTTCCTACCACCTGGTT Found at i:1260595 original size:38 final size:38 Alignment explanation

Indices: 1260544--1260709 Score: 332 Period size: 38 Copynumber: 4.4 Consensus size: 38 1260534 NNNNNNNNNN 1260544 AAGTCAACAGTCATGTCAACTCAATGCCAAATACCCAG 1 AAGTCAACAGTCATGTCAACTCAATGCCAAATACCCAG 1260582 AAGTCAACAGTCATGTCAACTCAATGCCAAATACCCAG 1 AAGTCAACAGTCATGTCAACTCAATGCCAAATACCCAG 1260620 AAGTCAACAGTCATGTCAACTCAATGCCAAATACCCAG 1 AAGTCAACAGTCATGTCAACTCAATGCCAAATACCCAG 1260658 AAGTCAACAGTCATGTCAACTCAATGCCAAATACCCAG 1 AAGTCAACAGTCATGTCAACTCAATGCCAAATACCCAG 1260696 AAGTCAACAGTCAT 1 AAGTCAACAGTCAT 1260710 TAACTAGATG Statistics Matches: 128, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 38 128 1.00 ACGTcount: A:0.40, C:0.28, G:0.13, T:0.19 Consensus pattern (38 bp): AAGTCAACAGTCATGTCAACTCAATGCCAAATACCCAG Found at i:1275037 original size:28 final size:28 Alignment explanation

Indices: 1275012--1275187 Score: 262 Period size: 28 Copynumber: 6.3 Consensus size: 28 1275002 ACATTGTAAA 1275012 TATCGTTATCCTTAGTGTACAGTGTAGC 1 TATCGTTATCCTTAGTGTACAGTGTAGC * * 1275040 TATTGTTATCCTTAGTGAACAGTGTAGC 1 TATCGTTATCCTTAGTGTACAGTGTAGC * * 1275068 TATTGTTATCCTTAGTGTAAAGTGTAGC 1 TATCGTTATCCTTAGTGTACAGTGTAGC * * 1275096 TATCGTAATCCTTAGTGAACAGTGTAGC 1 TATCGTTATCCTTAGTGTACAGTGTAGC * * 1275124 TATCGTTATCTTTAGTATACAGTGTAGC 1 TATCGTTATCCTTAGTGTACAGTGTAGC * * 1275152 TATCATTATCCTTAGTGTAAAGTGTAGC 1 TATCGTTATCCTTAGTGTACAGTGTAGC 1275180 TATCGTTA 1 TATCGTTA 1275188 GAGAATGGTA Statistics Matches: 131, Mismatches: 17, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 28 131 1.00 ACGTcount: A:0.26, C:0.15, G:0.20, T:0.40 Consensus pattern (28 bp): TATCGTTATCCTTAGTGTACAGTGTAGC Found at i:1276820 original size:2 final size:2 Alignment explanation

Indices: 1276813--1276852 Score: 80 Period size: 2 Copynumber: 20.0 Consensus size: 2 1276803 AGTGGATGAT 1276813 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1276853 ACTTTGTATA Statistics Matches: 38, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 38 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:1282747 original size:34 final size:34 Alignment explanation

Indices: 1282683--1282748 Score: 96 Period size: 34 Copynumber: 1.9 Consensus size: 34 1282673 ACATGTGATG * * * 1282683 CTATGCTCTGTGAATTTTGCTATGACATATGACA 1 CTATGCTCTGTGAATTATGCTAGGAAATATGACA * 1282717 CTATGCTCTGTGAATTATGCTGGGAAATATGA 1 CTATGCTCTGTGAATTATGCTAGGAAATATGA 1282749 TGTGATGCTC Statistics Matches: 28, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 34 28 1.00 ACGTcount: A:0.27, C:0.15, G:0.21, T:0.36 Consensus pattern (34 bp): CTATGCTCTGTGAATTATGCTAGGAAATATGACA Found at i:1286740 original size:13 final size:13 Alignment explanation

Indices: 1286722--1286748 Score: 54 Period size: 13 Copynumber: 2.1 Consensus size: 13 1286712 TACGAGTAAA 1286722 AGAATCAAACAGG 1 AGAATCAAACAGG 1286735 AGAATCAAACAGG 1 AGAATCAAACAGG 1286748 A 1 A 1286749 TGTACTGTAT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 14 1.00 ACGTcount: A:0.56, C:0.15, G:0.22, T:0.07 Consensus pattern (13 bp): AGAATCAAACAGG Found at i:1286773 original size:27 final size:28 Alignment explanation

Indices: 1286735--1286787 Score: 99 Period size: 27 Copynumber: 1.9 Consensus size: 28 1286725 ATCAAACAGG 1286735 AGAATCAAACAGGATGT-ACTGTATGAA 1 AGAATCAAACAGGATGTAACTGTATGAA 1286762 AGAATCAAACAGGATGTAACTGTATG 1 AGAATCAAACAGGATGTAACTGTATG 1286788 TTAATGAACA Statistics Matches: 25, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 27 17 0.68 28 8 0.32 ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23 Consensus pattern (28 bp): AGAATCAAACAGGATGTAACTGTATGAA Found at i:1303157 original size:38 final size:38 Alignment explanation

Indices: 1303115--1303204 Score: 180 Period size: 38 Copynumber: 2.4 Consensus size: 38 1303105 AACAAGTCAC 1303115 TGATTACATCAACATTTTACAAATCTACATACAGAATA 1 TGATTACATCAACATTTTACAAATCTACATACAGAATA 1303153 TGATTACATCAACATTTTACAAATCTACATACAGAATA 1 TGATTACATCAACATTTTACAAATCTACATACAGAATA 1303191 TGATTACATCAACA 1 TGATTACATCAACA 1303205 AGTCTCTACT Statistics Matches: 52, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 38 52 1.00 ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31 Consensus pattern (38 bp): TGATTACATCAACATTTTACAAATCTACATACAGAATA Found at i:1303240 original size:20 final size:20 Alignment explanation

Indices: 1303191--1303481 Score: 127 Period size: 20 Copynumber: 14.7 Consensus size: 20 1303181 ATACAGAATA 1303191 TGATTACATCAACAAGTCTC 1 TGATTACATCAACAAGTCTC * 1303211 ----TACTTCAACAAGTCTC 1 TGATTACATCAACAAGTCTC 1303227 TGATTACATCAACAAGTCTC 1 TGATTACATCAACAAGTCTC * * 1303247 TGATTACATCAAC-ATTTTAC 1 TGATTACATCAACAAGTCT-C ** ** * 1303267 AAATATACAT--AC-AGAATA 1 TGAT-TACATCAACAAGTCTC * 1303285 TGATTACATCAATAAGTCTC 1 TGATTACATCAACAAGTCTC 1303305 TGATTACATCACACTTTACAAG--TC 1 TGATTACAT--CA----ACAAGTCTC * ** * 1303329 TGATTACATTAAC-AGAATA 1 TGATTACATCAACAAGTCTC * ** * 1303348 TGATTACACCAGTAAGTCAC 1 TGATTACATCAACAAGTCTC ** * * 1303368 TGATGGCATTAACAAGTTTC 1 TGATTACATCAACAAGTCTC ** * 1303388 TGATGGCATTAACAAGTCTC 1 TGATTACATCAACAAGTCTC *** * * 1303408 TGATGGTATTAACAAGTCTG 1 TGATTACATCAACAAGTCTC ** * * 1303428 TGATGCCATTAATAAGTCTC 1 TGATTACATCAACAAGTCTC * 1303448 TGATTACATTAACAAGTCTC 1 TGATTACATCAACAAGTCTC 1303468 TGATTACATCAACA 1 TGATTACATCAACA 1303482 TTTTACAAAT Statistics Matches: 207, Mismatches: 46, Indels: 36 0.72 0.16 0.12 Matches are distributed among these distances: 16 15 0.07 17 7 0.03 18 4 0.02 19 18 0.09 20 140 0.68 21 5 0.02 22 3 0.01 24 11 0.05 26 4 0.02 ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32 Consensus pattern (20 bp): TGATTACATCAACAAGTCTC Found at i:1303302 original size:58 final size:62 Alignment explanation

Indices: 1303227--1303371 Score: 183 Period size: 58 Copynumber: 2.4 Consensus size: 62 1303217 AACAAGTCTC * * 1303227 TGATTACATCAACAAGTCTCTGATTACATCAACATTTTACAA-AT-A-TACA-T-ACAGAATA 1 TGATTACATCAATAAGTCTCTGATTACATC-ACACTTTACAAGATGATTACATTAACAGAATA * 1303285 TGATTACATCAATAAGTCTCTGATTACATCACACTTTACAAGTCTGATTACATTAACAGAATA 1 TGATTACATCAATAAGTCTCTGATTACATCACACTTTACAAG-ATGATTACATTAACAGAATA * * * 1303348 TGATTACACCAGTAAGTCACTGAT 1 TGATTACATCAATAAGTCTCTGAT 1303372 GGCATTAACA Statistics Matches: 75, Mismatches: 6, Indels: 7 0.85 0.07 0.08 Matches are distributed among these distances: 57 10 0.13 58 29 0.39 59 1 0.01 60 1 0.01 61 4 0.05 62 1 0.01 63 29 0.39 ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32 Consensus pattern (62 bp): TGATTACATCAATAAGTCTCTGATTACATCACACTTTACAAGATGATTACATTAACAGAATA Found at i:1303411 original size:40 final size:40 Alignment explanation

Indices: 1303361--1303471 Score: 150 Period size: 40 Copynumber: 2.8 Consensus size: 40 1303351 TTACACCAGT * * * 1303361 AAGTCACTGATGGCATTAACAAGTTTCTGATGGCATTAAC 1 AAGTCTCTGATGGCATTAACAAGTCTCTGATGCCATTAAC * * * 1303401 AAGTCTCTGATGGTATTAACAAGTCTGTGATGCCATTAAT 1 AAGTCTCTGATGGCATTAACAAGTCTCTGATGCCATTAAC ** 1303441 AAGTCTCTGATTACATTAACAAGTCTCTGAT 1 AAGTCTCTGATGGCATTAACAAGTCTCTGAT 1303472 TACATCAACA Statistics Matches: 61, Mismatches: 10, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 40 61 1.00 ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33 Consensus pattern (40 bp): AAGTCTCTGATGGCATTAACAAGTCTCTGATGCCATTAAC Found at i:1303530 original size:58 final size:60 Alignment explanation

Indices: 1303448--1303592 Score: 179 Period size: 63 Copynumber: 2.4 Consensus size: 60 1303438 AATAAGTCTC * * 1303448 TGATTACATTAACAAGTCTCTGATTACATCAACATTTTACAAATC-TACA-T-ACAGAATA 1 TGATTACATCAATAAGTCTCTGATTACATC-ACATTTTACAAATCTTACATTAACAGAATA * * 1303506 TGTTTACATCAATAAGTCTCTGATTACATCACATTTTACAAGTCTGATTACATTAACAGAATA 1 TGATTACATCAATAAGTCTCTGATTACATCACATTTTACAAATC---TTACATTAACAGAATA * * 1303569 TGATTACATCAGTAAGTCACTGAT 1 TGATTACATCAATAAGTCTCTGAT 1303593 GGCATTAACA Statistics Matches: 74, Mismatches: 7, Indels: 7 0.84 0.08 0.08 Matches are distributed among these distances: 57 13 0.18 58 27 0.36 61 4 0.05 62 1 0.01 63 29 0.39 ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34 Consensus pattern (60 bp): TGATTACATCAATAAGTCTCTGATTACATCACATTTTACAAATCTTACATTAACAGAATA Found at i:1303603 original size:221 final size:221 Alignment explanation

Indices: 1303220--1303681 Score: 836 Period size: 221 Copynumber: 2.1 Consensus size: 221 1303210 CTACTTCAAC 1303220 AAGTCTCTGATTACATCAACAAGTCTCTGATTACATCAACATTTTACAAATATACATACAGAATA 1 AAGTCTCTGATTACATCAACAAGTCTCTGATTACATCAACATTTTACAAATATACATACAGAATA 1303285 TGATTACATCAATAAGTCTCTGATTACATCACACTTTACAAGTCTGATTACATTAACAGAATATG 66 TGATTACATCAATAAGTCTCTGATTACATCACACTTTACAAGTCTGATTACATTAACAGAATATG * 1303350 ATTACACCAGTAAGTCACTGATGGCATTAACAAGTTTCTGATGGCATTAACAAGTCTCTGATGGT 131 ATTACACCAGTAAGTCACTGATGGCATTAACAAGTTTCTGATGGCATTAACAAGTCTCTGATGAT 1303415 ATTAACAAGTCTGTGATGCCATTAAT 196 ATTAACAAGTCTGTGATGCCATTAAT * * 1303441 AAGTCTCTGATTACATTAACAAGTCTCTGATTACATCAACATTTTACAAATCTACATACAGAATA 1 AAGTCTCTGATTACATCAACAAGTCTCTGATTACATCAACATTTTACAAATATACATACAGAATA * * 1303506 TGTTTACATCAATAAGTCTCTGATTACATCACATTTTACAAGTCTGATTACATTAACAGAATATG 66 TGATTACATCAATAAGTCTCTGATTACATCACACTTTACAAGTCTGATTACATTAACAGAATATG * * 1303571 ATTACATCAGTAAGTCACTGATGGCATTAACAAGTTTCTGATGGCATTAACAAGTCTTTGATGAT 131 ATTACACCAGTAAGTCACTGATGGCATTAACAAGTTTCTGATGGCATTAACAAGTCTCTGATGAT * 1303636 ATTAACAAGTCTGTGATGGCATTAAT 196 ATTAACAAGTCTGTGATGCCATTAAT * 1303662 -AGTCTCTGATTAAATCAACA 1 AAGTCTCTGATTACATCAACA 1303682 TTTTACAAGT Statistics Matches: 231, Mismatches: 10, Indels: 1 0.95 0.04 0.00 Matches are distributed among these distances: 220 18 0.08 221 213 0.92 ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33 Consensus pattern (221 bp): AAGTCTCTGATTACATCAACAAGTCTCTGATTACATCAACATTTTACAAATATACATACAGAATA TGATTACATCAATAAGTCTCTGATTACATCACACTTTACAAGTCTGATTACATTAACAGAATATG ATTACACCAGTAAGTCACTGATGGCATTAACAAGTTTCTGATGGCATTAACAAGTCTCTGATGAT ATTAACAAGTCTGTGATGCCATTAAT Found at i:1303605 original size:20 final size:20 Alignment explanation

Indices: 1303582--1303671 Score: 110 Period size: 20 Copynumber: 4.5 Consensus size: 20 1303572 TTACATCAGT * 1303582 AAGTCACTGATGGCATTAAC 1 AAGTCTCTGATGGCATTAAC * 1303602 AAGTTTCTGATGGCATTAAC 1 AAGTCTCTGATGGCATTAAC * ** 1303622 AAGTCTTTGATGATATTAAC 1 AAGTCTCTGATGGCATTAAC * 1303642 AAGTCTGTGATGGCATTAA- 1 AAGTCTCTGATGGCATTAAC * 1303661 TAGTCTCTGAT 1 AAGTCTCTGAT 1303672 TAAATCAACA Statistics Matches: 59, Mismatches: 11, Indels: 1 0.83 0.15 0.01 Matches are distributed among these distances: 19 9 0.15 20 50 0.85 ACGTcount: A:0.31, C:0.14, G:0.20, T:0.34 Consensus pattern (20 bp): AAGTCTCTGATGGCATTAAC Found at i:1303715 original size:45 final size:45 Alignment explanation

Indices: 1303663--1303751 Score: 151 Period size: 45 Copynumber: 2.0 Consensus size: 45 1303653 GGCATTAATA * * 1303663 GTCTCTGATTAAATCAACATTTTACAAGTCTTATTACATTAACAT 1 GTCTCTGATTAAATCAACATTTCACAAGTCTGATTACATTAACAT * 1303708 GTCTCTGATTACATCAACATTTCACAAGTCTGATTACATTAACA 1 GTCTCTGATTAAATCAACATTTCACAAGTCTGATTACATTAACA 1303752 GAATTCACAG Statistics Matches: 41, Mismatches: 3, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 45 41 1.00 ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37 Consensus pattern (45 bp): GTCTCTGATTAAATCAACATTTCACAAGTCTGATTACATTAACAT Found at i:1303740 original size:25 final size:24 Alignment explanation

Indices: 1303666--1303751 Score: 81 Period size: 25 Copynumber: 3.7 Consensus size: 24 1303656 ATTAATAGTC * 1303666 TCTGATTAAATCAACATTTTACAAG 1 TCTGATTACATCAACA-TTTACAAG * * * 1303691 TCTTATTACATTAACATGT-C--- 1 TCTGATTACATCAACATTTACAAG 1303711 TCTGATTACATCAACATTTCACAAG 1 TCTGATTACATCAACATTT-ACAAG * 1303736 TCTGATTACATTAACA 1 TCTGATTACATCAACA 1303752 GAATTCACAG Statistics Matches: 48, Mismatches: 8, Indels: 10 0.73 0.12 0.15 Matches are distributed among these distances: 20 16 0.33 22 1 0.02 23 1 0.02 24 2 0.04 25 28 0.58 ACGTcount: A:0.36, C:0.20, G:0.07, T:0.37 Consensus pattern (24 bp): TCTGATTACATCAACATTTACAAG Found at i:1303758 original size:27 final size:25 Alignment explanation

Indices: 1303711--1303760 Score: 64 Period size: 25 Copynumber: 1.9 Consensus size: 25 1303701 TTAACATGTC * 1303711 TCTGATTACATCAACATTTCACAAG 1 TCTGATTACATCAACAATTCACAAG * 1303736 TCTGATTACATTAACAGAATTCACA 1 TCTGATTACATCAAC--AATTCACA 1303761 GTAAACTTGA Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 25 14 0.67 27 7 0.33 ACGTcount: A:0.38, C:0.22, G:0.08, T:0.32 Consensus pattern (25 bp): TCTGATTACATCAACAATTCACAAG Found at i:1312616 original size:47 final size:47 Alignment explanation

Indices: 1312534--1312724 Score: 283 Period size: 47 Copynumber: 4.1 Consensus size: 47 1312524 TACATGTCCC * * * * * * 1312534 AATGATTCCCTACTTTTGAGGGAATAGCTCTGAGTTTTAATGGTACA 1 AATGATTTCTTACCTTTGAGAGAGTAGCTCTGAGTTTTGATGGTACA * * * * 1312581 ATTGATTTCTCACCTTTGAGAGAGTAGTTCCGAGTTTTGATGGTACA 1 AATGATTTCTTACCTTTGAGAGAGTAGCTCTGAGTTTTGATGGTACA 1312628 AATGATTTCTTACCTTTGAGAGAGTAGCTCTGAGTTTTGATGGTACA 1 AATGATTTCTTACCTTTGAGAGAGTAGCTCTGAGTTTTGATGGTACA * 1312675 AATGATTTCTTACCTTTGAGAGAGTAGCTCTGAGTTTTGGTGGTACA 1 AATGATTTCTTACCTTTGAGAGAGTAGCTCTGAGTTTTGATGGTACA 1312722 AAT 1 AAT 1312725 CAGCCGGTTA Statistics Matches: 129, Mismatches: 15, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 47 129 1.00 ACGTcount: A:0.26, C:0.14, G:0.23, T:0.38 Consensus pattern (47 bp): AATGATTTCTTACCTTTGAGAGAGTAGCTCTGAGTTTTGATGGTACA Found at i:1315249 original size:85 final size:85 Alignment explanation

Indices: 1315106--1315277 Score: 344 Period size: 85 Copynumber: 2.0 Consensus size: 85 1315096 GGCCACCGAC 1315106 GTATCTCCCGATGGAGCTAGAGCCTGAAAATAACGGCCAACAGGTCAGACTCCACAAATAATGCT 1 GTATCTCCCGATGGAGCTAGAGCCTGAAAATAACGGCCAACAGGTCAGACTCCACAAATAATGCT 1315171 AATACAAGTATAGTCAGTTT 66 AATACAAGTATAGTCAGTTT 1315191 GTATCTCCCGATGGAGCTAGAGCCTGAAAATAACGGCCAACAGGTCAGACTCCACAAATAATGCT 1 GTATCTCCCGATGGAGCTAGAGCCTGAAAATAACGGCCAACAGGTCAGACTCCACAAATAATGCT 1315256 AATACAAGTATAGTCAGTTT 66 AATACAAGTATAGTCAGTTT 1315276 GT 1 GT 1315278 CAGTCTCGGG Statistics Matches: 87, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 85 87 1.00 ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23 Consensus pattern (85 bp): GTATCTCCCGATGGAGCTAGAGCCTGAAAATAACGGCCAACAGGTCAGACTCCACAAATAATGCT AATACAAGTATAGTCAGTTT Found at i:1315862 original size:33 final size:33 Alignment explanation

Indices: 1315775--1316060 Score: 493 Period size: 33 Copynumber: 8.7 Consensus size: 33 1315765 GCATGGTTAN * 1315775 TACCATACATGTAATACAGTAAGGTGGCATAGG 1 TACCATACATGTAACACAGTAAGGTGGCATAGG * * * 1315808 TACCATACTTG-AACACCGTAAGGTAGCATAGG 1 TACCATACATGTAACACAGTAAGGTGGCATAGG * 1315840 TACCATACATGTAACACAGTAAGGTGGCATATG 1 TACCATACATGTAACACAGTAAGGTGGCATAGG 1315873 TACCATACATGTAACACAGTAAGGTGGCATAGG 1 TACCATACATGTAACACAGTAAGGTGGCATAGG * 1315906 TATCATACATGTAACACAGTAAGGTGGCATAGG 1 TACCATACATGTAACACAGTAAGGTGGCATAGG 1315939 TACCATACATGTAACACAGTAAGGTGGCATAGG 1 TACCATACATGTAACACAGTAAGGTGGCATAGG * 1315972 TACCATACATGTAATACAGTAAGGTGGCATAGG 1 TACCATACATGTAACACAGTAAGGTGGCATAGG * 1316005 TACCATACATGTAACACAGTAAGGTAGCATAGG 1 TACCATACATGTAACACAGTAAGGTGGCATAGG 1316038 TACCATACATGTAACACAGTAAG 1 TACCATACATGTAACACAGTAAG 1316061 CAGCGACTTA Statistics Matches: 238, Mismatches: 14, Indels: 2 0.94 0.06 0.01 Matches are distributed among these distances: 32 28 0.12 33 210 0.88 ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23 Consensus pattern (33 bp): TACCATACATGTAACACAGTAAGGTGGCATAGG Found at i:1317188 original size:166 final size:166 Alignment explanation

Indices: 1316749--1317375 Score: 911 Period size: 166 Copynumber: 3.8 Consensus size: 166 1316739 GTGAATATGC * * * * * * * 1316749 AAAATAAGCAAAGTCGA-CATTTAACAGAAAGCTGGCATCCGATTGGTACAGAAATATATCCCAC 1 AAAATAAACAAAGTC-ATCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCAC * 1316813 AATATGGCATGCCTAAACAAATAGTGTGTTAAAAA-TTCAAGCATCTGCGATAAATAGCTGCTGA 65 AATATGACATGCCTAAACAAATAGTGTG-TAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGA * 1316877 GAAATCTTTGAGGAAAATTTGTTTGAAAATTTTGGCT- 129 GAAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA * * * 1316914 AAAATAAACAAAGT-ACTCATTTAACAGGAAGTTGACGTCCAATTGGTACAAAAATATGTCCCAC 1 AAAATAAACAAAGTCA-TCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCAC * * * * 1316978 GATATGACATGCCTTAACAAACACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAG 65 AATATGACATGCCTAAACAAATAGTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAG 1317043 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA 130 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA * * * 1317080 AAAATAAACAAAGTCATTATTTAACAAGAAGTTGACGTCCGACTGATACAAAAATATATCCCACA 1 AAAATAAACAAAGTCATCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCACA * * * * * * * 1317145 ATATGGCAAGCCAAAACAAATAGTGTATTACAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA 66 ATATGACATGCCTAAACAAATAGTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGA * * 1317210 AATCTTTGACAAAAATTTGTTTGAAAATTTTTGCTA 131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA * * * 1317246 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAACTATATCCCACG 1 AAAATAAACAAAGTCATCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCACA * 1317311 ATATGACATGCCTAAACAAATAGTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA 66 ATATGACATGCCTAAACAAATAGTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGA 1317376 TAAATGCGAC Statistics Matches: 412, Mismatches: 45, Indels: 9 0.88 0.10 0.02 Matches are distributed among these distances: 163 1 0.00 164 6 0.01 165 141 0.34 166 263 0.64 167 1 0.00 ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28 Consensus pattern (166 bp): AAAATAAACAAAGTCATCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCACA ATATGACATGCCTAAACAAATAGTGTGTAAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGA AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA Done.