Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold149

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: 1065560
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30

Warning! 107426 characters in sequence are not A, C, G, or T


File 5 of 4

Found at i:912439 original size:2 final size:2

Alignment explanation

Indices: 912432--912466 Score: 70 Period size: 2 Copynumber: 17.5 Consensus size: 2 912422 ACCCAAGATG 912432 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C 912467 ATATTAAGGT Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 33 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:914182 original size:36 final size:36 Alignment explanation

Indices: 914135--914313 Score: 313 Period size: 36 Copynumber: 4.9 Consensus size: 36 914125 ACTTACGCTG * 914135 AGATCCTGTACACAACATCATTGAATGACATGTAAC 1 AGATCTTGTACACAACATCATTGAATGACATGTAAC 914171 AGATCTTGTACACAACATCATTGAATGACATGTAAC 1 AGATCTTGTACACAACATCATTGAATGACATGTAAC 914207 AGATCTTGTACACAACATCATTGAATGACATGTAAC 1 AGATCTTGTACACAACATCATTGAATGACATGTAAC 914243 AGATCTTGTACACAACATCATTGAATGACATGTAAC 1 AGATCTTGTACACAACATCATTGAATGACATGTAAC * * 914279 AGATCTTGTACACAAAATCTTTGAACTGTACATGT 1 AGATCTTGTACACAACATCATTGAA-TG-ACATGT 914314 CATATAGATC Statistics Matches: 138, Mismatches: 3, Indels: 2 0.97 0.02 0.01 Matches are distributed among these distances: 36 130 0.94 37 2 0.01 38 6 0.04 ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28 Consensus pattern (36 bp): AGATCTTGTACACAACATCATTGAATGACATGTAAC Found at i:915130 original size:22 final size:22 Alignment explanation

Indices: 915105--915236 Score: 192 Period size: 22 Copynumber: 5.7 Consensus size: 22 915095 CTTTACTGTG * 915105 ACTATAACATGACTACAGCATT 1 ACTATAACATGACTACAACATT * 915127 ACTACCGGTATAACATGACTACAGCATT 1 ACTA------TAACATGACTACAACATT 915155 ACTATAACATGACTACAACATT 1 ACTATAACATGACTACAACATT 915177 ACTATAACATGACTACAACATT 1 ACTATAACATGACTACAACATT 915199 ACTATAACATGACTACAACATT 1 ACTATAACATGACTACAACATT 915221 ACTATAACATGACTAC 1 ACTATAACATGACTAC 915237 CTACCCAGAT Statistics Matches: 103, Mismatches: 1, Indels: 12 0.89 0.01 0.10 Matches are distributed among these distances: 22 81 0.79 28 22 0.21 ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27 Consensus pattern (22 bp): ACTATAACATGACTACAACATT Found at i:915169 original size:11 final size:11 Alignment explanation

Indices: 915135--915235 Score: 121 Period size: 11 Copynumber: 9.2 Consensus size: 11 915125 TTACTACCGG 915135 TATAACATGAC 1 TATAACATGAC * * * 915146 TACAGCATTAC 1 TATAACATGAC 915157 TATAACATGAC 1 TATAACATGAC * * 915168 TACAACATTAC 1 TATAACATGAC 915179 TATAACATGAC 1 TATAACATGAC * * 915190 TACAACATTAC 1 TATAACATGAC 915201 TATAACATGAC 1 TATAACATGAC * * 915212 TACAACATTAC 1 TATAACATGAC 915223 TATAACATGAC 1 TATAACATGAC 915234 TA 1 TA 915236 CCTACCCAGA Statistics Matches: 72, Mismatches: 18, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 11 72 1.00 ACGTcount: A:0.45, C:0.22, G:0.06, T:0.28 Consensus pattern (11 bp): TATAACATGAC Found at i:916501 original size:2 final size:2 Alignment explanation

Indices: 916494--916556 Score: 126 Period size: 2 Copynumber: 31.5 Consensus size: 2 916484 GTAAAACTCA 916494 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 916536 CT CT CT CT CT CT CT CT CT CT C 1 CT CT CT CT CT CT CT CT CT CT C 916557 NNNNNNNNNN Statistics Matches: 61, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 61 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:917223 original size:36 final size:36 Alignment explanation

Indices: 917173--917280 Score: 191 Period size: 36 Copynumber: 3.0 Consensus size: 36 917163 ACATGGACAG * 917173 CTAG-TGTCATGTTGTAAATTTTGTATATACTGTCA 1 CTAGTTGTCATGTTGTAAATTTTGTATTTACTGTCA * 917208 CTAGTTGTCAAGTTGTAAATTTTGTATTTACTGTCA 1 CTAGTTGTCATGTTGTAAATTTTGTATTTACTGTCA 917244 CTAGTTGTCATGTTGTAAATTTTGTATTTACTGTCA 1 CTAGTTGTCATGTTGTAAATTTTGTATTTACTGTCA 917280 C 1 C 917281 CCGGTAAATT Statistics Matches: 69, Mismatches: 3, Indels: 1 0.95 0.04 0.01 Matches are distributed among these distances: 35 4 0.06 36 65 0.94 ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47 Consensus pattern (36 bp): CTAGTTGTCATGTTGTAAATTTTGTATTTACTGTCA Found at i:917575 original size:4 final size:4 Alignment explanation

Indices: 917568--917644 Score: 77 Period size: 4 Copynumber: 19.8 Consensus size: 4 917558 CCTCCCTCTT * * * * 917568 TAAA TAAA TAGA TAAA TAAA T-AA TAAA -AAA AAAA TGAA TGAA TAAA 1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA * * * 917614 TAAA TAGA CAAA TAGA TAAA TAAA TAAA TAA 1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA 917645 CAAAGATTAT Statistics Matches: 60, Mismatches: 11, Indels: 4 0.80 0.15 0.05 Matches are distributed among these distances: 3 6 0.10 4 54 0.90 ACGTcount: A:0.70, C:0.01, G:0.06, T:0.22 Consensus pattern (4 bp): TAAA Found at i:919353 original size:18 final size:18 Alignment explanation

Indices: 919330--919449 Score: 91 Period size: 18 Copynumber: 6.7 Consensus size: 18 919320 TTCATTATAT * 919330 CACAGAATCATAAATTAC 1 CACAGAATCACAAATTAC * 919348 CACAGAATCACCAATTAC 1 CACAGAATCACAAATTAC * 919366 CACAGAATCAC-ACTGTAC 1 CACAGAATCACAAAT-TAC * * * * * 919384 CATATAATTATACATTAC 1 CACAGAATCACAAATTAC * * * 919402 AACATAATCACACATTAC 1 CACAGAATCACAAATTAC * * 919420 CACATAATCACACATTAC 1 CACAGAATCACAAATTAC 919438 CAC-GAAATCACA 1 CACAG-AATCACA 919450 CTGTACCACT Statistics Matches: 84, Mismatches: 15, Indels: 6 0.80 0.14 0.06 Matches are distributed among these distances: 17 2 0.02 18 81 0.96 19 1 0.01 ACGTcount: A:0.46, C:0.28, G:0.04, T:0.22 Consensus pattern (18 bp): CACAGAATCACAAATTAC Found at i:919450 original size:18 final size:18 Alignment explanation

Indices: 919343--919495 Score: 152 Period size: 18 Copynumber: 8.5 Consensus size: 18 919333 AGAATCATAA * 919343 ATTACCACAGAATCAC-C 1 ATTACCACATAATCACAC * 919360 AATTACCACAGAATCACAC 1 -ATTACCACATAATCACAC * * * 919379 -TGTACCATATAATTATAC 1 AT-TACCACATAATCACAC * 919397 ATTACAACATAATCACAC 1 ATTACCACATAATCACAC 919415 ATTACCACATAATCACAC 1 ATTACCACATAATCACAC 919433 ATTACCACGA-AATCACAC 1 ATTACCAC-ATAATCACAC * * 919451 -TGTACCACTTAATCATAC 1 AT-TACCACATAATCACAC * 919469 ATTACAACATAATCACAC 1 ATTACCACATAATCACAC * 919487 ATTATCACA 1 ATTACCACA 919496 CCGTACCACA Statistics Matches: 112, Mismatches: 16, Indels: 14 0.79 0.11 0.10 Matches are distributed among these distances: 17 2 0.02 18 106 0.95 19 4 0.04 ACGTcount: A:0.44, C:0.29, G:0.03, T:0.24 Consensus pattern (18 bp): ATTACCACATAATCACAC Found at i:919452 original size:72 final size:72 Alignment explanation

Indices: 919343--919495 Score: 231 Period size: 72 Copynumber: 2.1 Consensus size: 72 919333 AGAATCATAA * 919343 ATTACCACAGAATCACCAATTACCACAGAATCACACTGTACCA-TATAATTATACATTACAACAT 1 ATTACCACAGAATCACCAATTACCACAGAATCACACTGTACCACT-TAATCATACATTACAACAT 919407 AATCACAC 65 AATCACAC * 919415 ATTACCACATAATCA-CACATTACCAC-GAAATCACACTGTACCACTTAATCATACATTACAACA 1 ATTACCACAGAATCACCA-ATTACCACAG-AATCACACTGTACCACTTAATCATACATTACAACA 919478 TAATCACAC 64 TAATCACAC * 919487 ATTATCACA 1 ATTACCACA 919496 CCGTACCACA Statistics Matches: 75, Mismatches: 3, Indels: 6 0.89 0.04 0.07 Matches are distributed among these distances: 71 3 0.04 72 71 0.95 73 1 0.01 ACGTcount: A:0.44, C:0.29, G:0.03, T:0.24 Consensus pattern (72 bp): ATTACCACAGAATCACCAATTACCACAGAATCACACTGTACCACTTAATCATACATTACAACATA ATCACAC Found at i:919507 original size:28 final size:29 Alignment explanation

Indices: 919475--919550 Score: 77 Period size: 28 Copynumber: 2.7 Consensus size: 29 919465 ATACATTACA * * 919475 ACATAATCACACATTATCACACCGTA-C-C 1 ACATAAACACACATTA-CACACCGAATCAC * * 919503 ACATAAAAACACATTGC-CACCGAATCAC 1 ACATAAACACACATTACACACCGAATCAC * 919531 ACATAACCACACATTACACA 1 ACATAAACACACATTACACA 919551 TAATCTTGTT Statistics Matches: 38, Mismatches: 7, Indels: 5 0.76 0.14 0.10 Matches are distributed among these distances: 26 6 0.16 27 2 0.05 28 28 0.74 29 2 0.05 ACGTcount: A:0.45, C:0.34, G:0.04, T:0.17 Consensus pattern (29 bp): ACATAAACACACATTACACACCGAATCAC Found at i:919718 original size:18 final size:18 Alignment explanation

Indices: 919697--920121 Score: 294 Period size: 18 Copynumber: 24.1 Consensus size: 18 919687 TCATGATATT 919697 TTACCACATAATCACACA 1 TTACCACATAATCACACA * * 919715 TTACCACAGAACCACACA 1 TTACCACATAATCACACA * * * * 919733 TTGCAACAAAATCACAAA 1 TTACCACATAATCACACA * * 919751 TTATCAGAT-AT-A-AC- 1 TTACCACATAATCACACA * 919765 -TA-CA-AAAAT-ACACA 1 TTACCACATAATCACACA * * 919779 TTACCACATTATCATACA 1 TTACCACATAATCACACA * * * * * 919797 TCACAACATTATTACAAA 1 TTACCACATAATCACACA * * * 919815 TAACTACAGAATCACACA 1 TTACCACATAATCACACA * 919833 TTACCACATCATCACACA 1 TTACCACATAATCACACA * * 919851 TTAACACAGAATCACACA 1 TTACCACATAATCACACA * * 919869 TTACCATATTATCACACA 1 TTACCACATAATCACACA * * 919887 TTACCATATTATCACACA 1 TTACCACATAATCACACA * * 919905 -TATCTACAGAATCACACA 1 TTA-CCACATAATCACACA * * 919923 TTAACACAGAATCACACA 1 TTACCACATAATCACACA * * * 919941 TTTCCATATTATCACACA 1 TTACCACATAATCACACA * * * 919959 TAACTACAGAATCACACA 1 TTACCACATAATCACACA * 919977 TTACCACATCATCACACA 1 TTACCACATAATCACACA * * * 919995 TTAACACAGAATCACATA 1 TTACCACATAATCACACA * * 920013 TTACCATATTATCACACA 1 TTACCACATAATCACACA * * 920031 TTACCATATTATCACACA 1 TTACCACATAATCACACA * * * * 920049 TAACAACAGAATCACTCA 1 TTACCACATAATCACACA * 920067 TTACCACAGAATCACACA 1 TTACCACATAATCACACA * * * 920085 -TATCTACAGAATCATACA 1 TTA-CCACATAATCACACA 920103 TTACCACATAATCACACA 1 TTACCACATAATCACACA 920121 T 1 T 920122 ATCTACAGAA Statistics Matches: 313, Mismatches: 83, Indels: 22 0.75 0.20 0.05 Matches are distributed among these distances: 11 1 0.00 12 5 0.02 13 4 0.01 15 3 0.01 16 3 0.01 17 9 0.03 18 284 0.91 19 4 0.01 ACGTcount: A:0.45, C:0.28, G:0.03, T:0.24 Consensus pattern (18 bp): TTACCACATAATCACACA Found at i:919840 original size:10 final size:9 Alignment explanation

Indices: 919827--920049 Score: 58 Period size: 8 Copynumber: 24.8 Consensus size: 9 919817 ACTACAGAAT 919827 CACACATTA 1 CACACATTA * 919836 C-CACATCA 1 CACACATTA 919844 TCACACATTA 1 -CACACATTA ** 919854 -ACACAGAA 1 CACACATTA 919862 TCACACATTA 1 -CACACATTA * 919872 C-CATATTA 1 CACACATTA 919880 TCACACATTA 1 -CACACATTA * 919890 C-CATATTA 1 CACACATTA 919898 TCACACA-TA 1 -CACACATTA * * 919907 TCTACAGAAT- 1 -C-ACACATTA 919917 CACACATTA 1 CACACATTA ** 919926 -ACACAGAA 1 CACACATTA * 919934 TCACACATTT 1 -CACACATTA * 919944 C-CATATTA 1 CACACATTA * 919952 TCACACATAA 1 -CACACATTA * * 919962 CTACAGAAT- 1 C-ACACATTA 919971 CACACATTA 1 CACACATTA * 919980 C-CACATCA 1 CACACATTA 919988 TCACACATTA 1 -CACACATTA ** 919998 -ACACAGAA 1 CACACATTA * 920006 TCACATATTA 1 -CACACATTA * 920016 C-CATATTA 1 CACACATTA 920024 TCACACATTA 1 -CACACATTA * 920034 C-CATATTA 1 CACACATTA 920042 TCACACAT 1 -CACACAT 920050 AACAACAGAA Statistics Matches: 152, Mismatches: 37, Indels: 49 0.64 0.16 0.21 Matches are distributed among these distances: 8 70 0.46 9 21 0.14 10 60 0.39 11 1 0.01 ACGTcount: A:0.43, C:0.30, G:0.02, T:0.26 Consensus pattern (9 bp): CACACATTA Found at i:920168 original size:72 final size:72 Alignment explanation

Indices: 919824--920177 Score: 195 Period size: 72 Copynumber: 4.9 Consensus size: 72 919814 ATAACTACAG * * ** * * * * * * ** 919824 AATCACACATTACCACATCATCACACATTAACACAGAATCACACATTACCATATTATCACACATT 1 AATCACACATAACAACAGAATCACACACTACCACAGAACCACACATAACGAAAGAATCACACATT * 919889 ACCATAT 66 ACCACAT * * * * * * ** * * ** * 919896 TATCACACATATCTACAGAATCACACATTAACACAGAATCACACATTTCCATATTATCACACATA 1 AATCACACATAACAACAGAATCACACACTACCACAGAACCACACATAACGAAAGAATCACACATT * * 919961 ACTACAG 66 ACCACAT * * ** * * * * * * * ** 919968 AATCACACATTACCACATCATCACACATTAACACAGAATCACATATTACCATATTATCACACATT 1 AATCACACATAACAACAGAATCACACACTACCACAGAACCACACATAACGAAAGAATCACACATT * 920033 ACCATAT 66 ACCACAT * * * * * * * * 920040 TATCACACATAACAACAGAATCACTCATTACCACAGAATCACACATATCTACAGAATCATACATT 1 AATCACACATAACAACAGAATCACACACTACCACAGAACCACACATAACGAAAGAATCACACATT 920105 ACCACAT 66 ACCACAT * * * ** * * 920112 AATCACACATATCTACAGAATCACACACTATCACATCACCACATATAACGAAAGAATTACACATT 1 AATCACACATAACAACAGAATCACACACTACCACAGAACCACACATAACGAAAGAATCACACATT 920177 A 66 A 920178 ACGCATTGTC Statistics Matches: 228, Mismatches: 54, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 72 228 1.00 ACGTcount: A:0.44, C:0.29, G:0.03, T:0.24 Consensus pattern (72 bp): AATCACACATAACAACAGAATCACACACTACCACAGAACCACACATAACGAAAGAATCACACATT ACCACAT Found at i:920370 original size:18 final size:18 Alignment explanation

Indices: 920344--920380 Score: 56 Period size: 18 Copynumber: 2.1 Consensus size: 18 920334 TTGCCACATC * 920344 GTATCACACATTACTTCA 1 GTATCACACATTACCTCA * 920362 GTATTACACATTACCTCA 1 GTATCACACATTACCTCA 920380 G 1 G 920381 CATACAACGC Statistics Matches: 17, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 18 17 1.00 ACGTcount: A:0.32, C:0.27, G:0.08, T:0.32 Consensus pattern (18 bp): GTATCACACATTACCTCA Found at i:920430 original size:18 final size:18 Alignment explanation

Indices: 920404--920455 Score: 61 Period size: 18 Copynumber: 2.9 Consensus size: 18 920394 AGCAAACATT * 920404 ACCAAAGCAGTATACCTC 1 ACCACAGCAGTATACCTC * * 920422 ACCACAGCA-TGATACTTT 1 ACCACAGCAGT-ATACCTC 920440 ACCACAGCAGTATACC 1 ACCACAGCAGTATACC 920456 CCATTACAGC Statistics Matches: 28, Mismatches: 4, Indels: 4 0.78 0.11 0.11 Matches are distributed among these distances: 17 1 0.04 18 26 0.93 19 1 0.04 ACGTcount: A:0.37, C:0.33, G:0.12, T:0.19 Consensus pattern (18 bp): ACCACAGCAGTATACCTC Found at i:920449 original size:36 final size:36 Alignment explanation

Indices: 920402--920478 Score: 118 Period size: 36 Copynumber: 2.1 Consensus size: 36 920392 ATAGCAAACA * 920402 TTACCAAAGCAGTATACCTCACCACAGCATGATACT 1 TTACCAAAGCAGTATACCCCACCACAGCATGATACT * ** 920438 TTACCACAGCAGTATACCCCATTACAGCATGATACT 1 TTACCAAAGCAGTATACCCCACCACAGCATGATACT 920474 TTACC 1 TTACC 920479 TTAGACGGTA Statistics Matches: 37, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 36 37 1.00 ACGTcount: A:0.34, C:0.31, G:0.10, T:0.25 Consensus pattern (36 bp): TTACCAAAGCAGTATACCCCACCACAGCATGATACT Found at i:921690 original size:47 final size:47 Alignment explanation

Indices: 921621--921714 Score: 179 Period size: 47 Copynumber: 2.0 Consensus size: 47 921611 CGTACATACC 921621 TACCCTTAAATGACAGATGGACGTGATTCCAGTCGGGCTCGGGTGTG 1 TACCCTTAAATGACAGATGGACGTGATTCCAGTCGGGCTCGGGTGTG * 921668 TACCCTTAAATGACAGATGGACGTGATTCCAGTGGGGCTCGGGTGTG 1 TACCCTTAAATGACAGATGGACGTGATTCCAGTCGGGCTCGGGTGTG 921715 GGGTCTGTAG Statistics Matches: 46, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 47 46 1.00 ACGTcount: A:0.21, C:0.20, G:0.33, T:0.26 Consensus pattern (47 bp): TACCCTTAAATGACAGATGGACGTGATTCCAGTCGGGCTCGGGTGTG Found at i:923016 original size:20 final size:20 Alignment explanation

Indices: 922991--923031 Score: 82 Period size: 20 Copynumber: 2.0 Consensus size: 20 922981 CGAGTCGCGA 922991 GTACTATAGTGTGGTACTGG 1 GTACTATAGTGTGGTACTGG 923011 GTACTATAGTGTGGTACTGG 1 GTACTATAGTGTGGTACTGG 923031 G 1 G 923032 AGAATCCTGT Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 20 21 1.00 ACGTcount: A:0.20, C:0.10, G:0.37, T:0.34 Consensus pattern (20 bp): GTACTATAGTGTGGTACTGG Found at i:924533 original size:2 final size:2 Alignment explanation

Indices: 924526--924575 Score: 84 Period size: 2 Copynumber: 25.5 Consensus size: 2 924516 CTTGCATAAA * 924526 CT CT CT CT CT CT CT CT TT CT CT CT CT CT CT CT CT CT -T CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 924567 CT CT CT CT C 1 CT CT CT CT C 924576 ATGCGAGATT Statistics Matches: 45, Mismatches: 2, Indels: 2 0.92 0.04 0.04 Matches are distributed among these distances: 1 1 0.02 2 44 0.98 ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52 Consensus pattern (2 bp): CT Found at i:925474 original size:20 final size:20 Alignment explanation

Indices: 925449--925488 Score: 71 Period size: 20 Copynumber: 2.0 Consensus size: 20 925439 AGGAAATCAT 925449 CTGGCCCCACTGTCATTAAC 1 CTGGCCCCACTGTCATTAAC * 925469 CTGGCCCCGCTGTCATTAAC 1 CTGGCCCCACTGTCATTAAC 925489 GTTTCTTAAG Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 20 19 1.00 ACGTcount: A:0.17, C:0.40, G:0.17, T:0.25 Consensus pattern (20 bp): CTGGCCCCACTGTCATTAAC Found at i:926053 original size:46 final size:46 Alignment explanation

Indices: 926003--927316 Score: 1577 Period size: 46 Copynumber: 28.8 Consensus size: 46 925993 TGAAACTGCT * * 926003 GTGTGGTTTCTGTGTAGGTTCTACCACTAGTCGATCTGTAACTGCC 1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC ** * * 926049 GTGTGGTTTTTGTGTAGGTTCTACCACTAGTCGATGTGTAACTGCC 1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC * * * * * 926095 GTGTGGATTCCGTCGTAAGTTTTACCACTAGTCGATGTGAAACTGTC 1 GTGTGGTTTCCGT-GTAGGTTCTACCACTAGTCGATCTGTAACTGTC * * * * 926142 --GTGCTTTCCGTTTAGGTTCTACCACTAGTCGATGTGTAACTGAC 1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC * * * 926186 GTGTGGTTTCTGTGTAGGTTCTACCACTAGTCGATGTGTAACTGCC 1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC * * 926232 GTGTGGTTTCCGTGTATGTTTTACCACTAGTCGATCTGTAACTGTC 1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC * * * 926278 GTTTGGTTTCCGTGTATGTTTTACCACTAGTCGATCTGTAACTGTC 1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC * * * * 926324 GTGTTGTTTCTGTGTAGCTTCTACCACTAGTCGATCTGTAACTGCC 1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC * * * * 926370 GTTTGGTTTCCGTGTATGTTTTACCACTAGTCGATGTGTAACTGTC 1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC * * * * * * 926416 GTGTTGTTTCTGTCTATGTTTTACCGCTAGTCGATCTGTAACTGTC 1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC * * * 926462 GTTTGGTTTCTGTGTAGGTTCTACCACTAGTCGATGTGTAACTGTC 1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC * * * * 926508 GTGTTGTTTCTGTGTATGTTTTACCACTAGTCGATCTGTAACTGTC 1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC * * * * 926554 GTTTGGTTTCTGTGTAGGTTCTACCACTAGTCGATGTGTAACTGAC 1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC * * * 926600 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATGTATAACTGCC 1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC * 926646 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTA 1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC * * * * * 926692 ATATGTTTTCCGTGT--GTTTTACCACTAGTCGATCTGTAACTGCC 1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC * * * 926736 GTTTGGTTTCCGTGTATGTTTTACCACTAGTCGATCTGTAACTGTC 1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC * * * * 926782 GTGTTGTTTCTGTGTAGCTTCTACCACTAGTCGATCTGTAACTGCC 1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC * * * * 926828 GTTTGGTTTCCGTGTATGTTTTACCACTAGTCGATGTGTAACTGTC 1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC * * * * * * 926874 GTGTTGTTTCTGTCTATGTTTTACCGCTAGTCGATCTGTAACTGTC 1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC * * * 926920 GTTTGGTTTCTGTGTAGGTTCTACCACTAGTCGATGTGTAACTGTC 1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC * * * * 926966 GTGTTGTTTCTGTGTATGTTTTACCACTAGTCGATCTGTAACTGTC 1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC * * * 927012 GTGTGGTTTCTGTGTAGGTTCTACCACTAGTCGATGTGTAACTGAC 1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC * * * 927058 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATGTATAACTGCC 1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC * 927104 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTA 1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC * * * * * 927150 ATATGTTTTCCGTGT--GTTTTACCACTAGTCGATCTGTAACTGCC 1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC * * * * 927194 GTTTGGTTTCCGTGTATGTTTTACCACTAGTCGATCTGTAACTGTA 1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC * * * * * * 927240 ATATGTTTTCCGTGT--GTTTTACCACTAGTCGATGTGTAACTGTA 1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC * * ** * 927284 ATATATTTTCCGTGT--GTTTTACCACTAGTCGAT 1 GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGAT 927317 ATGAACTTGG Statistics Matches: 1117, Mismatches: 144, Indels: 16 0.87 0.11 0.01 Matches are distributed among these distances: 44 164 0.15 45 9 0.01 46 915 0.82 47 29 0.03 ACGTcount: A:0.16, C:0.19, G:0.24, T:0.40 Consensus pattern (46 bp): GTGTGGTTTCCGTGTAGGTTCTACCACTAGTCGATCTGTAACTGTC Found at i:928310 original size:2 final size:2 Alignment explanation

Indices: 928303--928338 Score: 72 Period size: 2 Copynumber: 18.0 Consensus size: 2 928293 GACCGGAATA 928303 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 928339 AGTAACCTAC Statistics Matches: 34, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 34 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:930062 original size:2 final size:2 Alignment explanation

Indices: 930055--930097 Score: 59 Period size: 2 Copynumber: 21.5 Consensus size: 2 930045 NNNNNNNNNN * * * 930055 TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA TC TA TA TC TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 930097 T 1 T 930098 GCTGTTGAAT Statistics Matches: 35, Mismatches: 6, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 2 35 1.00 ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53 Consensus pattern (2 bp): TA Found at i:930489 original size:24 final size:24 Alignment explanation

Indices: 930461--930557 Score: 81 Period size: 24 Copynumber: 3.8 Consensus size: 24 930451 AACGTTCTAC * 930461 ATTTTTTGTTTTTGTTGTACG-AT 1 ATTTTTTTTTTTTGTTGTACGTAT * 930484 ATTTTTATTTTTTTGTTGT-GGTAT 1 ATTTTT-TTTTTTTGTTGTACGTAT * 930508 ATTTTTTTATTGTTGTTGTACAATGTTAT 1 ATTTTTTT-TTTTTGTTGTAC---G-TAT 930537 ATTTTTTTATTTTTTGTTGTA 1 A-TTTTTT-TTTTTTGTTGTA 930558 GATCTTCAGC Statistics Matches: 59, Mismatches: 5, Indels: 13 0.77 0.06 0.17 Matches are distributed among these distances: 23 9 0.15 24 28 0.47 28 1 0.02 29 4 0.07 30 16 0.27 31 1 0.02 ACGTcount: A:0.15, C:0.02, G:0.14, T:0.68 Consensus pattern (24 bp): ATTTTTTTTTTTTGTTGTACGTAT Found at i:931206 original size:21 final size:21 Alignment explanation

Indices: 931180--931596 Score: 200 Period size: 21 Copynumber: 18.7 Consensus size: 21 931170 AATACGCTGA * 931180 TATACAATGTTACATGCAGTG 1 TATACAATGTTACATACAGTG * 931201 TATACAATGTTACATATAGTG 1 TATACAATGTTACATACAGTG * 931222 TATACAATGTTACA-ACATGCAATT 1 TATACAATGTTACATACA-G---TG * * * 931246 TATACATTGGTACATATAGTG 1 TATACAATGTTACATACAGTG * 931267 TATACAATTAATGTTACA-ACATGCAATC 1 TATAC----AATGTTACATACA-G---TG * * * 931295 TATACATTGGTACATATAGTG 1 TATACAATGTTACATACAGTG * 931316 TATACAATGTTACA-ACATGCAATC 1 TATACAATGTTACATACA-G---TG * * * 931340 TATACATTGGTACATATAGTG 1 TATACAATGTTACATACAGTG * 931361 TATACAATGTTACA-ACATGCAATC 1 TATACAATGTTACATACA-G---TG * * * 931385 TATACATTGGTACATATAGTG 1 TATACAATGTTACATACAGTG * 931406 TATACAATGTTACATGCAGTG 1 TATACAATGTTACATACAGTG * 931427 TATACAATGTTACATATAGTG 1 TATACAATGTTACATACAGTG * 931448 TATACAATGTTACA-ACATGCAATC 1 TATACAATGTTACATACA-G---TG * * * 931472 TATACATTGGTACATATAGTG 1 TATACAATGTTACATACAGTG * * 931493 TATACAGTGTTACA-ACAAGCAATC 1 TATACAATGTTACATAC-AG---TG * * * 931517 TATACATTGGTACATATAGTG 1 TATACAATGTTACATACAGTG * 931538 TATACAATGTTACA-ACAAGCAATC 1 TATACAATGTTACATAC-AG---TG * * * 931562 TATACATTGGTACATATAGTG 1 TATACAATGTTACATACAGTG 931583 TATACAATGTTACA 1 TATACAATGTTACA 931597 ACATGCAATC Statistics Matches: 295, Mismatches: 62, Indels: 78 0.68 0.14 0.18 Matches are distributed among these distances: 20 10 0.03 21 163 0.55 24 96 0.33 25 20 0.07 28 6 0.02 ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34 Consensus pattern (21 bp): TATACAATGTTACATACAGTG Found at i:931260 original size:45 final size:45 Alignment explanation

Indices: 931180--931688 Score: 778 Period size: 45 Copynumber: 11.3 Consensus size: 45 931170 AATACGCTGA * * * * 931180 TATACAATGTT---ACATGCAGTGTATACAATGTTACATATAGTG 1 TATACAATGTTACAACATGCAATCTATACATTGGTACATATAGTG * 931222 TATACAATGTTACAACATGCAATTTATACATTGGTACATATAGTG 1 TATACAATGTTACAACATGCAATCTATACATTGGTACATATAGTG 931267 TATACAATTAATGTTACAACATGCAATCTATACATTGGTACATATAGTG 1 TATAC----AATGTTACAACATGCAATCTATACATTGGTACATATAGTG 931316 TATACAATGTTACAACATGCAATCTATACATTGGTACATATAGTG 1 TATACAATGTTACAACATGCAATCTATACATTGGTACATATAGTG 931361 TATACAATGTTACAACATGCAATCTATACATTGGTACATATAGTG 1 TATACAATGTTACAACATGCAATCTATACATTGGTACATATAGTG * * * * 931406 TATACAATGTT---ACATGCAGTGTATACAATGTTACATATAGTG 1 TATACAATGTTACAACATGCAATCTATACATTGGTACATATAGTG 931448 TATACAATGTTACAACATGCAATCTATACATTGGTACATATAGTG 1 TATACAATGTTACAACATGCAATCTATACATTGGTACATATAGTG * * 931493 TATACAGTGTTACAACAAGCAATCTATACATTGGTACATATAGTG 1 TATACAATGTTACAACATGCAATCTATACATTGGTACATATAGTG * 931538 TATACAATGTTACAACAAGCAATCTATACATTGGTACATATAGTG 1 TATACAATGTTACAACATGCAATCTATACATTGGTACATATAGTG * 931583 TATACAATGTTACAACATGCAATCTATACATTGGTGCATATAGTG 1 TATACAATGTTACAACATGCAATCTATACATTGGTACATATAGTG * 931628 TATACAATTAATGTTACAACATGCAATCTATACATTAGTACATATAGTG 1 TATAC----AATGTTACAACATGCAATCTATACATTGGTACATATAGTG 931677 TATACAATGTTA 1 TATACAATGTTA 931689 TACCATGCGA Statistics Matches: 433, Mismatches: 20, Indels: 25 0.91 0.04 0.05 Matches are distributed among these distances: 42 49 0.11 45 297 0.69 49 87 0.20 ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34 Consensus pattern (45 bp): TATACAATGTTACAACATGCAATCTATACATTGGTACATATAGTG Found at i:931809 original size:24 final size:24 Alignment explanation

Indices: 931675--931817 Score: 200 Period size: 24 Copynumber: 6.0 Consensus size: 24 931665 GTACATATAG * * * * 931675 TGTATACAATGTTATACCATGCGA 1 TGTATTCAATGTTACACAATGCAA 931699 TGTATTCATAATG--ACACAATGCAA 1 TGTATTC--AATGTTACACAATGCAA 931723 TGTATTCAATGTTACACAATGCAA 1 TGTATTCAATGTTACACAATGCAA 931747 TGTATTCAATGTTACACAATGCAA 1 TGTATTCAATGTTACACAATGCAA 931771 TGTATTCAATGTTACACAATGCAA 1 TGTATTCAATGTTACACAATGCAA * * 931795 TGTATTCAATATTACACCATGCA 1 TGTATTCAATGTTACACAATGCA 931818 TTAAGGCACC Statistics Matches: 109, Mismatches: 6, Indels: 8 0.89 0.05 0.07 Matches are distributed among these distances: 22 4 0.04 24 101 0.93 26 4 0.04 ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33 Consensus pattern (24 bp): TGTATTCAATGTTACACAATGCAA Found at i:938144 original size:4 final size:4 Alignment explanation

Indices: 938135--938187 Score: 79 Period size: 4 Copynumber: 13.2 Consensus size: 4 938125 TTAGAATCTA * * * 938135 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TCTC TCTC TCTC 1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC 938183 TGTC T 1 TGTC T 938188 CTGTCTCTCT Statistics Matches: 47, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 4 47 1.00 ACGTcount: A:0.00, C:0.30, G:0.19, T:0.51 Consensus pattern (4 bp): TGTC Found at i:938176 original size:2 final size:2 Alignment explanation

Indices: 938169--938225 Score: 96 Period size: 2 Copynumber: 28.5 Consensus size: 2 938159 TGTCTGTCTG * * 938169 TC TC TC TC TC TC TC TG TC TC TG 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 938211 TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC T 938226 GTTTCCTGTA Statistics Matches: 51, Mismatches: 4, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 2 51 1.00 ACGTcount: A:0.00, C:0.46, G:0.04, T:0.51 Consensus pattern (2 bp): TC Found at i:938188 original size:8 final size:8 Alignment explanation

Indices: 938135--938221 Score: 88 Period size: 8 Copynumber: 11.1 Consensus size: 8 938125 TTAGAATCTA * 938135 TGTCTGTC 1 TGTCTCTC * 938143 TGTCTGTC 1 TGTCTCTC * 938151 TGTCTGTC 1 TGTCTCTC * 938159 TGTCTGTC 1 TGTCTCTC 938167 TGTCTCTC 1 TGTCTCTC * 938175 TCTCTCTC 1 TGTCTCTC 938183 TG--TCTC 1 TGTCTCTC 938189 TGTCTCTC 1 TGTCTCTC * 938197 TCTCTCTC 1 TGTCTCTC * 938205 TCTCTCTC 1 TGTCTCTC * 938213 TCTCTCTC 1 TGTCTCTC 938221 T 1 T 938222 CTCTGTTTCC Statistics Matches: 73, Mismatches: 4, Indels: 4 0.90 0.05 0.05 Matches are distributed among these distances: 6 6 0.08 8 67 0.92 ACGTcount: A:0.00, C:0.37, G:0.13, T:0.51 Consensus pattern (8 bp): TGTCTCTC Found at i:938188 original size:12 final size:12 Alignment explanation

Indices: 938141--938227 Score: 97 Period size: 12 Copynumber: 7.4 Consensus size: 12 938131 TCTATGTCTG * * 938141 TCTGTCTGTCTG 1 TCTGTCTCTCTC * * 938153 TCTGTCTGTCTG 1 TCTGTCTCTCTC 938165 TCTGTCTCTCTC 1 TCTGTCTCTCTC * 938177 TC--TCTCTGTC 1 TCTGTCTCTCTC 938187 TCTGTCTCTCTC 1 TCTGTCTCTCTC * 938199 TCTCTCTCTCTC 1 TCTGTCTCTCTC * 938211 TCTCTCTCTCTC 1 TCTGTCTCTCTC 938223 TCTGT 1 TCTGT 938228 TTCCTGTAAG Statistics Matches: 67, Mismatches: 6, Indels: 4 0.87 0.08 0.05 Matches are distributed among these distances: 10 9 0.13 12 58 0.87 ACGTcount: A:0.00, C:0.38, G:0.11, T:0.51 Consensus pattern (12 bp): TCTGTCTCTCTC Found at i:938576 original size:44 final size:44 Alignment explanation

Indices: 938513--938622 Score: 148 Period size: 44 Copynumber: 2.5 Consensus size: 44 938503 CATAAGATCA * 938513 TTAGGATCGTAGGACCTTGACGGAAGGATCATAGGCCAAAGACG 1 TTAGGATCATAGGACCTTGACGGAAGGATCATAGGCCAAAGACG **** * * * 938557 TTAGGATCATAGGACCTTGATTTTAGGATTATAGGCCAATGCCG 1 TTAGGATCATAGGACCTTGACGGAAGGATCATAGGCCAAAGACG 938601 TTAGGATCATAGGACCTTGACG 1 TTAGGATCATAGGACCTTGACG 938623 TTGGAAGGCT Statistics Matches: 56, Mismatches: 10, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 44 56 1.00 ACGTcount: A:0.29, C:0.17, G:0.28, T:0.25 Consensus pattern (44 bp): TTAGGATCATAGGACCTTGACGGAAGGATCATAGGCCAAAGACG Found at i:938582 original size:22 final size:22 Alignment explanation

Indices: 938513--938624 Score: 102 Period size: 22 Copynumber: 5.1 Consensus size: 22 938503 CATAAGATCA * 938513 TTAGGATCGTAGGACCTTGACG 1 TTAGGATCATAGGACCTTGACG ** ** 938535 GAAGGATCATAGG-CCAAAGACG 1 TTAGGATCATAGGACC-TTGACG ** 938557 TTAGGATCATAGGACCTTGATT 1 TTAGGATCATAGGACCTTGACG * * * 938579 TTAGGATTATAGG-CCAATGCCG 1 TTAGGATCATAGGACC-TTGACG 938601 TTAGGATCATAGGACCTTGACG 1 TTAGGATCATAGGACCTTGACG 938623 TT 1 TT 938625 GGAAGGCTAG Statistics Matches: 67, Mismatches: 19, Indels: 8 0.71 0.20 0.09 Matches are distributed among these distances: 21 4 0.06 22 59 0.88 23 4 0.06 ACGTcount: A:0.29, C:0.17, G:0.28, T:0.27 Consensus pattern (22 bp): TTAGGATCATAGGACCTTGACG Found at i:939546 original size:2 final size:2 Alignment explanation

Indices: 939539--939596 Score: 116 Period size: 2 Copynumber: 29.0 Consensus size: 2 939529 AATCAGGTAC 939539 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 939581 AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG 939597 NATAATTCAA Statistics Matches: 56, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 56 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): AG Found at i:939790 original size:251 final size:250 Alignment explanation

Indices: 939347--939826 Score: 933 Period size: 251 Copynumber: 1.9 Consensus size: 250 939337 ATTTAATGAT 939347 ATAATTCAATTAGATAAATGAAATGATTATGGCACGCCTGCTCTCTGTCTCCCACAGAACTATGC 1 ATAATTCAATTAGATAAATGAAATGATTATGGCACGCCTGCTCTCTGTCTCCCACAGAACTATGC 939412 CAAGAAACTGGTCATCGCTGACCGTGCCTCCCTATTCCTGGTGGACACCAAGAGTCGCGAGCTGT 66 CAAGAAACTGGTCATCGCTGACCGTGCCTCCCTATTCCTGGTGGACACCAAGAGTCGCGAGCTGT * 939477 ACGCGCGAATCTTTGACACTGGACGTGTGGAGGAACATATACCTCAGAAAGAAATCAGGTACAGA 131 ACGCGCGAATCTTTGACACTGGACGTGTGGAGGAACATATACCTAAGAAAGAAATCAGGTACAGA 939542 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 196 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG 939597 NATAATTCAATTAGATAAATGAAATGATTATGGCACGCCTGCTCTCTGTCTCCCACAGAACTATG 1 -ATAATTCAATTAGATAAATGAAATGATTATGGCACGCCTGCTCTCTGTCTCCCACAGAACTATG 939662 CCAAGAAACTGGTCATCGCTGACCGTGCCTCCCTATTCCTGGTGGACACCAAGAGTCGCGAGCTG 65 CCAAGAAACTGGTCATCGCTGACCGTGCCTCCCTATTCCTGGTGGACACCAAGAGTCGCGAGCTG * 939727 TACGCGCGAATCTTTGACACTGGACGTGTGTAGGAACATATACCTAAGAAAGAAATCAGGTACAG 130 TACGCGCGAATCTTTGACACTGGACGTGTGGAGGAACATATACCTAAGAAAGAAATCAGGTACAG 939792 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 195 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 939827 ATATACCTAA Statistics Matches: 227, Mismatches: 2, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 251 227 1.00 ACGTcount: A:0.34, C:0.20, G:0.28, T:0.19 Consensus pattern (250 bp): ATAATTCAATTAGATAAATGAAATGATTATGGCACGCCTGCTCTCTGTCTCCCACAGAACTATGC CAAGAAACTGGTCATCGCTGACCGTGCCTCCCTATTCCTGGTGGACACCAAGAGTCGCGAGCTGT ACGCGCGAATCTTTGACACTGGACGTGTGGAGGAACATATACCTAAGAAAGAAATCAGGTACAGA GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG Found at i:939797 original size:2 final size:2 Alignment explanation

Indices: 939790--939826 Score: 74 Period size: 2 Copynumber: 18.5 Consensus size: 2 939780 AATCAGGTAC 939790 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A 939827 ATATACCTAA Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 35 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:940654 original size:20 final size:20 Alignment explanation

Indices: 940629--940693 Score: 55 Period size: 20 Copynumber: 3.3 Consensus size: 20 940619 ACGTGCCCAT 940629 TCCTAGCGACATTCCCGACA 1 TCCTAGCGACATTCCCGACA * * * 940649 TCCTAGAGTA-AGTTCTC-A-T 1 TCCTAGCG-ACA-TTCCCGACA * 940668 TTCTAGCGACATTCCCGACA 1 TCCTAGCGACATTCCCGACA 940688 TCCTAG 1 TCCTAG 940694 AGTAAGTTTT Statistics Matches: 32, Mismatches: 8, Indels: 10 0.64 0.16 0.20 Matches are distributed among these distances: 18 5 0.16 19 8 0.25 20 14 0.44 21 5 0.16 ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28 Consensus pattern (20 bp): TCCTAGCGACATTCCCGACA Found at i:940685 original size:39 final size:39 Alignment explanation

Indices: 940626--942045 Score: 1364 Period size: 39 Copynumber: 36.9 Consensus size: 39 940616 AGAACGTGCC * * 940626 CATTCCTAGCGACATTCCCGACATCCTAGAGTAAGTTCT 1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT * 940665 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTTT 1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT * ** * * * 940704 CATTCCTAGC-ATTTTTCCCAACATCCTAGAGTTAGTTAC 1 CATTTCTAGCGA-CATTCCCGACATCCTAGAGTAAGTTAT * * * 940743 CATTTCTATCGACATTCCCGACATCTTAGAGTTAGTTAT 1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT * * * * 940782 CATTCCTACCGACATTCCCGACATCTTAGAGTAAGTTTT 1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT * * * 940821 CA-TTCTAAGCGACACTCCTGAAATCCTAGAGTAAGTTAT 1 CATTTCT-AGCGACATTCCCGACATCCTAGAGTAAGTTAT * * * * 940860 CATTTCTAGCGATATTCCTGACATCCTAGAGTTAGATAT 1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT * * ** * * 940899 CATTTTTAGCCACACCCCCGA-ATTCTTAGAGTTAGTTAT 1 CATTTCTAGCGACATTCCCGACA-TCCTAGAGTAAGTTAT * * * * 940938 CATTCCTATCGACATTCCCGACATCTTAGAGTTAGTTAT 1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT * * * * * 940977 CATTCCTATCGACATTCTCGACATCTTAGAGTTAGTTAT 1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT * * * ** 941016 CA-TTCTTAGAGAAACTCTTGACATCCTAGAGTAAGTTAT 1 CATTTC-TAGCGACATTCCCGACATCCTAGAGTAAGTTAT * * * 941055 CATTTCTGGCGACATTCCCGACATCCTAGAATAAGTTCT 1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT * * * * 941094 CATTCCAAGCGACATTCCCGATATCCTAGAGTTAGTTAT 1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT * * * * * 941133 CATTCCTATCGACATTCCCGACATCTTAGAGTAATTTCT 1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT * * 941172 CATTCCAAGCGACATTCCCGACATCCTAGAGTAAGTTAT 1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT * * * 941211 -A-AT-T-----C-TTACCGACATCCTAGAGTAAGTTCT 1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT * * * * 941241 CATTCCAAGCGACATTCCCGATATCCTAGAGTAAGTTCT 1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT * 941280 CATTCCTAG-GAACATTCCCGACATCCTAGAGTAAGTTAT 1 CATTTCTAGCG-ACATTCCCGACATCCTAGAGTAAGTTAT * 941319 CA-TTCTTAACGACATTCCCGACATCCTAGAGTAAGTTAT 1 CATTTC-TAGCGACATTCCCGACATCCTAGAGTAAGTTAT * * 941358 CA-TTCTTAACGACATTCCCGACATCCTAGAGTAAGTTTT 1 CATTTC-TAGCGACATTCCCGACATCCTAGAGTAAGTTAT * * * * * 941397 CATTCCTAGC-ATTATTCCCAACATCTTAGAGTTAGTTAT 1 CATTTCTAGCGA-CATTCCCGACATCCTAGAGTAAGTTAT * * 941436 CA--T-T--C--C--TACCGACATCCTAGAGTAAGTTCT 1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT * * * * 941466 CATTCCAAGCGACATTCCCGATATCCTAGAGTAAGTAAT 1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT * * 941505 -A-AT-T-----C-TTGCCGACATCCTAGAGTAAGTTAT 1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT * * * *** 941535 CATTCCTACCAACATTCTTAACATCCTAGAGTAAGTTAT 1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT * * 941574 CATTTCTAGCGACATTCCTGACATCCTAGAGTAAGTTCT 1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT ** * 941613 CATTTCTAGCGACATTCCTAACATCCTAGAGTAAGTTCT 1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT 941652 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT 1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT * 941691 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTCT 1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT * * * * 941730 CATTTCTAGCGATATTCCTGACATCTTAAAGTAAGTTAT 1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT * ** * 941769 CA-TTCTTAGCGACACTCCTTACATCCTAAAGTAAGTTAT 1 CATTTC-TAGCGACATTCCCGACATCCTAGAGTAAGTTAT * * * * 941808 CATTTCTAGCGATATTCTCGACATCCTAGAGTTAGATAT 1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT * * * 941847 CATTTCTAGCGATATTCCCGACATCTTAGAGTTAGTTAT 1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT * * * * 941886 CATTTCTAGCGATATTCTCGACATCCTAGAGTTAGATAT 1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT * * 941925 CATTTCTAGCGATATTCCCGACATCCTAGCCGGAGTAAATTAT 1 CATTTCTAGCGACATTCCCGACATCCTA----GAGTAAGTTAT * * * * * 941968 TATTCCCAGCGACATTCCTGACATCCTAGAGTAAGTTAC 1 CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT * * 942007 CATCTCTAGCGACAAATTCCCGACATCCTAGAGTCAGTT 1 CATTTCTAGCGAC--ATTCCCGACATCCTAGAGTAAGTT 942046 CCTTGCGACA Statistics Matches: 1152, Mismatches: 181, Indels: 94 0.81 0.13 0.07 Matches are distributed among these distances: 30 66 0.06 31 4 0.00 33 1 0.00 34 1 0.00 35 1 0.00 36 1 0.00 37 1 0.00 38 18 0.02 39 991 0.86 40 15 0.01 41 22 0.02 43 31 0.03 ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33 Consensus pattern (39 bp): CATTTCTAGCGACATTCCCGACATCCTAGAGTAAGTTAT Found at i:941254 original size:30 final size:30 Alignment explanation

Indices: 941189--941255 Score: 89 Period size: 30 Copynumber: 2.2 Consensus size: 30 941179 AGCGACATTC ** 941189 CCGACATCCTAGAGTAAGTTATAATTCTTA 1 CCGACATCCTAGAGTAAGTTATAATTCCAA * * 941219 CCGACATCCTAGAGTAAGTTCTCATTCCAA 1 CCGACATCCTAGAGTAAGTTATAATTCCAA * 941249 GCGACAT 1 CCGACAT 941256 TCCCGATATC Statistics Matches: 32, Mismatches: 5, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 30 32 1.00 ACGTcount: A:0.31, C:0.25, G:0.15, T:0.28 Consensus pattern (30 bp): CCGACATCCTAGAGTAAGTTATAATTCCAA Found at i:941288 original size:19 final size:19 Alignment explanation

Indices: 941225--941288 Score: 60 Period size: 19 Copynumber: 3.3 Consensus size: 19 941215 CTTACCGACA 941225 TCCTAGAGTAAGTTCTCAT 1 TCCTAGAGTAAGTTCTCAT * * * 941244 TCCAAGCG-ACA-TTCCCGAT 1 TCCTAGAGTA-AGTTCTC-AT 941263 ATCCTAGAGTAAGTTCTCAT 1 -TCCTAGAGTAAGTTCTCAT 941283 TCCTAG 1 TCCTAG 941289 GAACATTCCC Statistics Matches: 34, Mismatches: 6, Indels: 10 0.68 0.12 0.20 Matches are distributed among these distances: 18 5 0.15 19 15 0.44 20 9 0.26 21 5 0.15 ACGTcount: A:0.27, C:0.27, G:0.16, T:0.31 Consensus pattern (19 bp): TCCTAGAGTAAGTTCTCAT Found at i:941451 original size:30 final size:30 Alignment explanation

Indices: 941417--941480 Score: 83 Period size: 30 Copynumber: 2.1 Consensus size: 30 941407 ATTATTCCCA * * * 941417 ACATCTTAGAGTTAGTTATCATTCCTACCG 1 ACATCCTAGAGTAAGTTATCATTCCAACCG * * 941447 ACATCCTAGAGTAAGTTCTCATTCCAAGCG 1 ACATCCTAGAGTAAGTTATCATTCCAACCG 941477 ACAT 1 ACAT 941481 TCCCGATATC Statistics Matches: 29, Mismatches: 5, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 30 29 1.00 ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31 Consensus pattern (30 bp): ACATCCTAGAGTAAGTTATCATTCCAACCG Found at i:950701 original size:10 final size:10 Alignment explanation

Indices: 950686--950723 Score: 67 Period size: 10 Copynumber: 3.8 Consensus size: 10 950676 TTCCGCTTGA 950686 ATTTGGGTCC 1 ATTTGGGTCC * 950696 ATTTGGGTTC 1 ATTTGGGTCC 950706 ATTTGGGTCC 1 ATTTGGGTCC 950716 ATTTGGGT 1 ATTTGGGT 950724 AAATCGACGC Statistics Matches: 26, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 10 26 1.00 ACGTcount: A:0.11, C:0.13, G:0.32, T:0.45 Consensus pattern (10 bp): ATTTGGGTCC Found at i:950711 original size:20 final size:20 Alignment explanation

Indices: 950686--950723 Score: 76 Period size: 20 Copynumber: 1.9 Consensus size: 20 950676 TTCCGCTTGA 950686 ATTTGGGTCCATTTGGGTTC 1 ATTTGGGTCCATTTGGGTTC 950706 ATTTGGGTCCATTTGGGT 1 ATTTGGGTCCATTTGGGT 950724 AAATCGACGC Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 20 18 1.00 ACGTcount: A:0.11, C:0.13, G:0.32, T:0.45 Consensus pattern (20 bp): ATTTGGGTCCATTTGGGTTC Found at i:952138 original size:10 final size:10 Alignment explanation

Indices: 952123--952160 Score: 67 Period size: 10 Copynumber: 3.8 Consensus size: 10 952113 TTCCGCTTGA 952123 ATTTGGGTCC 1 ATTTGGGTCC * 952133 ATTTGGGTTC 1 ATTTGGGTCC 952143 ATTTGGGTCC 1 ATTTGGGTCC 952153 ATTTGGGT 1 ATTTGGGT 952161 AAATCGACGC Statistics Matches: 26, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 10 26 1.00 ACGTcount: A:0.11, C:0.13, G:0.32, T:0.45 Consensus pattern (10 bp): ATTTGGGTCC Found at i:952148 original size:20 final size:20 Alignment explanation

Indices: 952123--952160 Score: 76 Period size: 20 Copynumber: 1.9 Consensus size: 20 952113 TTCCGCTTGA 952123 ATTTGGGTCCATTTGGGTTC 1 ATTTGGGTCCATTTGGGTTC 952143 ATTTGGGTCCATTTGGGT 1 ATTTGGGTCCATTTGGGT 952161 AAATCGACGC Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 20 18 1.00 ACGTcount: A:0.11, C:0.13, G:0.32, T:0.45 Consensus pattern (20 bp): ATTTGGGTCCATTTGGGTTC Found at i:964360 original size:33 final size:33 Alignment explanation

Indices: 964311--965071 Score: 370 Period size: 33 Copynumber: 21.6 Consensus size: 33 964301 GAGTCAATTA * * 964311 ACATAGTGGTAAGTGTTGTGGAGTCTTTGGTTG 1 ACATAGCGGTAAGTGTTGTTGAGTCTTTGGTTG * * * * 964344 ACAAAGCGGTAGGTGTTGTTAAGT-TCTCGGTTG 1 ACATAGCGGTAAGTGTTGTTGAGTCT-TTGGTTG * * ** * 964377 ACATAACGGTAAGTGATGAAGAGTCTTCGGTTG 1 ACATAGCGGTAAGTGTTGTTGAGTCTTTGGTTG ** * 964410 ACATAGTAGTAGGTGTTGTTGAGTTCTCGGTTGCGGTTG 1 ACATAGCGGTAAGTGTTGTTGAG-TCT---TT--GGTTG * 964449 A-AGTAGAGGTACGAGTAAGTGTCGTTGAGTCTTTGGTTG 1 ACA-T--A-G--CG-GTAAGTGTTGTTGAGTCTTTGGTTG * ** * 964488 ACATGGAAGTAAGTGTTGTGGAGTCTTTGGTTG 1 ACATAGCGGTAAGTGTTGTTGAGTCTTTGGTTG * 964521 ACATAGCGGTAGGTGTTGTTGAGT-TCTTGGTTG 1 ACATAGCGGTAAGTGTTGTTGAGTCT-TTGGTTG *** * * 964554 ACATAGAAATAAGTGTTGTAGAGTCTTCGGTTG 1 ACATAGCGGTAAGTGTTGTTGAGTCTTTGGTTG * ** * * 964587 ATATAGTAGTAGGTGTTGTTGAGT-TCTCGGTTG 1 ACATAGCGGTAAGTGTTGTTGAGTCT-TTGGTTG * * 964620 ACATAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTG 1 ACAT--A-G--CG-GTAAGTGTTGTTGAGTCTTTGGTTG ** * 964659 ACATAGAAGTAAGTGTTGTGGAGTCTTTGGTTG 1 ACATAGCGGTAAGTGTTGTTGAGTCTTTGGTTG * 964692 ACATAGCGGT-AGCTGTTGTTGAGT-TCTCGGTTG 1 ACATAGCGGTAAG-TGTTGTTGAGTCT-TTGGTTG * ** 964725 ACATAGAGATACGAGTAAGTGTCGTTGAGTCTCCGGTTG 1 ACAT--AG---CG-GTAAGTGTTGTTGAGTCTTTGGTTG * ** * 964764 ATATAGTAGTAGGTGTTGTTGAGTTCTCGGTTGCGGTTG 1 ACATAGCGGTAAGTGTTGTTGAG-TCT---TT--GGTTG * * 964803 A-AGTAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTG 1 ACA-T--A-G--CG-GTAAGTGTTGTTGAGTCTTTGGTTG ** * 964842 ACATAGAAGTAAGTGTTGTGGAGTCTTTGGTTG 1 ACATAGCGGTAAGTGTTGTTGAGTCTTTGGTTG * * * 964875 ACATAGCGGTAGGTGTTGTTAAGT-TCTCGGTTG 1 ACATAGCGGTAAGTGTTGTTGAGTCT-TTGGTTG * * 964908 ACATAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTG 1 ACAT--A-G--CG-GTAAGTGTTGTTGAGTCTTTGGTTG * ** * * 964947 ATATAGTAGTAGGTGTTGTTGAGT-TCTCGGTTG 1 ACATAGCGGTAAGTGTTGTTGAGTCT-TTGGTTG * * 964980 ACATAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTG 1 ACAT--A-G--CG-GTAAGTGTTGTTGAGTCTTTGGTTG ** * 965019 ACATAGAAGTAAGTGTTGTGGAGTCTTTGGTTG 1 ACATAGCGGTAAGTGTTGTTGAGTCTTTGGTTG * 965052 ACATAGCGGTAGGTGTTGTT 1 ACATAGCGGTAAGTGTTGTT 965072 NNNNNNNNNN Statistics Matches: 555, Mismatches: 107, Indels: 132 0.70 0.13 0.17 Matches are distributed among these distances: 32 8 0.01 33 344 0.62 34 8 0.01 35 5 0.01 36 8 0.01 37 7 0.01 38 6 0.01 39 122 0.22 40 8 0.01 41 5 0.01 42 2 0.00 44 6 0.01 45 26 0.05 ACGTcount: A:0.21, C:0.10, G:0.34, T:0.35 Consensus pattern (33 bp): ACATAGCGGTAAGTGTTGTTGAGTCTTTGGTTG Found at i:964615 original size:177 final size:174 Alignment explanation

Indices: 964319--965071 Score: 1128 Period size: 177 Copynumber: 4.3 Consensus size: 174 964309 TAACATAGTG * 964319 GTAAGTGTTGTGGAGTCTTTGGTTGACAAAGCGGTAGGTGTTGTTAAGTTCTCGGTTGACAT--A 1 GTAAGTGTTGTGGAGTCTTTGGTTGACATAGCGGTAGGTGTTGTTAAGTTCTCGGTTGACATAGA * * * 964382 -ACGGTAAGTGAT-GAAGAGTCTTCGGTTGACATAGTAGTAGGTGTTGTTGAGTTCTCGGTTG-C 66 GACAGTAAGTG-TCGTAGAGTCTTCGGTTGATATAGTAGTAGGTGTTGTTGAGTTCTCGGTTGAC * * 964444 GGTTGAAGTAGAGGTACGAGTAAGTGTCGTTGAGTCTTTGGTTGACATGGAA 130 ------A-TAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGAA * * 964496 GTAAGTGTTGTGGAGTCTTTGGTTGACATAGCGGTAGGTGTTGTTGAGTTCTTGGTTGACATAGA 1 GTAAGTGTTGTGGAGTCTTTGGTTGACATAGCGGTAGGTGTTGTTAAGTTCTCGGTTGACATAGA * 964561 -A-A-TAAGTGTTGTAGAGTCTTCGGTTGATATAGTAGTAGGTGTTGTTGAGTTCTCGGTTGACA 66 GACAGTAAGTGTCGTAGAGTCTTCGGTTGATATAGTAGTAGGTGTTGTTGAGTTCTCGGTTGACA 964623 TAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGAA 131 TAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGAA * * 964667 GTAAGTGTTGTGGAGTCTTTGGTTGACATAGCGGTAGCTGTTGTTGAGTTCTCGGTTGACATAGA 1 GTAAGTGTTGTGGAGTCTTTGGTTGACATAGCGGTAGGTGTTGTTAAGTTCTCGGTTGACATAGA * * 964732 GATACGAGTAAGTGTCGTTGAGTCTCCGGTTGATATAGTAGTAGGTGTTGTTGAGTTCTCGGTTG 66 G--AC-AGTAAGTGTCGTAGAGTCTTCGGTTGATATAGTAGTAGGTGTTGTTGAGTTCTCGGTTG 964797 -CGGTTGAAGTAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGAA 128 AC------A-TAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGAA 964850 GTAAGTGTTGTGGAGTCTTTGGTTGACATAGCGGTAGGTGTTGTTAAGTTCTCGGTTGACATAGA 1 GTAAGTGTTGTGGAGTCTTTGGTTGACATAGCGGTAGGTGTTGTTAAGTTCTCGGTTGACATAGA * 964915 GGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGATATAGTAGTAGGTGTTGTTGAGTTCTCGGTTG 66 -G-AC-AGTAAGTGTCGTAGAGTCTTCGGTTGATATAGTAGTAGGTGTTGTTGAGTTCTCGGTTG 964980 ACATAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGAA 128 ACATAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGAA 965027 GTAAGTGTTGTGGAGTCTTTGGTTGACATAGCGGTAGGTGTTGTT 1 GTAAGTGTTGTGGAGTCTTTGGTTGACATAGCGGTAGGTGTTGTT 965072 NNNNNNNNNN Statistics Matches: 541, Mismatches: 16, Indels: 38 0.91 0.03 0.06 Matches are distributed among these distances: 171 105 0.19 172 1 0.00 174 1 0.00 176 3 0.01 177 255 0.47 178 2 0.00 179 2 0.00 182 1 0.00 183 169 0.31 184 2 0.00 ACGTcount: A:0.21, C:0.10, G:0.34, T:0.35 Consensus pattern (174 bp): GTAAGTGTTGTGGAGTCTTTGGTTGACATAGCGGTAGGTGTTGTTAAGTTCTCGGTTGACATAGA GACAGTAAGTGTCGTAGAGTCTTCGGTTGATATAGTAGTAGGTGTTGTTGAGTTCTCGGTTGACA TAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGAA Found at i:964683 original size:105 final size:105 Alignment explanation

Indices: 964462--965062 Score: 392 Period size: 105 Copynumber: 5.7 Consensus size: 105 964452 TAGAGGTACG * * * * * * 964462 AGTAAGTGTCGTTGAGTCTTTGGTTGACATGGAAGTAAGTGTTGTGGAG-TCTTTGGTTGACATA 1 AGTAAGTGTTGTTGAGTCTTCGGTTGACATAGAAGTAGGTGTTGTTGAGTTC-TCGGTTGACATA * 964526 GCGGTA-G-GT--GT-T-GTTGAGTTCTT-GGTTGACATAGA 65 GAGGTACGAGTAAGTGTCGTTGAG-TCTTCGGTTGACATAGA * * * * 964561 AATAAGTGTTGTAGAGTCTTCGGTTGATATAGTAGTAGGTGTTGTTGAGTTCTCGGTTGACATAG 1 AGTAAGTGTTGTTGAGTCTTCGGTTGACATAGAAGTAGGTGTTGTTGAGTTCTCGGTTGACATAG 964626 AGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGA 66 AGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGA * * ** * 964666 AGTAAGTGTTGTGGAGTCTTTGGTTGACATAGCGGTAGCTGTTGTTGAGTTCTCGGTTGACATAG 1 AGTAAGTGTTGTTGAGTCTTCGGTTGACATAGAAGTAGGTGTTGTTGAGTTCTCGGTTGACATAG * * * * 964731 AGATACGAGTAAGTGTCGTTGAGTCTCCGGTTGATATAGT 66 AGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGA * * 964771 AGTAGGTGTTGTTGAGTTCTCGGTTGCGGTTGA-AGTAGAGGTACGAGTAAGTGTCGTTGAG-TC 1 AGTAAGTGTTGTTGAG---TC--TT-CGGTTGACA-TAGAAGTA-G-GT--GT-T-GTTGAGTTC * * * * 964834 TTCGGTTGACAT--A-G-A--AGTAAGTGTTGTGGAGTCTTTGGTTGACATAGC 53 -TCGGTTGACATAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGA * * * * 964882 GGTAGGTGTTGTTAAGT-TCTCGGTTGACATAGAGGTACGAGTAAGTGTCGTTGAG-TCTTCGGT 1 AGTAAGTGTTGTTGAGTCT-TCGGTTGACATAGAAGTA-G-GT--GT-T-GTTGAGTTC-TCGGT * 964945 TGATATAGTA-GTA-G-GT--GT-T-GTTGAGT-TCTCGGTTGACATAGAGGTA 58 TGACATAG-AGGTACGAGTAAGTGTCGTTGAGTCT-TCGGTTGACAT--A-G-A * * * * 964991 CGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGAAGTAAGTGTTGTGGAG-TCTTTGGTTGACA 1 --AGTAAGTGTTGTTGAGTCTTCGGTTGACATAGAAGTAGGTGTTGTTGAGTTC-TCGGTTGACA * 965055 TAGCGGTA 63 TAGAGGTA 965063 GGTGTTGTTN Statistics Matches: 414, Mismatches: 50, Indels: 70 0.78 0.09 0.13 Matches are distributed among these distances: 99 56 0.14 100 3 0.01 101 2 0.00 103 2 0.00 104 6 0.01 105 211 0.51 106 4 0.01 107 5 0.01 108 6 0.01 109 5 0.01 110 3 0.01 111 84 0.20 112 2 0.00 113 2 0.00 115 3 0.01 116 3 0.01 117 17 0.04 ACGTcount: A:0.21, C:0.10, G:0.33, T:0.35 Consensus pattern (105 bp): AGTAAGTGTTGTTGAGTCTTCGGTTGACATAGAAGTAGGTGTTGTTGAGTTCTCGGTTGACATAG AGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGA Found at i:964691 original size:72 final size:71 Alignment explanation

Indices: 964462--965063 Score: 422 Period size: 72 Copynumber: 8.5 Consensus size: 71 964452 TAGAGGTACG * * * * * 964462 AGTAAGTGTCGTTGAGTCTTTGGTTGACAT---GG-A-AGTAAGTGTTGTGGAGTCTTTGGTTGA 1 AGTAAGTGTTGTTGAGTCTTCGGTTGACATAGAGGTAGAGTAAGTGTCGTTGAGTCTTCGGTTGA * 964522 CATAGC 66 CATAGA * * * * 964528 GGTAGGTGTTGTTGAGTTCTT-GGTTGACATAGA---A-A-TAAGTGTTGTAGAGTCTTCGGTTG 1 AGTAAGTGTTGTTGAG-TCTTCGGTTGACATAGAGGTAGAGTAAGTGTCGTTGAGTCTTCGGTTG * * 964587 ATATAGT 65 ACATAGA * 964594 AGTAGGTGTTGTTGAGT-TCTCGGTTGACATAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTT 1 AGTAAGTGTTGTTGAGTCT-TCGGTTGACATAGAGGTA-GAGTAAGTGTCGTTGAGTCTTCGGTT 964658 GACATAGA 64 GACATAGA * * * * 964666 AGTAAGTGTTGTGGAGTCTTTGGTTGACATAGCGGTAG-CT--GT-T-GTTGAGT-TCTCGGTTG 1 AGTAAGTGTTGTTGAGTCTTCGGTTGACATAGAGGTAGAGTAAGTGTCGTTGAGTCT-TCGGTTG 964725 ACATAGAGATA 65 ACAT--AG--A * * * 964736 CGAGTAAGTGTCGTTGAGTCTCCGGTTGATATAGTA-GTAG-GT--GT-T-GTTGAGTTCTCGGT 1 --AGTAAGTGTTGTTGAGTCTTCGGTTGACATAG-AGGTAGAGTAAGTGTCGTTGAG---TC--T 964795 TGCGGTTGA-AGTAGAGGTA 58 T-CGGTTGACA-T--A-G-A * * * * 964814 CGAGTAAGTGTCGTTGAGTCTTCGGTTGACAT--A-G-A-AGTAAGTGTTGTGGAGTCTTTGGTT 1 --AGTAAGTGTTGTTGAGTCTTCGGTTGACATAGAGGTAGAGTAAGTGTCGTTGAGTCTTCGGTT * 964874 GACATAGC 64 GACATAGA * * * 964882 GGTAGGTGTTGTTAAGT-TCTCGGTTGACATAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTT 1 AGTAAGTGTTGTTGAGTCT-TCGGTTGACATAGAGGTA-GAGTAAGTGTCGTTGAGTCTTCGGTT * * 964946 GATATAGT 64 GACATAGA * 964954 AGTAGGTGTTGTTGAGT-TCTCGGTTGACATAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTT 1 AGTAAGTGTTGTTGAGTCT-TCGGTTGACATAGAGGTA-GAGTAAGTGTCGTTGAGTCTTCGGTT 965018 GACATAGA 64 GACATAGA * * * 965026 AGTAAGTGTTGTGGAGTCTTTGGTTGACATAGCGGTAG 1 AGTAAGTGTTGTTGAGTCTTCGGTTGACATAGAGGTAG 965064 GTGTTGTTNN Statistics Matches: 446, Mismatches: 46, Indels: 83 0.78 0.08 0.14 Matches are distributed among these distances: 64 1 0.00 65 4 0.01 66 118 0.26 67 7 0.02 68 5 0.01 69 3 0.01 70 4 0.01 71 3 0.01 72 233 0.52 73 5 0.01 74 3 0.01 75 5 0.01 76 2 0.00 77 3 0.01 78 49 0.11 79 1 0.00 ACGTcount: A:0.21, C:0.10, G:0.34, T:0.35 Consensus pattern (71 bp): AGTAAGTGTTGTTGAGTCTTCGGTTGACATAGAGGTAGAGTAAGTGTCGTTGAGTCTTCGGTTGA CATAGA Found at i:964874 original size:78 final size:78 Alignment explanation

Indices: 964719--964865 Score: 224 Period size: 78 Copynumber: 1.9 Consensus size: 78 964709 GTTGAGTTCT * * * * 964719 CGGTTGACATAGAGATACGAGTAAGTGTCGTTGAGTCTCCGGTTGATATAGTAGTAGGTGTTGTT 1 CGGTTGACATAGAGATACGAGTAAGTGTCGTTGAGTCTCCGGTTGACATAGAAGTAAGTGTTGTG 964784 GAGTTCTCGGTTG 66 GAGTTCTCGGTTG * * 964797 CGGTTGA-AGTAGAGGTACGAGTAAGTGTCGTTGAGTCTTCGGTTGACATAGAAGTAAGTGTTGT 1 CGGTTGACA-TAGAGATACGAGTAAGTGTCGTTGAGTCTCCGGTTGACATAGAAGTAAGTGTTGT 964861 GGAGT 65 GGAGT 964866 CTTTGGTTGA Statistics Matches: 62, Mismatches: 6, Indels: 2 0.89 0.09 0.03 Matches are distributed among these distances: 77 1 0.02 78 61 0.98 ACGTcount: A:0.22, C:0.10, G:0.35, T:0.33 Consensus pattern (78 bp): CGGTTGACATAGAGATACGAGTAAGTGTCGTTGAGTCTCCGGTTGACATAGAAGTAAGTGTTGTG GAGTTCTCGGTTG Found at i:973662 original size:112 final size:112 Alignment explanation

Indices: 973465--973745 Score: 544 Period size: 112 Copynumber: 2.5 Consensus size: 112 973455 NNNNNNNNNN * 973465 GAACTAACACAGAATATACAAGATATACACAACAGTTGTGTCGTGTGCCCAGGTGCATGTTTGTG 1 GAACTAACACAGAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCATGTTTGTG 973530 TATATCTAGTTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTG 66 TATATCTAGTTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTG * 973577 GAACTAACACAGAATATACAAGATAAACACAACAGGTGTGTCGTGTGCCCAGGTGCATGTTTGTG 1 GAACTAACACAGAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCATGTTTGTG 973642 TATATCTAGTTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTG 66 TATATCTAGTTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTG 973689 GAACTAACACAGAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA 1 GAACTAACACAGAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA 973746 CGTCAGGGTT Statistics Matches: 166, Mismatches: 3, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 112 166 1.00 ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27 Consensus pattern (112 bp): GAACTAACACAGAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCATGTTTGTG TATATCTAGTTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTG Found at i:974625 original size:11 final size:11 Alignment explanation

Indices: 974609--974662 Score: 99 Period size: 11 Copynumber: 4.9 Consensus size: 11 974599 ATTTTTTTAA 974609 TGGCTTAAAGG 1 TGGCTTAAAGG 974620 TGGCTTAAAGG 1 TGGCTTAAAGG * 974631 TAGCTTAAAGG 1 TGGCTTAAAGG 974642 TGGCTTAAAGG 1 TGGCTTAAAGG 974653 TGGCTTAAAG 1 TGGCTTAAAG 974663 AAGTTTAGAC Statistics Matches: 41, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 11 41 1.00 ACGTcount: A:0.30, C:0.09, G:0.33, T:0.28 Consensus pattern (11 bp): TGGCTTAAAGG Found at i:974710 original size:11 final size:11 Alignment explanation

Indices: 974694--974722 Score: 58 Period size: 11 Copynumber: 2.6 Consensus size: 11 974684 ATAAGTTGTC 974694 CTTAAAGGTGG 1 CTTAAAGGTGG 974705 CTTAAAGGTGG 1 CTTAAAGGTGG 974716 CTTAAAG 1 CTTAAAG 974723 ATAGTCTTTA Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 18 1.00 ACGTcount: A:0.31, C:0.10, G:0.31, T:0.28 Consensus pattern (11 bp): CTTAAAGGTGG Found at i:974804 original size:11 final size:11 Alignment explanation

Indices: 974788--974819 Score: 55 Period size: 11 Copynumber: 2.9 Consensus size: 11 974778 GCAATACATA 974788 TAGCTTAAAGG 1 TAGCTTAAAGG 974799 TAGCTTAAAGG 1 TAGCTTAAAGG * 974810 TGGCTTAAAG 1 TAGCTTAAAG 974820 ATCGTCTTTA Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 11 20 1.00 ACGTcount: A:0.34, C:0.09, G:0.28, T:0.28 Consensus pattern (11 bp): TAGCTTAAAGG Found at i:974841 original size:11 final size:11 Alignment explanation

Indices: 974825--974863 Score: 53 Period size: 11 Copynumber: 3.6 Consensus size: 11 974815 TAAAGATCGT 974825 CTTTAAGCTAC 1 CTTTAAGCTAC * 974836 CTTTAAAC-AC 1 CTTTAAGCTAC * 974846 CTTTAAGCTAT 1 CTTTAAGCTAC 974857 CTTTAAG 1 CTTTAAG 974864 GAGAAGTTAA Statistics Matches: 24, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 10 9 0.38 11 15 0.62 ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38 Consensus pattern (11 bp): CTTTAAGCTAC Found at i:978566 original size:2 final size:2 Alignment explanation

Indices: 978561--978590 Score: 51 Period size: 2 Copynumber: 15.0 Consensus size: 2 978551 TATATATATT * 978561 TG TG TG TG TG TG TG TG TG TT TG TG TG TG TG 1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG 978591 GAGATAAATA Statistics Matches: 26, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 2 26 1.00 ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53 Consensus pattern (2 bp): TG Found at i:981210 original size:9 final size:9 Alignment explanation

Indices: 981192--981223 Score: 55 Period size: 9 Copynumber: 3.6 Consensus size: 9 981182 AAAATTGCGG * 981192 GGTGATTTT 1 GGTGAGTTT 981201 GGTGAGTTT 1 GGTGAGTTT 981210 GGTGAGTTT 1 GGTGAGTTT 981219 GGTGA 1 GGTGA 981224 AGTAGGTCCA Statistics Matches: 22, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 9 22 1.00 ACGTcount: A:0.12, C:0.00, G:0.44, T:0.44 Consensus pattern (9 bp): GGTGAGTTT Found at i:983428 original size:98 final size:98 Alignment explanation

Indices: 983255--983438 Score: 271 Period size: 98 Copynumber: 1.9 Consensus size: 98 983245 TCATGATCAA * * * * 983255 AGGCTAATTGCTGCTGCTTATACAAACAGCATTATTGAGCACAATTAAAGTTGATCTGACAGAAG 1 AGGCTAATTGCTGCTGCTTATACAAACAGCATTATTGAACACAATAAAAGATGATCTGACAAAAG * 983320 GCACGCTTCTGCCAAAAGTATATGTGTACTGTT 66 GCAAGCTTCTGCCAAAAGTATATGTGTACTGTT ** * 983353 AGGCTAATTGCTGCTGCTTATACAAACAGTGTTATTGAACATAATAAAAGATGATCTGA-AAAAG 1 AGGCTAATTGCTGCTGCTTATACAAACAGCATTATTGAACACAATAAAAGATGATCTGACAAAA- * 983417 GGCAAGGTTCTGCCAAAAGTAT 65 GGCAAGCTTCTGCCAAAAGTAT 983439 TTGAATACTT Statistics Matches: 76, Mismatches: 9, Indels: 2 0.87 0.10 0.02 Matches are distributed among these distances: 97 3 0.04 98 73 0.96 ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28 Consensus pattern (98 bp): AGGCTAATTGCTGCTGCTTATACAAACAGCATTATTGAACACAATAAAAGATGATCTGACAAAAG GCAAGCTTCTGCCAAAAGTATATGTGTACTGTT Found at i:983616 original size:22 final size:24 Alignment explanation

Indices: 983586--983631 Score: 69 Period size: 22 Copynumber: 2.0 Consensus size: 24 983576 AATATTTGCC 983586 CTTACATACTAGT-A-TACAATAT 1 CTTACATACTAGTAATTACAATAT * 983608 CTTATATACTAGTAATTACAATAT 1 CTTACATACTAGTAATTACAATAT 983632 AATTTATAAG Statistics Matches: 21, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 22 12 0.57 23 1 0.05 24 8 0.38 ACGTcount: A:0.41, C:0.15, G:0.04, T:0.39 Consensus pattern (24 bp): CTTACATACTAGTAATTACAATAT Found at i:996939 original size:12 final size:12 Alignment explanation

Indices: 996922--996946 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 996912 ACAAATTATA 996922 TATAATAATAAT 1 TATAATAATAAT 996934 TATAATAATAAT 1 TATAATAATAAT 996946 T 1 T 996947 GCAAGTTTTT Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 13 1.00 ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44 Consensus pattern (12 bp): TATAATAATAAT Found at i:998726 original size:18 final size:18 Alignment explanation

Indices: 998703--998738 Score: 63 Period size: 18 Copynumber: 2.0 Consensus size: 18 998693 CAGACTTGTC * 998703 TTTGAGTTTTTTCTCAAA 1 TTTGAGATTTTTCTCAAA 998721 TTTGAGATTTTTCTCAAA 1 TTTGAGATTTTTCTCAAA 998739 CGTGCGTGCC Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 17 1.00 ACGTcount: A:0.25, C:0.11, G:0.11, T:0.53 Consensus pattern (18 bp): TTTGAGATTTTTCTCAAA Found at i:999831 original size:21 final size:21 Alignment explanation

Indices: 999745--1000016 Score: 203 Period size: 21 Copynumber: 13.0 Consensus size: 21 999735 AATTATGATC * 999745 TTTTCCATTTGTATTATATAAA 1 TTTTCCATTTGTATTGTAT-AA * ** 999767 TATTT--ATTTGTAATGTACCA 1 T-TTTCCATTTGTATTGTATAA * * * 999787 TTTTCTATTTGTAATGTATCA 1 TTTTCCATTTGTATTGTATAA * * 999808 TTTTCTATTTGTATTCTATAA 1 TTTTCCATTTGTATTGTATAA * 999829 TTTTCCATTTGCATTGTATAA 1 TTTTCCATTTGTATTGTATAA * 999850 ATTTCCATTTGTATTGTATAA 1 TTTTCCATTTGTATTGTATAA * * 999871 TTTTCTATTTGTTTTGTATAA 1 TTTTCCATTTGTATTGTATAA * * 999892 TTTTCCATTTGTATTCTTTAA 1 TTTTCCATTTGTATTGTATAA * 999913 TTGTCCATTTGTATTG-AGTAA 1 TTTTCCATTTGTATTGTA-TAA * * * ** 999934 TATTCTATTTGCATTGTACGA 1 TTTTCCATTTGTATTGTATAA * ** * 999955 GTTT-CATAAGTATTCTATAAA 1 TTTTCCATTTGTATTGTAT-AA * * * * 999976 TTTT-TATTTATATTCTCTAA 1 TTTTCCATTTGTATTGTATAA * 999996 TTTTCCATTTGTATTCTATAA 1 TTTTCCATTTGTATTGTATAA 1000017 GAAGATGGGT Statistics Matches: 196, Mismatches: 47, Indels: 15 0.76 0.18 0.06 Matches are distributed among these distances: 19 3 0.02 20 16 0.08 21 172 0.88 22 2 0.01 23 3 0.02 ACGTcount: A:0.26, C:0.11, G:0.08, T:0.55 Consensus pattern (21 bp): TTTTCCATTTGTATTGTATAA Found at i:1000815 original size:21 final size:21 Alignment explanation

Indices: 1000791--1001049 Score: 194 Period size: 21 Copynumber: 12.4 Consensus size: 21 1000781 TATAGAACAA * 1000791 AAATTGAAAATTATACAATAC 1 AAATGGAAAATTATACAATAC * 1000812 AAATGGAAAATGATACAATAC 1 AAATGGAAAATTATACAATAC * * ** 1000833 AAATAGCAAATGGTACAATAC 1 AAATGGAAAATTATACAATAC 1000854 AAAT--AAATATT-TACAAAATAC 1 AAATGGAAA-ATTATAC--AATAC * 1000875 AAATGGAAAATTATAGAATAC 1 AAATGGAAAATTATACAATAC * 1000896 AAATGGAAAATTATAGAATAC 1 AAATGGAAAATTATACAATAC * * * * * 1000917 AATTTGACATTTATATAATAC 1 AAATGGAAAATTATACAATAC * 1000938 AAGTGGAAAATTATACAATAC 1 AAATGGAAAATTATACAATAC * * * 1000959 AAA-AG-AAATTCATATAATGC 1 AAATGGAAAATT-ATACAATAC * 1000979 AAATGGAAAATTATAGAATAC 1 AAATGGAAAATTATACAATAC * * * 1001000 AAAT-AAAAAGTTAAACAATGC 1 AAATGGAAAA-TTATACAATAC 1001021 -AAT--AAATATTTATACAATAC 1 AAATGGAAA-A-TTATACAATAC * 1001041 CAATGGAAA 1 AAATGGAAA 1001050 TGATTGAGTA Statistics Matches: 192, Mismatches: 32, Indels: 26 0.77 0.13 0.10 Matches are distributed among these distances: 19 13 0.07 20 30 0.16 21 133 0.69 22 8 0.04 23 8 0.04 ACGTcount: A:0.56, C:0.09, G:0.10, T:0.25 Consensus pattern (21 bp): AAATGGAAAATTATACAATAC Found at i:1010397 original size:12 final size:13 Alignment explanation

Indices: 1010371--1010401 Score: 55 Period size: 12 Copynumber: 2.5 Consensus size: 13 1010361 CAGAAATTTA 1010371 AGATTTGAGGCTG 1 AGATTTGAGGCTG 1010384 AGATTTGA-GCTG 1 AGATTTGAGGCTG 1010396 AGATTT 1 AGATTT 1010402 TTATATGTTG Statistics Matches: 18, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 12 10 0.56 13 8 0.44 ACGTcount: A:0.26, C:0.06, G:0.32, T:0.35 Consensus pattern (13 bp): AGATTTGAGGCTG Found at i:1012670 original size:25 final size:25 Alignment explanation

Indices: 1012640--1012720 Score: 135 Period size: 25 Copynumber: 3.2 Consensus size: 25 1012630 AGTCTCACAG * 1012640 GCATCTTATAATATTCATTCCATAT 1 GCATCTTATCATATTCATTCCATAT * * 1012665 ACATCTTATCATATTCATACCATAT 1 GCATCTTATCATATTCATTCCATAT 1012690 GCATCTTATCATATTCATTCCATAT 1 GCATCTTATCATATTCATTCCATAT 1012715 GCATCT 1 GCATCT 1012721 CATTATGTCG Statistics Matches: 51, Mismatches: 5, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 25 51 1.00 ACGTcount: A:0.31, C:0.23, G:0.04, T:0.42 Consensus pattern (25 bp): GCATCTTATCATATTCATTCCATAT Found at i:1020696 original size:2 final size:2 Alignment explanation

Indices: 1020689--1020760 Score: 117 Period size: 2 Copynumber: 36.0 Consensus size: 2 1020679 AATTGAAATT * * * 1020689 TC TC TC TC TC TC TA TC TC TC TC TC TC TC TC TC CC TC GC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1020731 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 1020761 ATACCAACAT Statistics Matches: 64, Mismatches: 6, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 2 64 1.00 ACGTcount: A:0.01, C:0.50, G:0.01, T:0.47 Consensus pattern (2 bp): TC Found at i:1027197 original size:2 final size:2 Alignment explanation

Indices: 1027190--1027240 Score: 102 Period size: 2 Copynumber: 25.5 Consensus size: 2 1027180 CTTTATCATT 1027190 GA 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 GA 1027232 GA GA GA GA G 1 GA GA GA GA G 1027241 TGTGTGTGTG Statistics Matches: 49, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 49 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:1028018 original size:2 final size:2 Alignment explanation

Indices: 1028011--1028071 Score: 113 Period size: 2 Copynumber: 30.5 Consensus size: 2 1028001 AATTTTTGAT * 1028011 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG CG 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 1028053 AG AG AG AG AG AG AG AG AG A 1 AG AG AG AG AG AG AG AG AG A 1028072 ATGTTTCTGT Statistics Matches: 57, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 2 57 1.00 ACGTcount: A:0.49, C:0.02, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:1028638 original size:40 final size:40 Alignment explanation

Indices: 1028528--1028627 Score: 191 Period size: 40 Copynumber: 2.5 Consensus size: 40 1028518 TATTTCTATA 1028528 TTTAGAAAGTACAGGTCAATCTGAGTTTTTAAAGCTTATT 1 TTTAGAAAGTACAGGTCAATCTGAGTTTTTAAAGCTTATT 1028568 TTTAGAAAGTACAGGTCAATCTGAGTTTTTAAAGCTTATT 1 TTTAGAAAGTACAGGTCAATCTGAGTTTTTAAAGCTTATT * 1028608 TTTAGAAAGTACAGCTCAAT 1 TTTAGAAAGTACAGGTCAAT 1028628 TTGCATTTTT Statistics Matches: 59, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 40 59 1.00 ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38 Consensus pattern (40 bp): TTTAGAAAGTACAGGTCAATCTGAGTTTTTAAAGCTTATT Found at i:1035852 original size:4 final size:4 Alignment explanation

Indices: 1035843--1035893 Score: 57 Period size: 4 Copynumber: 12.8 Consensus size: 4 1035833 ACTAAAGTGG * * * * * 1035843 GACA GACA GACA GACA GACA GACA GACG GACG GTCG GACG GACA GACA 1 GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA 1035891 GAC 1 GAC 1035894 TGACGCAGAG Statistics Matches: 43, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 4 43 1.00 ACGTcount: A:0.39, C:0.25, G:0.33, T:0.02 Consensus pattern (4 bp): GACA Found at i:1042386 original size:21 final size:21 Alignment explanation

Indices: 1042362--1042453 Score: 98 Period size: 21 Copynumber: 4.4 Consensus size: 21 1042352 ATCTGACACC 1042362 ACTTGTCAGATAATTATGTCG 1 ACTTGTCAGATAATTATGTCG * 1042383 ACTTGTCAGAT-CTTGATGTCG 1 ACTTGTCAGATAATT-ATGTCG * 1042404 ACCTGTCAGATAATTATGTTC- 1 ACTTGTCAGATAATTATG-TCG * ** * 1042425 ACTTGTCAGTTCTTTAAGTCG 1 ACTTGTCAGATAATTATGTCG 1042446 ACTTGTCA 1 ACTTGTCA 1042454 CTTATTCACG Statistics Matches: 59, Mismatches: 8, Indels: 8 0.79 0.11 0.11 Matches are distributed among these distances: 20 4 0.07 21 51 0.86 22 4 0.07 ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39 Consensus pattern (21 bp): ACTTGTCAGATAATTATGTCG Found at i:1042412 original size:42 final size:42 Alignment explanation

Indices: 1042365--1042453 Score: 126 Period size: 42 Copynumber: 2.1 Consensus size: 42 1042355 TGACACCACT * 1042365 TGTCAGATAATTATG-TCGACTTGTCAGATCTTGATGTCGACC 1 TGTCAGATAATTATGTTC-ACTTGTCAGATCTTGAAGTCGACC * * * 1042407 TGTCAGATAATTATGTTCACTTGTCAGTTCTTTAAGTCGACT 1 TGTCAGATAATTATGTTCACTTGTCAGATCTTGAAGTCGACC 1042449 TGTCA 1 TGTCA 1042454 CTTATTCACG Statistics Matches: 42, Mismatches: 4, Indels: 2 0.88 0.08 0.04 Matches are distributed among these distances: 42 40 0.95 43 2 0.05 ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39 Consensus pattern (42 bp): TGTCAGATAATTATGTTCACTTGTCAGATCTTGAAGTCGACC Found at i:1042556 original size:21 final size:21 Alignment explanation

Indices: 1042530--1042689 Score: 196 Period size: 21 Copynumber: 7.7 Consensus size: 21 1042520 AATAATATTT * * 1042530 TCTGACAAGTCGACATTATGA 1 TCTGACAAGTCGACATAATTA * 1042551 TCTGACAAGTCGACATAATCA 1 TCTGACAAGTCGACATAATTA *** 1042572 TCTTTTAAGTCGACATAATTA 1 TCTGACAAGTCGACATAATTA * 1042593 TTTGACAAGTCGACATAATTA 1 TCTGACAAGTCGACATAATTA 1042614 TCTGACAAGTCGACATAATTA 1 TCTGACAAGTCGACATAATTA * * * 1042635 TTTGACAAGACGACATAA-CA 1 TCTGACAAGTCGACATAATTA * * * 1042655 TCTGACAAGACAACATCATTA 1 TCTGACAAGTCGACATAATTA 1042676 TCTGACAAGTCGAC 1 TCTGACAAGTCGAC 1042690 TTACAATATG Statistics Matches: 118, Mismatches: 20, Indels: 2 0.84 0.14 0.01 Matches are distributed among these distances: 20 16 0.14 21 102 0.86 ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28 Consensus pattern (21 bp): TCTGACAAGTCGACATAATTA Found at i:1042804 original size:42 final size:42 Alignment explanation

Indices: 1042743--1042825 Score: 130 Period size: 42 Copynumber: 2.0 Consensus size: 42 1042733 ATTCTTTCGG * * 1042743 TCAGATAATTATGTTAACTTCTCAGATCTTTATGTCGACTTT 1 TCAGATAATTATGTAAACTTCTCAGATATTTATGTCGACTTT * * 1042785 TCAGATGATTATGTAAACTTGTCAGATATTTATGTCGACTT 1 TCAGATAATTATGTAAACTTCTCAGATATTTATGTCGACTT 1042826 ATATGGTATT Statistics Matches: 37, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 42 37 1.00 ACGTcount: A:0.28, C:0.14, G:0.14, T:0.43 Consensus pattern (42 bp): TCAGATAATTATGTAAACTTCTCAGATATTTATGTCGACTTT Found at i:1042825 original size:21 final size:21 Alignment explanation

Indices: 1042742--1042825 Score: 80 Period size: 21 Copynumber: 4.0 Consensus size: 21 1042732 TATTCTTTCG * * 1042742 GTCAGATAATTATGTTAACTT 1 GTCAGATATTTATGTCAACTT * * * 1042763 CTCAGATCTTTATGTCGACTT 1 GTCAGATATTTATGTCAACTT * * 1042784 TTCAGATGA-TTATGTAAACTT 1 GTCAGAT-ATTTATGTCAACTT * 1042805 GTCAGATATTTATGTCGACTT 1 GTCAGATATTTATGTCAACTT 1042826 ATATGGTATT Statistics Matches: 49, Mismatches: 12, Indels: 4 0.75 0.18 0.06 Matches are distributed among these distances: 20 1 0.02 21 48 0.98 ACGTcount: A:0.27, C:0.14, G:0.15, T:0.43 Consensus pattern (21 bp): GTCAGATATTTATGTCAACTT Found at i:1042944 original size:21 final size:21 Alignment explanation

Indices: 1042919--1043012 Score: 82 Period size: 21 Copynumber: 4.5 Consensus size: 21 1042909 ATGGTTATTT * 1042919 TCTGACAAGTCAACATAAAGA 1 TCTGACAAGTCAACATAAATA ** 1042940 TCTGACAAGTTGACATAAATA 1 TCTGACAAGTCAACATAAATA * * * 1042961 TATGACAAGTCGACAT-TATCA 1 TCTGACAAGTCAACATAAAT-A * * * * 1042982 TATGAGAAGTTAACATAATTA 1 TCTGACAAGTCAACATAAATA 1043003 TCTGACAAGT 1 TCTGACAAGT 1043013 GGTGGCAGAT Statistics Matches: 58, Mismatches: 13, Indels: 4 0.77 0.17 0.05 Matches are distributed among these distances: 20 2 0.03 21 55 0.95 22 1 0.02 ACGTcount: A:0.43, C:0.15, G:0.15, T:0.28 Consensus pattern (21 bp): TCTGACAAGTCAACATAAATA Found at i:1044770 original size:21 final size:21 Alignment explanation

Indices: 1044722--1044770 Score: 62 Period size: 21 Copynumber: 2.3 Consensus size: 21 1044712 TACAAGATAA * * * * 1044722 ACGATAAGATATGATTCATGC 1 ACGATAGGATAGGATTAACGC 1044743 ACGATAGGATAGGATTAACGC 1 ACGATAGGATAGGATTAACGC 1044764 ACGATAG 1 ACGATAG 1044771 AACAGTATAC Statistics Matches: 24, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 21 24 1.00 ACGTcount: A:0.39, C:0.14, G:0.24, T:0.22 Consensus pattern (21 bp): ACGATAGGATAGGATTAACGC Found at i:1049484 original size:21 final size:21 Alignment explanation

Indices: 1049460--1049593 Score: 83 Period size: 21 Copynumber: 6.4 Consensus size: 21 1049450 CGATAAACCT 1049460 GATAGGATTAACGCACGATAG 1 GATAGGATTAACGCACGATAG * * 1049481 GATAGGAATAACACACGATAG 1 GATAGGATTAACGCACGATAG * * * *** 1049502 AAAAGTAAGCACGCACGATAG 1 GATAGGATTAACGCACGATAG * * 1049523 GATAGGATAAACGCATGATAG 1 GATAGGATTAACGCACGATAG * * * * 1049544 AACAGTA-TACACGCACGATAC 1 GATAGGATTA-ACGCACGATAG * * * 1049565 GATAGAATTGAA-ACACAATAG 1 GATAGGATT-AACGCACGATAG 1049586 GATAGGAT 1 GATAGGAT 1049594 AGGATTGTAA Statistics Matches: 82, Mismatches: 28, Indels: 6 0.71 0.24 0.05 Matches are distributed among these distances: 20 1 0.01 21 78 0.95 22 2 0.02 23 1 0.01 ACGTcount: A:0.45, C:0.15, G:0.24, T:0.16 Consensus pattern (21 bp): GATAGGATTAACGCACGATAG Found at i:1049517 original size:42 final size:42 Alignment explanation

Indices: 1049470--1049569 Score: 132 Period size: 42 Copynumber: 2.4 Consensus size: 42 1049460 GATAGGATTA 1049470 ACGCACGATAGGATAGGA-ATAACACACGATAGAAAAGTA-AGC 1 ACGCACGATAGGATAGGATA-AACACACGATAGAAAAGTATA-C * * * 1049512 ACGCACGATAGGATAGGATAAACGCATGATAGAACAGTATAC 1 ACGCACGATAGGATAGGATAAACACACGATAGAAAAGTATAC * 1049554 ACGCACGATACGATAG 1 ACGCACGATAGGATAG 1049570 AATTGAAACA Statistics Matches: 52, Mismatches: 4, Indels: 4 0.87 0.07 0.07 Matches are distributed among these distances: 42 50 0.96 43 2 0.04 ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14 Consensus pattern (42 bp): ACGCACGATAGGATAGGATAAACACACGATAGAAAAGTATAC Found at i:1053999 original size:8 final size:8 Alignment explanation

Indices: 1053988--1054035 Score: 53 Period size: 8 Copynumber: 6.1 Consensus size: 8 1053978 TGAAAAGTTC 1053988 ACAGACGG 1 ACAGACGG * 1053996 ACAGACAG 1 ACAGACGG 1054004 ACAGACGG 1 ACAGACGG * * 1054012 ACGGACAG 1 ACAGACGG * 1054020 ACGGACGG 1 ACAGACGG 1054028 AC-GACGG 1 ACAGACGG 1054035 A 1 A 1054036 TAAACTGTGA Statistics Matches: 35, Mismatches: 5, Indels: 1 0.85 0.12 0.02 Matches are distributed among these distances: 7 6 0.17 8 29 0.83 ACGTcount: A:0.38, C:0.25, G:0.38, T:0.00 Consensus pattern (8 bp): ACAGACGG Found at i:1054005 original size:12 final size:12 Alignment explanation

Indices: 1053988--1054035 Score: 53 Period size: 12 Copynumber: 4.1 Consensus size: 12 1053978 TGAAAAGTTC * * 1053988 ACAGACGGACAG 1 ACAGACAGACGG 1054000 ACAGACAGACGG 1 ACAGACAGACGG * 1054012 ACGGACAGACGG 1 ACAGACAGACGG * 1054024 ACGGAC-GACGG 1 ACAGACAGACGG 1054035 A 1 A 1054036 TAAACTGTGA Statistics Matches: 33, Mismatches: 3, Indels: 1 0.89 0.08 0.03 Matches are distributed among these distances: 11 6 0.18 12 27 0.82 ACGTcount: A:0.38, C:0.25, G:0.38, T:0.00 Consensus pattern (12 bp): ACAGACAGACGG Done.