Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold448

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: 1018568
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.28

Warning! 171214 characters in sequence are not A, C, G, or T


File 2 of 3

Found at i:3260 original size:13 final size:13

Alignment explanation

Indices: 3242--3267 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 3232 TAAATTCTCA 3242 ATAGATAGATTGT 1 ATAGATAGATTGT 3255 ATAGATAGATTGT 1 ATAGATAGATTGT 3268 GACAAGCATT Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38 Consensus pattern (13 bp): ATAGATAGATTGT Found at i:16204 original size:69 final size:67 Alignment explanation

Indices: 16107--16243 Score: 238 Period size: 67 Copynumber: 2.0 Consensus size: 67 16097 ATTTGTTCCA ** 16107 TTTCTTTACATGCATGCCTTTATTATTCTTTTTTTTTTTTTAAAAGTTTACGATATATAAAAGAA 1 TTTCTTTACATGCATGCCTTTATTATTC--TTTTTTTTTCGAAAAGTTTACGATATATAAAAGAA 16172 AGAG 64 AGAG 16176 TTTCTTTACATGCATGCCTTTATTATTCTTTTTTTTTCGAAAAGTTTACGATATATAAAAGAAAG 1 TTTCTTTACATGCATGCCTTTATTATTCTTTTTTTTTCGAAAAGTTTACGATATATAAAAGAAAG 16241 AG 66 AG 16243 T 1 T 16244 ATGTCCGACT Statistics Matches: 66, Mismatches: 2, Indels: 2 0.94 0.03 0.03 Matches are distributed among these distances: 67 38 0.58 69 28 0.42 ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47 Consensus pattern (67 bp): TTTCTTTACATGCATGCCTTTATTATTCTTTTTTTTTCGAAAAGTTTACGATATATAAAAGAAAG AG Found at i:24584 original size:29 final size:29 Alignment explanation

Indices: 24542--24632 Score: 173 Period size: 29 Copynumber: 3.1 Consensus size: 29 24532 GCATGAATCA * 24542 AAAAGTTTCTCTCTCCTACGTATATGGAT 1 AAAAGTTTCTCTCTCCTACGTATGTGGAT 24571 AAAAGTTTCTCTCTCCTACGTATGTGGAT 1 AAAAGTTTCTCTCTCCTACGTATGTGGAT 24600 AAAAGTTTCTCTCTCCTACGTATGTGGAT 1 AAAAGTTTCTCTCTCCTACGTATGTGGAT 24629 AAAA 1 AAAA 24633 ACTAGAACCA Statistics Matches: 61, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 29 61 1.00 ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36 Consensus pattern (29 bp): AAAAGTTTCTCTCTCCTACGTATGTGGAT Found at i:32275 original size:180 final size:180 Alignment explanation

Indices: 31973--32317 Score: 611 Period size: 180 Copynumber: 1.9 Consensus size: 180 31963 ATTGTATATT 31973 GGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATAT 1 GGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATAT * 32038 CAGAGGTGTGCAGATTGCTAGGATTTTGATTTCCAAAAATTTATTGAAAAAATACCAGCTTTCGA 66 CAGAGGTGTGCAGATTGCTAGGATGTTGATTTCCAAAAATTTATTGAAAAAATACCAGCTTTCGA * 32103 ACTTAGTCATTTTTTGGCAGAATATTGCATATAGGATACCCTCATTGTAC 131 ACTTAGTCATTTTTTGGCAAAATATTGCATATAGGATACCCTCATTGTAC * 32153 GGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATAT 1 GGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATAT * * * * 32218 CAGAGGTGTGCATATTGCTAGGATGTTGATTTCCAATAATTTA-TGAAATTAATACCAGCTTTTG 66 CAGAGGTGTGCAGATTGCTAGGATGTTGATTTCCAAAAATTTATTGAAA-AAATACCAGCTTTCG 32282 AACTTAGTCATTTTTTGGCAAAATATTGCATATAGG 130 AACTTAGTCATTTTTTGGCAAAATATTGCATATAGG 32318 GTACTCCATT Statistics Matches: 157, Mismatches: 7, Indels: 2 0.95 0.04 0.01 Matches are distributed among these distances: 179 5 0.03 180 152 0.97 ACGTcount: A:0.30, C:0.15, G:0.18, T:0.36 Consensus pattern (180 bp): GGATAACTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACATATAT CAGAGGTGTGCAGATTGCTAGGATGTTGATTTCCAAAAATTTATTGAAAAAATACCAGCTTTCGA ACTTAGTCATTTTTTGGCAAAATATTGCATATAGGATACCCTCATTGTAC Found at i:32814 original size:4 final size:4 Alignment explanation

Indices: 32805--32847 Score: 50 Period size: 4 Copynumber: 10.8 Consensus size: 4 32795 CTTTCCTCTG * * * * 32805 CGTC CGTC CGTC CGTC CGCC CGCC CGTC TGTC TGTC CGTC CGT 1 CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGT 32848 ACGTTTGTCT Statistics Matches: 35, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 4 35 1.00 ACGTcount: A:0.00, C:0.49, G:0.26, T:0.26 Consensus pattern (4 bp): CGTC Found at i:32841 original size:20 final size:20 Alignment explanation

Indices: 32808--32861 Score: 54 Period size: 20 Copynumber: 2.7 Consensus size: 20 32798 TCCTCTGCGT * * 32808 CCGTCCGTCCGTCCGCCCGC 1 CCGTCTGTCTGTCCGCCCGC * * 32828 CCGTCTGTCTGTCCGTCCGT 1 CCGTCTGTCTGTCCGCCCGC * * 32848 ACGTTTGTCTGTCC 1 CCGTCTGTCTGTCC 32862 CACTTCAGTT Statistics Matches: 28, Mismatches: 6, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 20 28 1.00 ACGTcount: A:0.02, C:0.44, G:0.24, T:0.30 Consensus pattern (20 bp): CCGTCTGTCTGTCCGCCCGC Found at i:36363 original size:166 final size:164 Alignment explanation

Indices: 36086--36448 Score: 414 Period size: 166 Copynumber: 2.2 Consensus size: 164 36076 GATGTATAGC * * * * 36086 TGTACCAATT-GGACGTAAACTTCCTGTTAAATGAGGACTTTGTTTATTATTAGCCTAAATTTTC 1 TGTACC-ATTCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTATTAACCAAAATTTTC * * * * 36150 AAACAAAATTTCGTCAAAGAATTCTCAGCAACTATTTATCGCAGATGCTTGAA-ATTTAAACA-T 65 AAACAAAATTTCGTCAAAGAATTCTCAGCAACAATTAAACCCAGATGCTT-AATATTTAAACACT * * * 36213 ACTTTGTGTTTAGGGATGCCAAAT-TGTGGGATATATTTT 129 A--TT-TATATAGCGATGCCAAATCT-TGGGATATATTTT * * 36252 TGTACCATTCGGACGTCAACTTCCTATTAAATGACGATTTTGTTTATT-TTCAACCAAAATTTTC 1 TGTACCATTCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTATT-AACCAAAATTTTC * * * * * 36316 TAACAAACTTTCGTC-AAGGATTTTGCAGCAACAATTAAACCCAGATGCTTAATATTTTAACACT 65 AAACAAAATTTCGTCAAAGAATTCT-CAGCAACAATTAAACCCAGATGCTTAATATTTAAACACT * * * 36380 ATTTATATAGCTATGCCATATCTTGGGATCTATTTT 129 ATTTATATAGCGATGCCAAATCTTGGGATATATTTT * 36416 TGTACCAATCGGACGTCAACTTCCTGTTAAATG 1 TGTACCATTCGGACGTCAACTTCCTGTTAAATG 36449 TTGAATTTGC Statistics Matches: 168, Mismatches: 23, Indels: 14 0.82 0.11 0.07 Matches are distributed among these distances: 164 56 0.33 165 17 0.10 166 93 0.55 167 2 0.01 ACGTcount: A:0.31, C:0.17, G:0.14, T:0.37 Consensus pattern (164 bp): TGTACCATTCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTATTAACCAAAATTTTCA AACAAAATTTCGTCAAAGAATTCTCAGCAACAATTAAACCCAGATGCTTAATATTTAAACACTAT TTATATAGCGATGCCAAATCTTGGGATATATTTT Found at i:40678 original size:2 final size:2 Alignment explanation

Indices: 40665--40720 Score: 94 Period size: 2 Copynumber: 28.0 Consensus size: 2 40655 GTTTCGCTCG * * 40665 CT CT CG CT CT CT CT CT CA 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 40707 CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT 40721 ATAGCTTTTG Statistics Matches: 50, Mismatches: 4, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 2 50 1.00 ACGTcount: A:0.02, C:0.50, G:0.02, T:0.46 Consensus pattern (2 bp): CT Found at i:43628 original size:29 final size:29 Alignment explanation

Indices: 43549--43629 Score: 144 Period size: 29 Copynumber: 2.8 Consensus size: 29 43539 TTTAATGTCA * 43549 CTTGCTTCTTCATAATGGAGTCATCTTCC 1 CTTGCTTCTTCATAATGGAGTTATCTTCC * 43578 CTTGCTTCTTCATAATGAAGTTATCTTCC 1 CTTGCTTCTTCATAATGGAGTTATCTTCC 43607 CTTGCTTCTTCATAATGGAGTTA 1 CTTGCTTCTTCATAATGGAGTTA 43630 ATAATCATTA Statistics Matches: 49, Mismatches: 3, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 29 49 1.00 ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43 Consensus pattern (29 bp): CTTGCTTCTTCATAATGGAGTTATCTTCC Found at i:45054 original size:20 final size:21 Alignment explanation

Indices: 45029--45069 Score: 59 Period size: 21 Copynumber: 2.0 Consensus size: 21 45019 TATCCAAATG 45029 ATTA-TTTTATGATTAT-ATTA 1 ATTATTTTTAT-ATTATGATTA 45049 ATTATTTTTATATTATGATTA 1 ATTATTTTTATATTATGATTA 45070 TAAAAACAAG Statistics Matches: 19, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 20 9 0.47 21 10 0.53 ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61 Consensus pattern (21 bp): ATTATTTTTATATTATGATTA Found at i:48085 original size:2 final size:2 Alignment explanation

Indices: 48073--48110 Score: 69 Period size: 2 Copynumber: 19.5 Consensus size: 2 48063 GCGCAGGTAA 48073 CT CT C- 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 CT CT C 48111 CACACACGAC Statistics Matches: 35, Mismatches: 0, Indels: 2 0.95 0.00 0.05 Matches are distributed among these distances: 1 1 0.03 2 34 0.97 ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47 Consensus pattern (2 bp): CT Found at i:51709 original size:42 final size:42 Alignment explanation

Indices: 51650--51737 Score: 140 Period size: 42 Copynumber: 2.1 Consensus size: 42 51640 TTGGCAACAT * * 51650 TTTAGGCCAGTTTCGGACAGAAACAAGCCAGTTCAATAAATG 1 TTTAGGCCAGTTTCGGACAGAAACAAGCCAATTCAAGAAATG * * 51692 TTTAGGCCAGTTTCGGACAGAAACGAGCCAATTCAAGAAATT 1 TTTAGGCCAGTTTCGGACAGAAACAAGCCAATTCAAGAAATG 51734 TTTA 1 TTTA 51738 CATTCTTATT Statistics Matches: 42, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 42 42 1.00 ACGTcount: A:0.35, C:0.18, G:0.20, T:0.26 Consensus pattern (42 bp): TTTAGGCCAGTTTCGGACAGAAACAAGCCAATTCAAGAAATG Found at i:53456 original size:6 final size:6 Alignment explanation

Indices: 53445--53551 Score: 115 Period size: 6 Copynumber: 17.8 Consensus size: 6 53435 TACAGCCACC * * * * 53445 ACTACT ACTACT ACTACC ACTACT ACTACC ACTACT CCTACT ACCACT 1 ACTACT ACTACT ACTACT ACTACT ACTACT ACTACT ACTACT ACTACT * * * * * * 53493 ACTACT ACCACT ACTCCT ACTACC ACTACT ACTACT ACTCCT ATTGCT 1 ACTACT ACTACT ACTACT ACTACT ACTACT ACTACT ACTACT ACTACT * 53541 ACTACA ACTAC 1 ACTACT ACTAC 53552 CCATCAATAC Statistics Matches: 81, Mismatches: 20, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 6 81 1.00 ACGTcount: A:0.31, C:0.40, G:0.01, T:0.28 Consensus pattern (6 bp): ACTACT Found at i:53466 original size:15 final size:15 Alignment explanation

Indices: 53442--53530 Score: 121 Period size: 15 Copynumber: 6.1 Consensus size: 15 53432 CTCTACAGCC 53442 ACCACTACTACTACT 1 ACCACTACTACTACT * * 53457 ACTACCACTACTACT 1 ACCACTACTACTACT * 53472 ACCACTACTCCTACT 1 ACCACTACTACTACT 53487 A-C-C-ACTACTACT 1 ACCACTACTACTACT * 53499 ACCACTACTCCTACT 1 ACCACTACTACTACT 53514 ACCACTACTACTACT 1 ACCACTACTACTACT 53529 AC 1 AC 53531 TCCTATTGCT Statistics Matches: 63, Mismatches: 8, Indels: 6 0.82 0.10 0.08 Matches are distributed among these distances: 12 9 0.14 13 2 0.03 14 2 0.03 15 50 0.79 ACGTcount: A:0.31, C:0.43, G:0.00, T:0.26 Consensus pattern (15 bp): ACCACTACTACTACT Found at i:53542 original size:27 final size:27 Alignment explanation

Indices: 53448--53527 Score: 151 Period size: 27 Copynumber: 3.0 Consensus size: 27 53438 AGCCACCACT * 53448 ACTACTACTACTACCACTACTACTACC 1 ACTACTCCTACTACCACTACTACTACC 53475 ACTACTCCTACTACCACTACTACTACC 1 ACTACTCCTACTACCACTACTACTACC 53502 ACTACTCCTACTACCACTACTACTAC 1 ACTACTCCTACTACCACTACTACTAC 53528 TACTCCTATT Statistics Matches: 52, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 27 52 1.00 ACGTcount: A:0.31, C:0.42, G:0.00, T:0.26 Consensus pattern (27 bp): ACTACTCCTACTACCACTACTACTACC Found at i:62053 original size:1 final size:1 Alignment explanation

Indices: 62047--62076 Score: 60 Period size: 1 Copynumber: 30.0 Consensus size: 1 62037 TTGCTCCCTT 62047 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 62077 ATGTCCTGAA Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 29 1.00 ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00 Consensus pattern (1 bp): C Found at i:62519 original size:169 final size:168 Alignment explanation

Indices: 62175--63006 Score: 1175 Period size: 169 Copynumber: 4.9 Consensus size: 168 62165 TGCTCACGTG * * ** * * 62175 TGGGAGTAGAGAAGAAGATTTTTTAAGATTTAAAACATTTTTAAAATATGACAATATTGGCCCCA 1 TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCA * * ** * * 62240 CCCTAGAGCCTAAACCCCTAACAAAGGGGTCAAT-AATTTTACAATTTTGGTAGAGGGCTTCATG 66 CCCTAGAGCCTGAACCCCTGACCCAGGGGTC-ATGAATTTCACAATTTTGGTAGAGGGCCTCATG * * * * * * 62304 GACATTATAACCAGGAATTTAGTTTTTAACAAATATATA 130 GACATCATAATCATGCATTTAGTTTTAAACAAATATAAA * * 62343 TGGGAGTAGAGAAGAAGATTTTCCAAGATTTAATACATTTTTACTATTTGGCCATATTGGCCCCA 1 TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCA * * * ** 62408 CCCTACAACCTGAACCCCATGACCGAGGGGTCATGAATTTCACAATTAAGGTAGAGGGCCTCATG 66 CCCTAGAGCCTGAACCCC-TGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATG 62473 GACATCATAATCATGCATTTAGTTTTAAACAAATA-AATA 130 GACATCATAATCATGCATTTAGTTTTAAACAAATATAA-A * * * 62512 TGGGAGTAAAGAAGAAGATTTTTTAAAGATTTAATACATTTATACTATATGGCCATATTGGCCCC 1 TGGGAGTAGAGAAGAAGATTTTCT-AAGATTTAATACATTTTTACTATATGGCCATATTGGCCCC 62577 ACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATG 65 ACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATG 62642 GACATCATAATCATGCATTTAGTTTTAAACAAATATAAA 130 GACATCATAATCATGCATTTAGTTTTAAACAAATATAAA * 62681 TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTAACTATATATATGGCCATATTGGC 1 TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTT---TA-CTATATGGCCATATTGGC * * * 62746 CCCACCCTACAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAAGGCCGC 62 CCCACCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTC * * 62811 ATGGACATCATAATCATGTATTTAGTTTTTAACAAATATAAA 127 ATGGACATCATAATCATGCATTTAGTTTTAAACAAATATAAA 62853 TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACA-TTTTACTATATGGCCATATTGGCCCCA 1 TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCA * ** * * * * * 62917 CCCTAGAGCCTGAACCCCTGAACTTGAGGCCATGAAATTCACAATTTTGGTAGAAGGCTTCATGG 66 CCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATGG * * 62982 ACATCATAACCATGCATTCAGTTTT 131 ACATCATAATCATGCATTTAGTTTT 63007 TTCTTCACAT Statistics Matches: 599, Mismatches: 56, Indels: 19 0.89 0.08 0.03 Matches are distributed among these distances: 167 99 0.17 168 93 0.16 169 189 0.32 170 57 0.10 171 5 0.01 172 156 0.26 ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30 Consensus pattern (168 bp): TGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCA CCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATGG ACATCATAATCATGCATTTAGTTTTAAACAAATATAAA Found at i:63031 original size:167 final size:167 Alignment explanation

Indices: 62081--63009 Score: 1043 Period size: 169 Copynumber: 5.5 Consensus size: 167 62071 CCCCCCATGT * ** * * 62081 CCTGAACCCCTGACCCAGAGGCCATGAATTTCACAATTAAGGTAG-AGGCGTTAGTGGACATCAT 1 CCTGAACCCCTGACCCAGGGGCCATGAATTTCACAATTTTGGTAGAAGGCCTCA-TGGACATCAT * ** * ** ** ** * * * 62145 AACTATTTATTCAGTTTTTT-TGCTCACGTGTGGGAGTAGAGAAGAAGATTTTTTAAGATTTAAA 65 AACCATGCATTTAGTTTTTTCAACAAATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAAT ** * * 62209 ACATTTTTAAAATATGACAATATTGGCCCCACCCTAGAG 130 ACA-TTTTACTATATGGCCATATTGGCCCCACCCTAGAG * * ** * * * * * 62248 CCTAAACCCCTAACAAAGGGGTCAAT-AATTTTACAATTTTGGTAGAGGGCTTCATGGACATTAT 1 CCTGAACCCCTGACCCAGGGG-CCATGAATTTCACAATTTTGGTAGAAGGCCTCATGGACATCAT * * * 62312 AACCAGGAATTTAG-TTTTT-AACAAATATATATGGGAGTAGAGAAGAAGATTTTCCAAGATTTA 65 AACCATGCATTTAGTTTTTTCAAC-AA-ATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTA * * * 62375 ATACATTTTTACTATTTGGCCATATTGGCCCCACCCTACAA 128 ATACA-TTTTACTATATGGCCATATTGGCCCCACCCTAGAG * * ** * 62416 CCTGAACCCCATGACCGAGGGGTCATGAATTTCACAATTAAGGTAGAGGGCCTCATGGACATCAT 1 CCTGAACCCC-TGACCCAGGGGCCATGAATTTCACAATTTTGGTAGAAGGCCTCATGGACATCAT * * * * 62481 AATCATGCATTTAG--TTTTAAACAAATAAATATGGGAGTAAAGAAGAAGATTTTTTAAAGATTT 65 AACCATGCATTTAGTTTTTTCAACAAAT--ATATGGGAGTAGAGAAGAAGATTTTCT-AAGATTT 62544 AATACATTTATACTATATGGCCATATTGGCCCCACCCTAGAG 127 AATACATTT-TACTATATGGCCATATTGGCCCCACCCTAGAG * * 62586 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATGGACATCATA 1 CCTGAACCCCTGACCCAGGGGCCATGAATTTCACAATTTTGGTAGAAGGCCTCATGGACATCATA * * 62651 ATCATGCATTTAG--TTTTAAACAAATATAAATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAA 66 ACCATGCATTTAGTTTTTTCAACAAATAT--ATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAA * 62714 TACATTTTAACTATATATATGGCCATATTGGCCCCACCCTACAG 129 TACATTTT-AC----TATATGGCCATATTGGCCCCACCCTAGAG * * 62758 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAAGGCCGCATGGACATCATA 1 CCTGAACCCCTGACCCAGGGGCCATGAATTTCACAATTTTGGTAGAAGGCCTCATGGACATCATA * * 62823 ATCATGTATTTAG-TTTTT-AACAAATATAAATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAA 66 ACCATGCATTTAGTTTTTTCAACAAATAT--ATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAA 62886 TACATTTTACTATATGGCCATATTGGCCCCACCCTAGAG 129 TACATTTTACTATATGGCCATATTGGCCCCACCCTAGAG * ** * * * 62925 CCTGAACCCCTGAACTTGAGGCCATGAAATTCACAATTTTGGTAGAAGGCTTCATGGACATCATA 1 CCTGAACCCCTGACCCAGGGGCCATGAATTTCACAATTTTGGTAGAAGGCCTCATGGACATCATA * 62990 ACCATGCATTCAGTTTTTTC 66 ACCATGCATTTAGTTTTTTC 63010 TTCACATGTG Statistics Matches: 665, Mismatches: 76, Indels: 40 0.85 0.10 0.05 Matches are distributed among these distances: 166 6 0.01 167 150 0.23 168 113 0.17 169 182 0.27 170 52 0.08 171 2 0.00 172 156 0.23 173 4 0.01 ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30 Consensus pattern (167 bp): CCTGAACCCCTGACCCAGGGGCCATGAATTTCACAATTTTGGTAGAAGGCCTCATGGACATCATA ACCATGCATTTAGTTTTTTCAACAAATATATGGGAGTAGAGAAGAAGATTTTCTAAGATTTAATA CATTTTACTATATGGCCATATTGGCCCCACCCTAGAG Found at i:64090 original size:2 final size:2 Alignment explanation

Indices: 64085--64142 Score: 116 Period size: 2 Copynumber: 29.0 Consensus size: 2 64075 AGGTAAATAA 64085 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC 1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC 64127 AC AC AC AC AC AC AC AC 1 AC AC AC AC AC AC AC AC 64143 TAATTATCGC 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:0.50, G:0.00, T:0.00 Consensus pattern (2 bp): AC Found at i:65239 original size:15 final size:15 Alignment explanation

Indices: 65219--65248 Score: 60 Period size: 15 Copynumber: 2.0 Consensus size: 15 65209 TTCCAGTCCG 65219 CAGCATTTCTAGAAA 1 CAGCATTTCTAGAAA 65234 CAGCATTTCTAGAAA 1 CAGCATTTCTAGAAA 65249 ATTGTGTTTT Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27 Consensus pattern (15 bp): CAGCATTTCTAGAAA Found at i:69191 original size:8 final size:8 Alignment explanation

Indices: 69180--69210 Score: 53 Period size: 8 Copynumber: 3.9 Consensus size: 8 69170 TGAAAAGTTT 69180 ACGGACAG 1 ACGGACAG 69188 ACGGACAG 1 ACGGACAG * 69196 ACAGACAG 1 ACGGACAG 69204 ACGGACA 1 ACGGACA 69211 AAATGTGATC Statistics Matches: 21, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 8 21 1.00 ACGTcount: A:0.42, C:0.26, G:0.32, T:0.00 Consensus pattern (8 bp): ACGGACAG Found at i:70259 original size:161 final size:161 Alignment explanation

Indices: 69977--70318 Score: 567 Period size: 161 Copynumber: 2.1 Consensus size: 161 69967 AACATCCACA * ** * 69977 AAGAAAATGAAAGTTAACTGCAAATATTTGGAATTTTTCTAAGTCCAAGGGCCATAACTCTGTCG 1 AAGAAAATGAACGGAAACTGCAAATATCTGGAATTTTTCTAAGTCCAAGGGCCATAACTCTGTCG * * 70042 AAAATGGCTCGATCGTACCCAATATCGAACTTGACCTAGATATTATCATGATAAACCTGTATACC 66 AAAATGGCTCGATCATACCCAATATCGAACTTGACCTAGATATTATCATAATAAACCTGTATACC 70107 AAATTTCATTTCAATATGTTCATCCTCTGCG 131 AAATTTCATTTCAATATGTTCATCCTCTGCG * * * 70138 AAGCAAATGAGCGGAAACTGCAAATATCTGGAATTTTTCTACGTCCAAGGGCCATAACTCTGTCG 1 AAGAAAATGAACGGAAACTGCAAATATCTGGAATTTTTCTAAGTCCAAGGGCCATAACTCTGTCG 70203 AAAATGGCTCGATCATACCCAATATCGAACTTGACCTAGATATTATCATAATAAACCTGTATACC 66 AAAATGGCTCGATCATACCCAATATCGAACTTGACCTAGATATTATCATAATAAACCTGTATACC * * * 70268 AAATTTTATTTCAATATGTTTATCCTCTGCT 131 AAATTTCATTTCAATATGTTCATCCTCTGCG * 70299 AAGAAAATGAATGGAAACTG 1 AAGAAAATGAACGGAAACTG 70319 TTGGTAGACC Statistics Matches: 166, Mismatches: 15, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 161 166 1.00 ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30 Consensus pattern (161 bp): AAGAAAATGAACGGAAACTGCAAATATCTGGAATTTTTCTAAGTCCAAGGGCCATAACTCTGTCG AAAATGGCTCGATCATACCCAATATCGAACTTGACCTAGATATTATCATAATAAACCTGTATACC AAATTTCATTTCAATATGTTCATCCTCTGCG Found at i:70617 original size:3 final size:3 Alignment explanation

Indices: 70611--70654 Score: 61 Period size: 3 Copynumber: 14.7 Consensus size: 3 70601 AACAACAACA * * * 70611 ACT ACT ACT TCT ACT ACT ACT ACT ACC ACT ACT ACT ACA ACT AC 1 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT AC 70655 CCAACAGCCA Statistics Matches: 35, Mismatches: 6, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 3 35 1.00 ACGTcount: A:0.34, C:0.36, G:0.00, T:0.30 Consensus pattern (3 bp): ACT Found at i:84005 original size:24 final size:24 Alignment explanation

Indices: 83978--84030 Score: 74 Period size: 24 Copynumber: 2.2 Consensus size: 24 83968 TGTAGAAACC 83978 TTTTTTATTT-ATTTTTCGT-TTAT 1 TTTTTTATTTCATTTTT-GTATTAT * 84001 TTTTTTATTTCATTTTTTTATTAT 1 TTTTTTATTTCATTTTTGTATTAT 84025 TTTTTT 1 TTTTTT 84031 TTGGCTCTGA Statistics Matches: 27, Mismatches: 1, Indels: 3 0.87 0.03 0.10 Matches are distributed among these distances: 23 11 0.41 24 16 0.59 ACGTcount: A:0.13, C:0.04, G:0.02, T:0.81 Consensus pattern (24 bp): TTTTTTATTTCATTTTTGTATTAT Found at i:84024 original size:16 final size:16 Alignment explanation

Indices: 83980--84026 Score: 51 Period size: 16 Copynumber: 2.9 Consensus size: 16 83970 TAGAAACCTT * 83980 TTTTATTTATT-TTTCG 1 TTTT-TTTATTATTTCA * 83996 TTTATTTTTTTATTTCA 1 TTT-TTTTATTATTTCA 84013 TTTTTTTATTATTT 1 TTTTTTTATTATTT 84027 TTTTTTGGCT Statistics Matches: 26, Mismatches: 3, Indels: 4 0.79 0.09 0.12 Matches are distributed among these distances: 16 18 0.69 17 8 0.31 ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79 Consensus pattern (16 bp): TTTTTTTATTATTTCA Found at i:84026 original size:11 final size:12 Alignment explanation

Indices: 83978--84030 Score: 65 Period size: 11 Copynumber: 4.5 Consensus size: 12 83968 TGTAGAAACC 83978 TTTTTTATTTA- 1 TTTTTTATTTAT ** 83989 TTTTTCGTTTAT 1 TTTTTTATTTAT 84001 TTTTTTATTTCAT 1 TTTTTTATTT-AT 84014 TTTTTTA-TTAT 1 TTTTTTATTTAT 84025 TTTTTT 1 TTTTTT 84031 TTGGCTCTGA Statistics Matches: 36, Mismatches: 4, Indels: 4 0.82 0.09 0.09 Matches are distributed among these distances: 11 17 0.47 12 10 0.28 13 9 0.25 ACGTcount: A:0.13, C:0.04, G:0.02, T:0.81 Consensus pattern (12 bp): TTTTTTATTTAT Found at i:84587 original size:2 final size:2 Alignment explanation

Indices: 84582--84621 Score: 71 Period size: 2 Copynumber: 20.0 Consensus size: 2 84572 ATTTTTTCCG * 84582 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CG 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 84622 AACTTTATAA Statistics Matches: 36, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 36 1.00 ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47 Consensus pattern (2 bp): CT Found at i:85095 original size:20 final size:20 Alignment explanation

Indices: 85070--85107 Score: 67 Period size: 20 Copynumber: 1.9 Consensus size: 20 85060 GCTTAAGTAC 85070 CTGGTTGAAGAATGTTTCAA 1 CTGGTTGAAGAATGTTTCAA * 85090 CTGGTTGAAGACTGTTTC 1 CTGGTTGAAGAATGTTTC 85108 TTTACAATGA Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 20 17 1.00 ACGTcount: A:0.24, C:0.13, G:0.26, T:0.37 Consensus pattern (20 bp): CTGGTTGAAGAATGTTTCAA Found at i:92455 original size:3 final size:3 Alignment explanation

Indices: 92449--92474 Score: 52 Period size: 3 Copynumber: 8.7 Consensus size: 3 92439 GATGATGATG 92449 ATC ATC ATC ATC ATC ATC ATC ATC AT 1 ATC ATC ATC ATC ATC ATC ATC ATC AT 92475 GATTATGATT Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 23 1.00 ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35 Consensus pattern (3 bp): ATC Found at i:94364 original size:44 final size:44 Alignment explanation

Indices: 94315--94403 Score: 178 Period size: 44 Copynumber: 2.0 Consensus size: 44 94305 TGCCCACAAT 94315 TTAAAAATATGACATCATAAAGTTTACCTTTTCCCGCCATTTTC 1 TTAAAAATATGACATCATAAAGTTTACCTTTTCCCGCCATTTTC 94359 TTAAAAATATGACATCATAAAGTTTACCTTTTCCCGCCATTTTC 1 TTAAAAATATGACATCATAAAGTTTACCTTTTCCCGCCATTTTC 94403 T 1 T 94404 CATTTCTAGC Statistics Matches: 45, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 44 45 1.00 ACGTcount: A:0.31, C:0.22, G:0.07, T:0.39 Consensus pattern (44 bp): TTAAAAATATGACATCATAAAGTTTACCTTTTCCCGCCATTTTC Found at i:96933 original size:10 final size:11 Alignment explanation

Indices: 96909--96934 Score: 52 Period size: 11 Copynumber: 2.4 Consensus size: 11 96899 GTTGTTGGGA 96909 TTTTTGTTTGT 1 TTTTTGTTTGT 96920 TTTTTGTTTGT 1 TTTTTGTTTGT 96931 TTTT 1 TTTT 96935 ATTTTTAGTT Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 15 1.00 ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85 Consensus pattern (11 bp): TTTTTGTTTGT Found at i:110756 original size:13 final size:13 Alignment explanation

Indices: 110738--110769 Score: 55 Period size: 13 Copynumber: 2.5 Consensus size: 13 110728 ATCATAAAGA * 110738 TTTATTTATTTTT 1 TTTATTTATTTAT 110751 TTTATTTATTTAT 1 TTTATTTATTTAT 110764 TTTATT 1 TTTATT 110770 CGTGACGACA Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 13 18 1.00 ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81 Consensus pattern (13 bp): TTTATTTATTTAT Found at i:119595 original size:18 final size:18 Alignment explanation

Indices: 119572--119608 Score: 74 Period size: 18 Copynumber: 2.1 Consensus size: 18 119562 TTGGGGGGAT 119572 GGTCACATTTAAATAAGA 1 GGTCACATTTAAATAAGA 119590 GGTCACATTTAAATAAGA 1 GGTCACATTTAAATAAGA 119608 G 1 G 119609 ATGTTTGATT Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 19 1.00 ACGTcount: A:0.43, C:0.11, G:0.19, T:0.27 Consensus pattern (18 bp): GGTCACATTTAAATAAGA Found at i:120865 original size:165 final size:166 Alignment explanation

Indices: 120435--121145 Score: 1176 Period size: 166 Copynumber: 4.3 Consensus size: 166 120425 GGTATTTTTC * * * *** * * 120435 AAAAATCTTCTTCTCAAAAACTATTAGGCCGGTAAAGCTTAAACTT-GTGTGGAGGCATCATCAG 1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAA-TTAAAATGGAAGCATCCTCAG * * * * 120499 GTAGTGTAGATTCAAGTTTGTTCAATTCATGGTCCCCGGGGGTTGGGTGGGGCCACAATTGGGGG 65 GAAGTGTTGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGG 120564 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT 130 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT * * * 120601 AAAAATTTTCTTCTCAAAAACTATTTGGCCAGAAAAACTCAAATTAAAATGGAAGCATCCTCAGG 1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG 120666 AAGTGTTGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGA 66 AAGTGTTGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGA 120731 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTTT 131 TCAAGTTTTACATAGGAATATATAGAGAAAATC-TTT * 120768 AAAAAT-TTCTT-TTAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG 1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG * * * 120831 AAGTGTTTATTCAAATTTGTTCAAATCATGGTCCCCGGGGGTTGGGTGGGGCCACAATTGGGGGA 66 AAGTGTTGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGA 120896 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT 131 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT * * 120932 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGTAAGCATCCTCATG 1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG * * 120997 TAGTGTTGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTTGGGGA 66 AAGTGTTGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGA 121062 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT 131 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT 121098 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAA 1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAA 121146 NGGGGTTATA Statistics Matches: 512, Mismatches: 29, Indels: 8 0.93 0.05 0.01 Matches are distributed among these distances: 164 9 0.02 165 151 0.29 166 343 0.67 167 9 0.02 ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29 Consensus pattern (166 bp): AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG AAGTGTTGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGA TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT Found at i:120903 original size:331 final size:333 Alignment explanation

Indices: 120430--121145 Score: 1197 Period size: 331 Copynumber: 2.2 Consensus size: 333 120420 TTGTTGGTAT * * * *** * 120430 TTTTCAAAAATCTTCTTCTCAAAAACTATTAGGCCGGTAAAGCTTAAACTT-GTGTGGAGGCATC 1 TTTT-AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAA-TTAAAATGGAAGCATC * * * 120494 ATCAGGTAGTGTAGATTCAAGTTTGTTCAATTCATGGTCCCCGGGGGTTGGGTGGGGCCACAATT 64 ATCAGGAAGTGTAGATTCAAATTTGTTCAAATCATGGTCCCCGGGGGTTGGGTGGGGCCACAATT * 120559 GGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATTTTCTTCTCAAAAACTA 129 GGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTA * 120624 TTTGGCCAGAAAAACTCAAATTAAAATGGAAGCATCCTCAGGAAGTGTTGATTCAAGTTTGTTCA 194 TTAGGCCAGAAAAACTCAAATTAAAATGGAAGCATCCTCAGGAAGTGTTGATTCAAGTTTGTTCA 120689 AATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTTACATAGGAATATAT 259 AATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTTACATAGGAATATAT 120754 AGAGAAAATC 324 AGAGAAAATC * * 120764 TTTTAAAAAT-TTCTT-TTAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCT 1 TTTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCAT ** 120827 CAGGAAGTGTTTATTCAAATTTGTTCAAATCATGGTCCCCGGGGGTTGGGTGGGGCCACAATTGG 66 CAGGAAGTGTAGATTCAAATTTGTTCAAATCATGGTCCCCGGGGGTTGGGTGGGGCCACAATTGG 120892 GGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATT 131 GGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATT * * * * 120957 AGGCCAGAAAAGCTCAAATTAAAATGTAAGCATCCTCATGTAGTGTTGATTCAAGTTTGTTCAAA 196 AGGCCAGAAAAACTCAAATTAAAATGGAAGCATCCTCAGGAAGTGTTGATTCAAGTTTGTTCAAA * 121022 TCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTTGGGGATCAAGTTTTACATAGGAATATATAG 261 TCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTTACATAGGAATATATAG 121087 AGAAAATC 326 AGAAAATC 121095 -TTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAA 1 TTTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAA 121146 NGGGGTTATA Statistics Matches: 357, Mismatches: 22, Indels: 8 0.92 0.06 0.02 Matches are distributed among these distances: 330 11 0.03 331 297 0.83 332 39 0.11 333 6 0.02 334 4 0.01 ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29 Consensus pattern (333 bp): TTTTAAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCAT CAGGAAGTGTAGATTCAAATTTGTTCAAATCATGGTCCCCGGGGGTTGGGTGGGGCCACAATTGG GGGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATT AGGCCAGAAAAACTCAAATTAAAATGGAAGCATCCTCAGGAAGTGTTGATTCAAGTTTGTTCAAA TCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGGGATCAAGTTTTACATAGGAATATATAG AGAAAATC Found at i:130207 original size:20 final size:21 Alignment explanation

Indices: 130165--130214 Score: 57 Period size: 21 Copynumber: 2.4 Consensus size: 21 130155 AGTATGTTGG ** 130165 TTTTTTTTGTTTTTGTTTAGT 1 TTTTTTTTGGCTTTGTTTAGT * 130186 TTTTTTTTGGCTTT-TTTCGT 1 TTTTTTTTGGCTTTGTTTAGT 130206 TTTTCTTTT 1 TTTT-TTTT 130215 TTTTTGAGGG Statistics Matches: 25, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 20 9 0.36 21 16 0.64 ACGTcount: A:0.02, C:0.06, G:0.12, T:0.80 Consensus pattern (21 bp): TTTTTTTTGGCTTTGTTTAGT Found at i:141950 original size:2 final size:2 Alignment explanation

Indices: 141943--141996 Score: 108 Period size: 2 Copynumber: 27.0 Consensus size: 2 141933 CCGCAAACAA 141943 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC 1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC 141985 AC AC AC AC AC AC 1 AC AC AC AC AC AC 141997 TTAATTTGAT Statistics Matches: 52, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 52 1.00 ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00 Consensus pattern (2 bp): AC Found at i:145754 original size:4 final size:4 Alignment explanation

Indices: 145745--145774 Score: 60 Period size: 4 Copynumber: 7.5 Consensus size: 4 145735 GTTACCCTGT 145745 TCCG TCCG TCCG TCCG TCCG TCCG TCCG TC 1 TCCG TCCG TCCG TCCG TCCG TCCG TCCG TC 145775 TGTCACGTTT Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 26 1.00 ACGTcount: A:0.00, C:0.50, G:0.23, T:0.27 Consensus pattern (4 bp): TCCG Found at i:146507 original size:165 final size:164 Alignment explanation

Indices: 146304--146698 Score: 564 Period size: 165 Copynumber: 2.4 Consensus size: 164 146294 AGTAGCTACG * * * * * 146304 TCATCTCTTGGGATATAATTGGGGCTGTCCTATAGATGTGCAATAAGGTTTTAAAAATTTAAATT 1 TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAATTTAAATT * * 146369 TCATCCTGGGAGTC-AAATAGTAGCAG-AAAATTGACGTTTATCACTAAAAAAAAACAAACATTG 66 TCATCCAGGGAGTCAAAAT-GTAGCAGAAAAATTGACGTTTATCACT--AAAAAAA-AAACATAG * 146432 ATCCAAGAGCTCCTATTATGATTTAATGGATAGACA-A 127 ATCCAAGAACTCCTATTATGATTTAATGGATAGACACA * * 146469 TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAGTAAGGTTTTTAAAATTTAAATT 1 TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAATTTAAATT * 146534 TCATCCAGGGAGTCAAAATGTAGCAGAAAAATTGACGTTTATCACTTAAAAAAAAACATAGATCC 66 TCATCCAGGGAGTCAAAATGTAGCAGAAAAATTGACGTTTATCACTAAAAAAAAAACATAGATCC * * 146599 TAGAACTCCTTTTATGATTTAATGGATAGACACA 131 AAGAACTCCTATTATGATTTAATGGATAGACACA * * * * 146633 TCATATCTTGGGATATGAAAGGAACTGTTCCATAGATGTGCATTAAGGTTTTGAAAAA-TTAAAT 1 TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTT-AAAAATTTAAAT 146697 TT 65 TT 146699 AACCCTGAGG Statistics Matches: 208, Mismatches: 18, Indels: 9 0.89 0.08 0.04 Matches are distributed among these distances: 163 40 0.19 164 63 0.30 165 82 0.39 166 23 0.11 ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32 Consensus pattern (164 bp): TCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAATTTAAATT TCATCCAGGGAGTCAAAATGTAGCAGAAAAATTGACGTTTATCACTAAAAAAAAAACATAGATCC AAGAACTCCTATTATGATTTAATGGATAGACACA Found at i:146697 original size:164 final size:163 Alignment explanation

Indices: 146335--146698 Score: 536 Period size: 164 Copynumber: 2.2 Consensus size: 163 146325 GGGCTGTCCT * 146335 ATAGATGTGCAATAAGGTTTTAAAAATTTAAATTTCATCCTGGGAGTCAAATAGTAGCAGAAAAT 1 ATAGATGTGCAATAAGGTTTTAAAAA-TTAAATTTCATCCAGGGAGTCAAATAGTAGCAGAAAAT * * 146400 TGACGTTTATCACTAAAAAAAAACAAACATTGATCCAAGAGCTCCTATTATGATTTAATGGATAG 65 TGACGTTTATCACT-AAAAAAAACAAACATAGATCCAAGAACTCCTATTATGATTTAATGGATAG * * * 146465 ACAATCATATCTTGGGATATGATAGGGACTGTTCT 129 ACAATCATATCTTGGGATATGAAAGGAACTGTTCC * * 146500 ATAGATGTGCAGTAAGGTTTTTAAAATTTAAATTTCATCCAGGGAGTCAAA-ATGTAGCAGAAAA 1 ATAGATGTGCAATAAGG-TTTTAAAAATTAAATTTCATCCAGGGAGTCAAATA-GTAGCAG-AAA * * * 146564 ATTGACGTTTATCACT-TAAAAAA-AAACATAGATCCTAGAACTCCTTTTATGATTTAATGGATA 63 ATTGACGTTTATCACTAAAAAAAACAAACATAGATCCAAGAACTCCTATTATGATTTAATGGATA 146627 GACACATCATATCTTGGGATATGAAAGGAACTGTTCC 128 GACA-ATCATATCTTGGGATATGAAAGGAACTGTTCC * 146664 ATAGATGTGCATTAAGGTTTTGAAAAATTAAATTT 1 ATAGATGTGCAATAAGGTTTT-AAAAATTAAATTT 146699 AACCCTGAGG Statistics Matches: 181, Mismatches: 13, Indels: 11 0.88 0.06 0.05 Matches are distributed among these distances: 163 44 0.24 164 64 0.35 165 46 0.25 166 27 0.15 ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32 Consensus pattern (163 bp): ATAGATGTGCAATAAGGTTTTAAAAATTAAATTTCATCCAGGGAGTCAAATAGTAGCAGAAAATT GACGTTTATCACTAAAAAAAACAAACATAGATCCAAGAACTCCTATTATGATTTAATGGATAGAC AATCATATCTTGGGATATGAAAGGAACTGTTCC Found at i:146894 original size:135 final size:135 Alignment explanation

Indices: 146746--147044 Score: 367 Period size: 134 Copynumber: 2.2 Consensus size: 135 146736 GATGCCCTTT * * 146746 AAGGATCAAGAATATATATGGTTAAGGGGTGGGGATCTCAACCGTTTTCG-AGATATT-CGTGCA 1 AAGGAACAAGAATATATATGGTTAAGGGGTGGGGATCTCAACCGTTTT-GAAGATATTAAG-GCA * * * * * * 146809 CTTCCTGTTCAAGGGGGGTCATGACCACCCCCGGGGCCCATGACCTACATACCGTTCGATGCCCC 64 CTTCCTGTTCAA-GGGCGTCAGGACCACCCACAGGGCCCATGACCTACATAACATTCGATGCCCC 146874 TTGACA-C 128 TTGACATC * * 146881 AAGGAACAAGAATATATATGGTTTAA-GGGTGGGGATCTCAACTGTTTTGAAGATATTAAGGGAC 1 AAGGAACAAGAATATATATGG-TTAAGGGGTGGGGATCTCAACCGTTTTGAAGATATTAAGGCAC * ** * 146945 TTGCTGTTTGAGGGCGTCAGGACCACCCACAGGGCCCATGACCTACATAACATTTGATGCCCCTT 65 TTCCTGTTCAAGGGCGTCAGGACCACCCACAGGGCCCATGACCTACATAACATTCGATGCCCCTT 147010 GACATC 130 GACATC * * 147016 -AGAAACATGAATATATATGGGTT-AGGGGT 1 AAGGAACAAGAATATATAT-GGTTAAGGGGT 147045 CATGATTATA Statistics Matches: 142, Mismatches: 16, Indels: 13 0.83 0.09 0.08 Matches are distributed among these distances: 133 1 0.01 134 74 0.52 135 62 0.44 136 5 0.04 ACGTcount: A:0.27, C:0.21, G:0.26, T:0.25 Consensus pattern (135 bp): AAGGAACAAGAATATATATGGTTAAGGGGTGGGGATCTCAACCGTTTTGAAGATATTAAGGCACT TCCTGTTCAAGGGCGTCAGGACCACCCACAGGGCCCATGACCTACATAACATTCGATGCCCCTTG ACATC Found at i:157152 original size:2 final size:2 Alignment explanation

Indices: 157145--157193 Score: 98 Period size: 2 Copynumber: 24.5 Consensus size: 2 157135 GTCAGAGCGG 157145 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 157187 AT AT AT A 1 AT AT AT A 157194 CGGCCCGTAT Statistics Matches: 47, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 47 1.00 ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49 Consensus pattern (2 bp): AT Found at i:159382 original size:21 final size:21 Alignment explanation

Indices: 159356--159400 Score: 72 Period size: 21 Copynumber: 2.1 Consensus size: 21 159346 GTAAAACGTA 159356 TGCAACAAATGCGAGAGCTCG 1 TGCAACAAATGCGAGAGCTCG ** 159377 TGCAACGTATGCGAGAGCTCG 1 TGCAACAAATGCGAGAGCTCG 159398 TGC 1 TGC 159401 GAAGCTCAAA Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 21 22 1.00 ACGTcount: A:0.27, C:0.24, G:0.31, T:0.18 Consensus pattern (21 bp): TGCAACAAATGCGAGAGCTCG Found at i:179723 original size:67 final size:67 Alignment explanation

Indices: 179650--179783 Score: 234 Period size: 67 Copynumber: 2.0 Consensus size: 67 179640 TAAAATATAC * 179650 ACAAATCATACAGGGTAAGTGATATATAAAAATAT-GAACAAAATATATACACGGGGCATAAAAT 1 ACAAATCATACAGGGTAAGTGATATATAAAAATATAG-ACAAAATATATACACGGAGCATAAAAT 179714 TCT 65 TCT * 179717 ACAAATCATACAGGGTAAGTGATTTATAAAAATATAGACAAAATATATACACGGAGCATAAAATT 1 ACAAATCATACAGGGTAAGTGATATATAAAAATATAGACAAAATATATACACGGAGCATAAAATT 179782 CT 66 CT 179784 GTAACAGTAC Statistics Matches: 64, Mismatches: 2, Indels: 2 0.94 0.03 0.03 Matches are distributed among these distances: 67 63 0.98 68 1 0.02 ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25 Consensus pattern (67 bp): ACAAATCATACAGGGTAAGTGATATATAAAAATATAGACAAAATATATACACGGAGCATAAAATT CT Found at i:181310 original size:30 final size:31 Alignment explanation

Indices: 181270--181332 Score: 101 Period size: 31 Copynumber: 2.1 Consensus size: 31 181260 TTCAAAGTGT * 181270 TTTTCCGAGCCTG-CGGAAAGGCCCGAGAAG 1 TTTTCAGAGCCTGCCGGAAAGGCCCGAGAAG * 181300 TTTTCAGAGCCTGCCGGAAAGGCCTGAGAAG 1 TTTTCAGAGCCTGCCGGAAAGGCCCGAGAAG 181331 TT 1 TT 181333 GCAATTGGTA Statistics Matches: 30, Mismatches: 2, Indels: 1 0.91 0.06 0.03 Matches are distributed among these distances: 30 12 0.40 31 18 0.60 ACGTcount: A:0.24, C:0.24, G:0.32, T:0.21 Consensus pattern (31 bp): TTTTCAGAGCCTGCCGGAAAGGCCCGAGAAG Found at i:182771 original size:48 final size:48 Alignment explanation

Indices: 182683--182775 Score: 116 Period size: 48 Copynumber: 1.9 Consensus size: 48 182673 TGTCATATGA * * 182683 AAAACCAAAACAACGTAAAAATTAAGGTGGCATATACAAAACATTTTG 1 AAAACAAAAACAACGTAAAAATTAAGGTGACATATACAAAACATTTTG * * ** 182731 AAAACAAAAACAATGTAAAATTTACTGTGACATA-AGCAAAACATT 1 AAAACAAAAACAACGTAAAAATTAAGGTGACATATA-CAAAACATT 182776 AAGGAGGGTG Statistics Matches: 38, Mismatches: 6, Indels: 2 0.83 0.13 0.04 Matches are distributed among these distances: 47 1 0.03 48 37 0.97 ACGTcount: A:0.54, C:0.14, G:0.11, T:0.22 Consensus pattern (48 bp): AAAACAAAAACAACGTAAAAATTAAGGTGACATATACAAAACATTTTG Found at i:183911 original size:38 final size:38 Alignment explanation

Indices: 183868--183953 Score: 120 Period size: 38 Copynumber: 2.3 Consensus size: 38 183858 TGAGGGTGGT * * * 183868 AGCAGACATAATTTGACCTA-TTGTGGGTTTAGGGTAGC 1 AGCAGACATAATCTGACCTACTT-TGGGTTCAGAGTAGC * 183906 AGCAGACATAATCTGACCTACTTTGGGTTCAGAGTAGT 1 AGCAGACATAATCTGACCTACTTTGGGTTCAGAGTAGC 183944 AGCAGACATA 1 AGCAGACATA 183954 TCCTGAATAG Statistics Matches: 43, Mismatches: 4, Indels: 2 0.88 0.08 0.04 Matches are distributed among these distances: 38 41 0.95 39 2 0.05 ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28 Consensus pattern (38 bp): AGCAGACATAATCTGACCTACTTTGGGTTCAGAGTAGC Found at i:185713 original size:108 final size:108 Alignment explanation

Indices: 185505--185791 Score: 283 Period size: 108 Copynumber: 2.7 Consensus size: 108 185495 TTATCAAACC * * * * * 185505 CAAACTTTGCATTTTTTCAATGTTGGGCACATTTGAGAGTTCCGGAGAACTTCTAGCTTTTTTAA 1 CAAACTTCGCATTTTTTCAATGTTGGGCACTTTTGAGAGATCCGGAAAACTCCTAGCTTTTTTAA * * ** * 185570 GAGTAA-TTGAATTAGAATCTGTTTGTGGTTTTCTTATCAACAT 66 GAG-AACGTGAATTAAAATCTGTTTGTGGTGCTCTTATCAACAA * * * * * * 185613 CAAACTTCGCATTGTTTCAATTTTTGACACTTTTGAGAGCTCCGGACAACTCCTAGCTTTTTTAA 1 CAAACTTCGCATTTTTTCAATGTTGGGCACTTTTGAGAGATCCGGAAAACTCCTAGCTTTTTTAA ** * 185678 GAGAACGTGTTTTAAAATCTGATGTT-T-GTGCTCTTATTAACAA 66 GAGAACGTGAATTAAAATCTG-T-TTGTGGTGCTCTTATCAACAA ** * * * * * * 185721 CAAACAACGCTTTTTTTCAATGTCGGGCACTTTTGAGAGATCTGGAAAACTCCTAACTTTTCTAG 1 CAAACTTCGCATTTTTTCAATGTTGGGCACTTTTGAGAGATCCGGAAAACTCCTAGCTTTTTTAA 185786 GAGAAC 66 GAGAAC 185792 AGGTGTTAGA Statistics Matches: 145, Mismatches: 31, Indels: 6 0.80 0.17 0.03 Matches are distributed among these distances: 107 2 0.01 108 139 0.96 109 2 0.01 110 2 0.01 ACGTcount: A:0.27, C:0.17, G:0.17, T:0.38 Consensus pattern (108 bp): CAAACTTCGCATTTTTTCAATGTTGGGCACTTTTGAGAGATCCGGAAAACTCCTAGCTTTTTTAA GAGAACGTGAATTAAAATCTGTTTGTGGTGCTCTTATCAACAA Found at i:186492 original size:33 final size:33 Alignment explanation

Indices: 186455--186555 Score: 157 Period size: 33 Copynumber: 3.1 Consensus size: 33 186445 TGGTTATTAT 186455 TTTTTTCAATTTGGCTTGTTTTATCAGGTTTTC 1 TTTTTTCAATTTGGCTTGTTTTATCAGGTTTTC * * 186488 TTTTTTTAATTTGTCTTGTTTTATCAGGTTTTC 1 TTTTTTCAATTTGGCTTGTTTTATCAGGTTTTC * * * 186521 TATTTTCAATTCGGCTTATTTTATCAGGTTTTC 1 TTTTTTCAATTTGGCTTGTTTTATCAGGTTTTC 186554 TT 1 TT 186556 CCGAAAAGGT Statistics Matches: 60, Mismatches: 8, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 33 60 1.00 ACGTcount: A:0.14, C:0.12, G:0.13, T:0.61 Consensus pattern (33 bp): TTTTTTCAATTTGGCTTGTTTTATCAGGTTTTC Found at i:186494 original size:18 final size:18 Alignment explanation

Indices: 186473--186526 Score: 53 Period size: 15 Copynumber: 3.1 Consensus size: 18 186463 ATTTGGCTTG 186473 TTTTATCAGGTTTTCTTT 1 TTTTATCAGGTTTTCTTT * 186491 TTTTA--A--TTTGTCTTG 1 TTTTATCAGGTTT-TCTTT 186506 TTTTATCAGGTTTTCTATT 1 TTTTATCAGGTTTTCT-TT 186525 TT 1 TT 186527 CAATTCGGCT Statistics Matches: 28, Mismatches: 2, Indels: 11 0.68 0.05 0.27 Matches are distributed among these distances: 14 3 0.11 15 9 0.32 16 1 0.04 17 1 0.04 18 8 0.29 19 6 0.21 ACGTcount: A:0.13, C:0.09, G:0.11, T:0.67 Consensus pattern (18 bp): TTTTATCAGGTTTTCTTT Found at i:186945 original size:24 final size:24 Alignment explanation

Indices: 186918--186995 Score: 84 Period size: 24 Copynumber: 3.2 Consensus size: 24 186908 TCTCTTCTTT * * 186918 ATTTTCATCGGTCATTTTCTGTTC 1 ATTTTCATCGGTCATTTGCTGTCC * * 186942 ATTTTCATTGGTCGTTTGCTGTCC 1 ATTTTCATCGGTCATTTGCTGTCC * * * * 186966 ATTTCCATCGTTCGTTTGCTGTCT 1 ATTTTCATCGGTCATTTGCTGTCC 186990 ATTTTC 1 ATTTTC 186996 GTCTGCTGTT Statistics Matches: 45, Mismatches: 9, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 24 45 1.00 ACGTcount: A:0.10, C:0.22, G:0.15, T:0.53 Consensus pattern (24 bp): ATTTTCATCGGTCATTTGCTGTCC Found at i:201804 original size:16 final size:16 Alignment explanation

Indices: 201780--201815 Score: 54 Period size: 16 Copynumber: 2.2 Consensus size: 16 201770 AAAGAAGTAT * 201780 GACGGACGGAAACACG 1 GACGCACGGAAACACG * 201796 GACGCACGGACACACG 1 GACGCACGGAAACACG 201812 GACG 1 GACG 201816 GACGCCCGGC Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 16 18 1.00 ACGTcount: A:0.33, C:0.31, G:0.36, T:0.00 Consensus pattern (16 bp): GACGCACGGAAACACG Found at i:207185 original size:161 final size:161 Alignment explanation

Indices: 206895--207185 Score: 374 Period size: 161 Copynumber: 1.8 Consensus size: 161 206885 GGAACATCCA * * * * * 206895 CAAAGAAAATGAACGTAAACTGCAAATATTTGGAATTTTTTTAAGTCAAAGGGGCATAACTCTGT 1 CAAAGAAAATGAACGGAAACTGCAAATACTTGGAATTTTTCTAAGTCAAAGAGCCATAACTCTGT * * * 206960 CCAAAATTGCTCTATCATAACCAAAATTAAACTTGACCTAGATATTATTTAAAAAATTCTGTATA 66 CCAAAATTGCTCTATCATAACCAAAATCAAACTTGACCTAGATATTATATAAAAAATCCTGTATA 207025 CCAAATTTTATATCAATATGTGCACCCTCTG 131 CCAAATTTTATATCAATATGTGCACCCTCTG ** * * 207056 CAAAGAAAATGAGTGGAAACTGCAAATAACTT-GAATTTTTCTATGTCCAAGAGCCATAACTCTG 1 CAAAGAAAATGAACGGAAACTGCAAAT-ACTTGGAATTTTTCTAAGTCAAAGAGCCATAACTCTG * * * * 207120 TCCAAAATTGCT-TGATCGT-ACCAAATATCCAACTTGACCTAGATATTATCATGATAAA-CCTG 65 TCCAAAATTGCTCT-ATCATAACCAAA-ATCAAACTTGACCTAGATATTAT-ATAAAAAATCCTG 207182 TATA 127 TATA 207186 AACAACTATC Statistics Matches: 110, Mismatches: 16, Indels: 8 0.82 0.12 0.06 Matches are distributed among these distances: 160 7 0.06 161 95 0.86 162 8 0.07 ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31 Consensus pattern (161 bp): CAAAGAAAATGAACGGAAACTGCAAATACTTGGAATTTTTCTAAGTCAAAGAGCCATAACTCTGT CCAAAATTGCTCTATCATAACCAAAATCAAACTTGACCTAGATATTATATAAAAAATCCTGTATA CCAAATTTTATATCAATATGTGCACCCTCTG Found at i:208853 original size:14 final size:14 Alignment explanation

Indices: 208836--208865 Score: 51 Period size: 14 Copynumber: 2.1 Consensus size: 14 208826 TAATGTTTCC * 208836 CACGAAATGCTTCA 1 CACGAAATGCTACA 208850 CACGAAATGCTACA 1 CACGAAATGCTACA 208864 CA 1 CA 208866 GTTTACACGA Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 14 15 1.00 ACGTcount: A:0.40, C:0.30, G:0.13, T:0.17 Consensus pattern (14 bp): CACGAAATGCTACA Found at i:210475 original size:21 final size:21 Alignment explanation

Indices: 210446--210550 Score: 102 Period size: 21 Copynumber: 5.0 Consensus size: 21 210436 GCTACACGCT * * 210446 CGCTAAACGGTTCACACGAAA 1 CGCTGAACGGTTTACACGAAA * 210467 CGCTGAACGGTTTACATGAAA 1 CGCTGAACGGTTTACACGAAA * * * * 210488 CGCTGCACGCTTTGCCCGAAA 1 CGCTGAACGGTTTACACGAAA * * * 210509 CGCTAAACGATATACACGAAA 1 CGCTGAACGGTTTACACGAAA * * 210530 TGCTGAATGGTTTACACGAAA 1 CGCTGAACGGTTTACACGAAA 210551 TGTTTCTCGC Statistics Matches: 65, Mismatches: 19, Indels: 0 0.77 0.23 0.00 Matches are distributed among these distances: 21 65 1.00 ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20 Consensus pattern (21 bp): CGCTGAACGGTTTACACGAAA Found at i:210769 original size:21 final size:21 Alignment explanation

Indices: 210743--210888 Score: 118 Period size: 21 Copynumber: 7.0 Consensus size: 21 210733 TACAAGATAA * * 210743 ACGATAGGATAGGATTTATGC 1 ACGATAGGATAGGATTAACGC * 210764 ACGATAGGATAGCATTAACGC 1 ACGATAGGATAGGATTAACGC * * * * 210785 ACGATAGAACAGTA-TACATGC 1 ACGATAGGATAGGATTA-ACGC * 210806 ACGAAAGGATAGGATTAACGC 1 ACGATAGGATAGGATTAACGC * * 210827 ACGATAGGACAGTA-TACACGC 1 ACGATAGGATAGGATTA-ACGC * * 210848 ACGATATGATAGGATTGATC-C 1 ACGATAGGATAGGATT-AACGC * * 210869 ACGATAGGAAAGGATAAACG 1 ACGATAGGATAGGATTAACG 210889 ATGTTCATGA Statistics Matches: 96, Mismatches: 23, Indels: 12 0.73 0.18 0.09 Matches are distributed among these distances: 20 6 0.06 21 85 0.89 22 4 0.04 23 1 0.01 ACGTcount: A:0.40, C:0.16, G:0.25, T:0.19 Consensus pattern (21 bp): ACGATAGGATAGGATTAACGC Found at i:210860 original size:42 final size:42 Alignment explanation

Indices: 210762--210877 Score: 162 Period size: 42 Copynumber: 2.8 Consensus size: 42 210752 TAGGATTTAT * * * 210762 GCACGATAGGATAGCATTAACGCACGATAGAACAGTATACAT 1 GCACGATAGGATAGGATTAACGCACGATAGGACAGTATACAC * 210804 GCACGAAAGGATAGGATTAACGCACGATAGGACAGTATACAC 1 GCACGATAGGATAGGATTAACGCACGATAGGACAGTATACAC * * 210846 GCACGATATGATAGGATTGATC-CACGATAGGA 1 GCACGATAGGATAGGATT-AACGCACGATAGGA 210878 AAGGATAAAC Statistics Matches: 66, Mismatches: 7, Indels: 2 0.88 0.09 0.03 Matches are distributed among these distances: 42 64 0.97 43 2 0.03 ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18 Consensus pattern (42 bp): GCACGATAGGATAGGATTAACGCACGATAGGACAGTATACAC Found at i:210872 original size:63 final size:63 Alignment explanation

Indices: 210743--210888 Score: 152 Period size: 63 Copynumber: 2.3 Consensus size: 63 210733 TACAAGATAA * * * * * 210743 ACGATAGGATAGGATTTATGCACGATAGGATAGCATTAACGCACGATAGAACAGTATACATGC 1 ACGATAGGATAGGATTAACGCACGATAGGACAGCATTAACGCACGATAGAACAGGATACATCC * * * ** 210806 ACGAAAGGATAGGATTAACGCACGATAGGACAGTA-TACACGCACGATATG-ATAGGATTGATCC 1 ACGATAGGATAGGATTAACGCACGATAGGACAGCATTA-ACGCACGATA-GAACAGGATACATCC * * 210869 ACGATAGGAAAGGATAAACG 1 ACGATAGGATAGGATTAACG 210889 ATGTTCATGA Statistics Matches: 68, Mismatches: 13, Indels: 4 0.80 0.15 0.05 Matches are distributed among these distances: 62 2 0.03 63 65 0.96 64 1 0.01 ACGTcount: A:0.40, C:0.16, G:0.25, T:0.19 Consensus pattern (63 bp): ACGATAGGATAGGATTAACGCACGATAGGACAGCATTAACGCACGATAGAACAGGATACATCC Found at i:211866 original size:21 final size:21 Alignment explanation

Indices: 211842--211925 Score: 107 Period size: 21 Copynumber: 4.0 Consensus size: 21 211832 CGATAAACCT 211842 GATAGGATTAACGCACGATAG 1 GATAGGATTAACGCACGATAG 211863 GATAGGATTAACGCACGATAG 1 GATAGGATTAACGCACGATAG * * * 211884 AACAGTA-TACACGCACGATAG 1 GATAGGATTA-ACGCACGATAG * * 211905 GATAGAATTAACACACGATAG 1 GATAGGATTAACGCACGATAG 211926 AACAGTTAAT Statistics Matches: 54, Mismatches: 7, Indels: 4 0.83 0.11 0.06 Matches are distributed among these distances: 20 2 0.04 21 50 0.93 22 2 0.04 ACGTcount: A:0.42, C:0.17, G:0.24, T:0.18 Consensus pattern (21 bp): GATAGGATTAACGCACGATAG Found at i:211899 original size:42 final size:45 Alignment explanation

Indices: 211852--211969 Score: 161 Period size: 42 Copynumber: 2.7 Consensus size: 45 211842 GATAGGATTA * 211852 ACGCACGATAGGATAGGATTAACGCACGATAGAACAG-T-AT-AC 1 ACGCACGATAGGATAGGATTAACACACGATAGAACAGTTAATAAC * * 211894 ACGCACGATAGGATAGAATTAACACACGATAGAACAGTTAATAAT 1 ACGCACGATAGGATAGGATTAACACACGATAGAACAGTTAATAAC * * * 211939 ACGCACGATACGATAGGATTGATACACGATA 1 ACGCACGATAGGATAGGATTAACACACGATA 211970 CGATAGGAAA Statistics Matches: 66, Mismatches: 7, Indels: 3 0.87 0.09 0.04 Matches are distributed among these distances: 42 35 0.53 43 1 0.02 44 2 0.03 45 28 0.42 ACGTcount: A:0.42, C:0.18, G:0.21, T:0.19 Consensus pattern (45 bp): ACGCACGATAGGATAGGATTAACACACGATAGAACAGTTAATAAC Found at i:212462 original size:124 final size:124 Alignment explanation

Indices: 212216--212589 Score: 662 Period size: 124 Copynumber: 3.0 Consensus size: 124 212206 TCAATATGTC 212216 GGTTTTTCAGTATTCGGCGGGATTTGTTTTTTCTTCTCACATTATTAATATTTTTATTGGTTTCA 1 GGTTTTTCAGTATTCGGCGGGATTTGTTTTTTCTTCTCAC---ATTAATATTTTTATTGGTTTCA * 212281 GAGAATACGATGT-AAAAATACTAACTGTAAATAAACCTGTGATTATTTACATTGATAATTT 63 GAGAATACGATGTAAAAAATACTTACTGTAAATAAACCTGTGATTATTTACATTGATAATTT 212342 GGTTTTTCAGTATTCGGCGGGATTTGTTTTTTCTTCTCACATTAATATTTTTATTGGTTTCAGAG 1 GGTTTTTCAGTATTCGGCGGGATTTGTTTTTTCTTCTCACATTAATATTTTTATTGGTTTCAGAG 212407 AATACGATGTAAAAAATACTTACTGTAAATAAACCTGTGATTATTTACATTGATAATTT 66 AATACGATGTAAAAAATACTTACTGTAAATAAACCTGTGATTATTTACATTGATAATTT * 212466 GGTTTTTCAGTATTCGGCGGGATTTGTTTTCTCTTCTCACATTAATATTTTTATTGGTTTCAGAG 1 GGTTTTTCAGTATTCGGCGGGATTTGTTTTTTCTTCTCACATTAATATTTTTATTGGTTTCAGAG * * 212531 AATACGATGTAAAAAATATTTGCTGTAAATAAACCTGT-ATTTATTTACATTGATAATTT 66 AATACGATGTAAAAAATACTTACTGTAAATAAACCTGTGA-TTATTTACATTGATAATTT 212590 TGAAAGTTAT Statistics Matches: 242, Mismatches: 4, Indels: 6 0.96 0.02 0.02 Matches are distributed among these distances: 123 36 0.15 124 166 0.69 126 40 0.17 ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45 Consensus pattern (124 bp): GGTTTTTCAGTATTCGGCGGGATTTGTTTTTTCTTCTCACATTAATATTTTTATTGGTTTCAGAG AATACGATGTAAAAAATACTTACTGTAAATAAACCTGTGATTATTTACATTGATAATTT Found at i:223809 original size:24 final size:24 Alignment explanation

Indices: 223768--223814 Score: 67 Period size: 24 Copynumber: 2.0 Consensus size: 24 223758 GAAATGCCTC 223768 TAATTGTACCGTGAACAATTAGTA 1 TAATTGTACCGTGAACAATTAGTA * * * 223792 TAATTGTTCCTTGGACAATTAGT 1 TAATTGTACCGTGAACAATTAGT 223815 CTACAAGTGA Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 24 20 1.00 ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38 Consensus pattern (24 bp): TAATTGTACCGTGAACAATTAGTA Found at i:224453 original size:16 final size:16 Alignment explanation

Indices: 224431--224474 Score: 54 Period size: 16 Copynumber: 2.8 Consensus size: 16 224421 AAGTGTGAAG * 224431 GACGGACACACGGAC- 1 GACGGACACACAGACA * 224446 GCACGGACCCACAGACA 1 G-ACGGACACACAGACA 224463 GACGGACACACA 1 GACGGACACACA 224475 AGGGTAAAAC Statistics Matches: 24, Mismatches: 3, Indels: 3 0.80 0.10 0.10 Matches are distributed among these distances: 15 1 0.04 16 22 0.92 17 1 0.04 ACGTcount: A:0.36, C:0.36, G:0.27, T:0.00 Consensus pattern (16 bp): GACGGACACACAGACA Found at i:226094 original size:13 final size:13 Alignment explanation

Indices: 226078--226102 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 226068 TATAATATTG 226078 ATATATGATTTAC 1 ATATATGATTTAC 226091 ATATATGATTTA 1 ATATATGATTTA 226103 ATTTACATGG 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:0.40, C:0.04, G:0.08, T:0.48 Consensus pattern (13 bp): ATATATGATTTAC Found at i:241851 original size:2 final size:2 Alignment explanation

Indices: 241844--241877 Score: 59 Period size: 2 Copynumber: 17.0 Consensus size: 2 241834 TACCCTAGAT * 241844 TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 241878 CACTTACTTG Statistics Matches: 30, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 2 30 1.00 ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50 Consensus pattern (2 bp): TA Found at i:253726 original size:2 final size:2 Alignment explanation

Indices: 253719--253761 Score: 86 Period size: 2 Copynumber: 21.5 Consensus size: 2 253709 NNNNNNNNNN 253719 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 253761 T 1 T 253762 GTTCATCCGG Statistics Matches: 41, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 41 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:254180 original size:112 final size:112 Alignment explanation

Indices: 253983--254205 Score: 392 Period size: 112 Copynumber: 2.0 Consensus size: 112 253973 AGTTTTGTTC * * 253983 GTTTGTGTATATCTAATTAAAGTCTATTTTTTGTCCAACTTAAGAAAACCCATGGAACTAACACA 1 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTAAAGAAAACCCATGGAACTAACACA * 254048 GAATATACAAGATATACACAACAGTTGTGTCGTGTGCCCAGGTGCAT 66 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCAT * * * 254095 GTTTGTGTATATCTAATTAAAGTTTATTGTTTGTCGAACTAAAGAAAACCCCTGGAACTAACACA 1 GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTAAAGAAAACCCATGGAACTAACACA 254160 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA 66 GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA 254206 CGTCAGGGTT Statistics Matches: 105, Mismatches: 6, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 112 105 1.00 ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30 Consensus pattern (112 bp): GTTTGTGTATATCTAATTAAAGTCTATTGTTTGTCCAACTAAAGAAAACCCATGGAACTAACACA GAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCAT Found at i:255118 original size:17 final size:16 Alignment explanation

Indices: 255078--255118 Score: 57 Period size: 17 Copynumber: 2.6 Consensus size: 16 255068 GCCGTGGGCG * 255078 TTTTTTTT-TTTTGTT 1 TTTTTTTTCTTTTCTT 255093 TTTTTTTTCTTCTTCTT 1 TTTTTTTTCTT-TTCTT 255110 TTTTTTTTC 1 TTTTTTTTC 255119 CATTTTATTT Statistics Matches: 23, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 15 8 0.35 16 2 0.09 17 13 0.57 ACGTcount: A:0.00, C:0.10, G:0.02, T:0.88 Consensus pattern (16 bp): TTTTTTTTCTTTTCTT Found at i:255232 original size:11 final size:11 Alignment explanation

Indices: 255216--255256 Score: 73 Period size: 11 Copynumber: 3.7 Consensus size: 11 255206 TTTTTTAATT 255216 GCTTAAAGGTG 1 GCTTAAAGGTG * 255227 GCTTAAAGGTA 1 GCTTAAAGGTG 255238 GCTTAAAGGTG 1 GCTTAAAGGTG 255249 GCTTAAAG 1 GCTTAAAG 255257 AAGTTTGGAC Statistics Matches: 28, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 11 28 1.00 ACGTcount: A:0.32, C:0.10, G:0.32, T:0.27 Consensus pattern (11 bp): GCTTAAAGGTG Found at i:255413 original size:11 final size:11 Alignment explanation

Indices: 255397--255435 Score: 53 Period size: 11 Copynumber: 3.6 Consensus size: 11 255387 TAAAGATCGT 255397 CTTTAAGCTAC 1 CTTTAAGCTAC * 255408 CTTTAAAC-AC 1 CTTTAAGCTAC * 255418 CTTTAAGCTAT 1 CTTTAAGCTAC 255429 CTTTAAG 1 CTTTAAG 255436 GAGGACTTAA 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:269300 original size:11 final size:11 Alignment explanation

Indices: 269284--269308 Score: 50 Period size: 11 Copynumber: 2.3 Consensus size: 11 269274 AATATCCTTT 269284 ATTTACACATA 1 ATTTACACATA 269295 ATTTACACATA 1 ATTTACACATA 269306 ATT 1 ATT 269309 ATATAAAATA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 14 1.00 ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40 Consensus pattern (11 bp): ATTTACACATA Found at i:287216 original size:12 final size:12 Alignment explanation

Indices: 287199--287240 Score: 75 Period size: 12 Copynumber: 3.4 Consensus size: 12 287189 AGGTTTGAAT 287199 AAAAAAAAAAAC 1 AAAAAAAAAAAC 287211 AAAAAAAAAAAC 1 AAAAAAAAAAAC 287223 AAAACAAAAAAAC 1 AAAA-AAAAAAAC 287236 AAAAA 1 AAAAA 287241 CAATACACGT Statistics Matches: 29, Mismatches: 0, Indels: 2 0.94 0.00 0.06 Matches are distributed among these distances: 12 17 0.59 13 12 0.41 ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00 Consensus pattern (12 bp): AAAAAAAAAAAC Found at i:287217 original size:13 final size:13 Alignment explanation

Indices: 287199--287240 Score: 68 Period size: 13 Copynumber: 3.3 Consensus size: 13 287189 AGGTTTGAAT 287199 AAAAAAAAAAAC- 1 AAAAAAAAAAACA 287211 AAAAAAAAAAACA 1 AAAAAAAAAAACA * 287224 AAACAAAAAAACA 1 AAAAAAAAAAACA 287237 AAAA 1 AAAA 287241 CAATACACGT Statistics Matches: 27, Mismatches: 2, Indels: 1 0.90 0.07 0.03 Matches are distributed among these distances: 12 12 0.44 13 15 0.56 ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00 Consensus pattern (13 bp): AAAAAAAAAAACA Found at i:294059 original size:201 final size:200 Alignment explanation

Indices: 293714--294114 Score: 784 Period size: 201 Copynumber: 2.0 Consensus size: 200 293704 GATTGAATCT * 293714 CCTATAAATCTCTAACCGTAATATTTCTTATTAATTTTCATGAATAAATATAGCCGGTATATGAC 1 CCTATAAATCTCTAACCGTAATATATCTTATTAATTTTCATGAATAAATATAGCCGGTATATGAC 293779 AATATTATTTGGACTGTATATGTATTTTTTTATCATATGGATATATGAATAATTCAATATCTGTT 66 AATATTATTTGGACTGTATATGTATTTTTTTATCATATGGATATATGAATAATTCAATATCTGTT 293844 GGTAATACAGAGTTATATATTCACTTCTCTGGAATCTATGTGTAGGCCACAGAGACTTGAGCCAA 131 GGTAATACAGAGTTATATATTCACTTCTCTGGAATCTATGTGTAGGCCACAGAGACTTGAGCCAA 293909 ACGTA 196 ACGTA 293914 NCCTATAAATCTCTAACCGTAATATATCTTATTAATTTTCATGAATAAATATAGCCGGTATATGA 1 -CCTATAAATCTCTAACCGTAATATATCTTATTAATTTTCATGAATAAATATAGCCGGTATATGA 293979 CAATATTATTTGGACTGTATATGTATTTTTTTATCATATGGATATATGAATAATTCAATATCTGT 65 CAATATTATTTGGACTGTATATGTATTTTTTTATCATATGGATATATGAATAATTCAATATCTGT 294044 TGGTAATACAGAGTTATATATTCACTTCTCTGGAATCTATGTGTAGGCCACAGAGACTTGAGCCA 130 TGGTAATACAGAGTTATATATTCACTTCTCTGGAATCTATGTGTAGGCCACAGAGACTTGAGCCA 294109 AACGTA 195 AACGTA 294115 TCATCCTGCA Statistics Matches: 199, Mismatches: 1, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 201 199 1.00 ACGTcount: A:0.33, C:0.14, G:0.14, T:0.38 Consensus pattern (200 bp): CCTATAAATCTCTAACCGTAATATATCTTATTAATTTTCATGAATAAATATAGCCGGTATATGAC AATATTATTTGGACTGTATATGTATTTTTTTATCATATGGATATATGAATAATTCAATATCTGTT GGTAATACAGAGTTATATATTCACTTCTCTGGAATCTATGTGTAGGCCACAGAGACTTGAGCCAA ACGTA Found at i:297038 original size:17 final size:17 Alignment explanation

Indices: 297016--297056 Score: 55 Period size: 17 Copynumber: 2.4 Consensus size: 17 297006 CAAATGAAAG * 297016 AATTTTCAAATGATTTA 1 AATTTTAAAATGATTTA * 297033 AATTTTAAAATGTTTTA 1 AATTTTAAAATGATTTA * 297050 AAATTTA 1 AATTTTA 297057 GATATTCACT Statistics Matches: 21, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 17 21 1.00 ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49 Consensus pattern (17 bp): AATTTTAAAATGATTTA Found at i:303525 original size:66 final size:66 Alignment explanation

Indices: 303455--303592 Score: 258 Period size: 66 Copynumber: 2.1 Consensus size: 66 303445 TGTAAAATAT 303455 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTACTATTATTCTATTGTTTCTTTTTCACTTTT 1 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTACTATTATTCTATTGTTTCTTTTTCACTTTT 303520 C 66 C * * 303521 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTGTATTGTTTCTTTTTCACTTTT 1 TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTACTATTATTCTATTGTTTCTTTTTCACTTTT 303586 C 66 C 303587 TTATTA 1 TTATTA 303593 TTCTTTTTTT Statistics Matches: 70, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 66 70 1.00 ACGTcount: A:0.17, C:0.21, G:0.14, T:0.49 Consensus pattern (66 bp): TTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTACTATTATTCTATTGTTTCTTTTTCACTTTT C Found at i:304401 original size:69 final size:69 Alignment explanation

Indices: 304290--304502 Score: 374 Period size: 69 Copynumber: 3.1 Consensus size: 69 304280 ACAGTCTTTA 304290 ATTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTATTGTTTCTTTTTCACTTT 1 ATTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTATTGTTTCTTTTTCACTTT 304355 TCTT 66 TCTT * 304359 ATTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCT-TCGGTTTCTTTTTCACTT 1 ATTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTAT-TGTTTCTTTTTCACTT 304423 TTCTT 65 TTCTT * * * 304428 CTTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTGTAATGTTTCTTTTTCACTTT 1 ATTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTATTGTTTCTTTTTCACTTT 304493 TCTT 66 TCTT 304497 ATTATT 1 ATTATT 304503 CTTTTTTTTT Statistics Matches: 136, Mismatches: 6, Indels: 4 0.93 0.04 0.03 Matches are distributed among these distances: 68 1 0.01 69 135 0.99 ACGTcount: A:0.16, C:0.22, G:0.14, T:0.49 Consensus pattern (69 bp): ATTATTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTATTGTTTCTTTTTCACTTT TCTT Found at i:320380 original size:51 final size:52 Alignment explanation

Indices: 320262--320394 Score: 232 Period size: 51 Copynumber: 2.6 Consensus size: 52 320252 AAAGAAACCG * * * 320262 TAGAAAAACAAAAGGGTCTTCCGTTGGAAACGGAAGACCCTAAAAAAAACAA 1 TAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCTAAAAAAAACAA 320314 TAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCT-AAAAAAACAA 1 TAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCTAAAAAAAACAA 320365 TAGAATAACAAGAGGGTCTTCCGTTGAAAA 1 TAGAATAACAAGAGGGTCTTCCGTTGAAAA 320395 AGAAAAACAA Statistics Matches: 78, Mismatches: 3, Indels: 1 0.95 0.04 0.01 Matches are distributed among these distances: 51 40 0.51 52 38 0.49 ACGTcount: A:0.47, C:0.17, G:0.20, T:0.17 Consensus pattern (52 bp): TAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCTAAAAAAAACAA Found at i:322193 original size:30 final size:30 Alignment explanation

Indices: 322154--322217 Score: 78 Period size: 31 Copynumber: 2.1 Consensus size: 30 322144 AAATATGAAA * 322154 AAAATCGAAT-ATTCCT-GGTACGACTTAAC 1 AAAATCGAATGATT-CTAAGTACGACTTAAC * 322183 AAAATACGAATGATTTTAAGTACGACTTAAC 1 AAAAT-CGAATGATTCTAAGTACGACTTAAC 322214 AAAA 1 AAAA 322218 ACCTTTCCGA Statistics Matches: 30, Mismatches: 2, Indels: 4 0.83 0.06 0.11 Matches are distributed among these distances: 29 5 0.17 30 6 0.20 31 19 0.63 ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27 Consensus pattern (30 bp): AAAATCGAATGATTCTAAGTACGACTTAAC Found at i:322992 original size:30 final size:30 Alignment explanation

Indices: 322953--323016 Score: 78 Period size: 31 Copynumber: 2.1 Consensus size: 30 322943 AAAAGATGAA 322953 AAAATCGAAT-ATTCCT-GGTACGACTTAAC 1 AAAATCGAATGATT-CTAGGTACGACTTAAC * * 322982 AAAATACGAATGATTTTAGGTATGACTTAAC 1 AAAAT-CGAATGATTCTAGGTACGACTTAAC 323013 AAAA 1 AAAA 323017 ACCTTTTCGA Statistics Matches: 30, Mismatches: 2, Indels: 4 0.83 0.06 0.11 Matches are distributed among these distances: 29 5 0.17 30 6 0.20 31 19 0.63 ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28 Consensus pattern (30 bp): AAAATCGAATGATTCTAGGTACGACTTAAC Found at i:323637 original size:21 final size:21 Alignment explanation

Indices: 323613--323653 Score: 64 Period size: 21 Copynumber: 2.0 Consensus size: 21 323603 AAAAATAAAG * 323613 AAAAAGAAAAAATATAATAAT 1 AAAAAGAAAAAATAGAATAAT * 323634 AAAAAGAAACAATAGAATAA 1 AAAAAGAAAAAATAGAATAA 323654 CAAGAGGGTC Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 21 18 1.00 ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15 Consensus pattern (21 bp): AAAAAGAAAAAATAGAATAAT Found at i:326474 original size:15 final size:15 Alignment explanation

Indices: 326444--326483 Score: 64 Period size: 15 Copynumber: 2.7 Consensus size: 15 326434 ATGTGACCAG 326444 ATAAATACTG-TTTT 1 ATAAATACTGTTTTT * 326458 ATAACTACTGTTTTT 1 ATAAATACTGTTTTT 326473 ATAAATACTGT 1 ATAAATACTGT 326484 CTAAACATGT Statistics Matches: 23, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 14 9 0.39 15 14 0.61 ACGTcount: A:0.35, C:0.10, G:0.07, T:0.47 Consensus pattern (15 bp): ATAAATACTGTTTTT Found at i:326550 original size:14 final size:14 Alignment explanation

Indices: 326531--326562 Score: 64 Period size: 14 Copynumber: 2.3 Consensus size: 14 326521 AGTATCTACA 326531 TTTATACAGAAAAT 1 TTTATACAGAAAAT 326545 TTTATACAGAAAAT 1 TTTATACAGAAAAT 326559 TTTA 1 TTTA 326563 CCAAAACATG Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 18 1.00 ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41 Consensus pattern (14 bp): TTTATACAGAAAAT Found at i:328842 original size:65 final size:66 Alignment explanation

Indices: 328735--328869 Score: 227 Period size: 65 Copynumber: 2.0 Consensus size: 66 328725 CAGAGAGCAG 328735 TCAGTCTACAGTCAGGAGGATGACGTCATGGATTTTACCCATAAGGTCATACGAGGTCAAGGTGG 1 TCAGTCTACAGTC--GAGGATGACGTCATGGATTTTACCCATAAGGTCATACGAGGTCAAGGTGG 328800 GAC 64 GAC * * 328803 TCAGTCTACAGTC-AGGATGACGTCATGGGTTTTCCCCATAAGGTCATACGAGGTCAAGGTGGGA 1 TCAGTCTACAGTCGAGGATGACGTCATGGATTTTACCCATAAGGTCATACGAGGTCAAGGTGGGA 328867 C 66 C 328868 TC 1 TC 328870 TACAGTCAGG Statistics Matches: 65, Mismatches: 2, Indels: 3 0.93 0.03 0.04 Matches are distributed among these distances: 65 52 0.80 68 13 0.20 ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24 Consensus pattern (66 bp): TCAGTCTACAGTCGAGGATGACGTCATGGATTTTACCCATAAGGTCATACGAGGTCAAGGTGGGA C Found at i:329116 original size:59 final size:59 Alignment explanation

Indices: 329024--329220 Score: 306 Period size: 59 Copynumber: 3.3 Consensus size: 59 329014 ACTCAAAGGA * * 329024 TTAGTTCACATAGCAACAGTTGAAGGATGATACCATACATATCTACTGTCAGGGTCACC 1 TTAGTTCACAGAGCAACAGTTGAAGGATGATACCATAAATATCTACTGTCAGGGTCACC * * * * 329083 TTAGTTCTCATAGCAACAGTTG-AGCGATGATACCATAAATATTTACTGACAGGGTCACC 1 TTAGTTCACAGAGCAACAGTTGAAG-GATGATACCATAAATATCTACTGTCAGGGTCACC * * 329142 TTAGTTCTCAGAGCAACAGTTGAAGGATGATACCATAAATATCAACTGTCAGGGTCACC 1 TTAGTTCACAGAGCAACAGTTGAAGGATGATACCATAAATATCTACTGTCAGGGTCACC 329201 TTAGTTCACAGAGCAACAGT 1 TTAGTTCACAGAGCAACAGT 329221 CAAGGGAGGG Statistics Matches: 127, Mismatches: 9, Indels: 4 0.91 0.06 0.03 Matches are distributed among these distances: 58 2 0.02 59 123 0.97 60 2 0.02 ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27 Consensus pattern (59 bp): TTAGTTCACAGAGCAACAGTTGAAGGATGATACCATAAATATCTACTGTCAGGGTCACC Found at i:334538 original size:40 final size:40 Alignment explanation

Indices: 334492--334639 Score: 161 Period size: 40 Copynumber: 3.9 Consensus size: 40 334482 CAGATACCTC 334492 GATTCTAATGATGTTCGATTTATCTGATTATCAGATTCTT 1 GATTCTAATGATGTTCGATTTATCTGATTATCAGATTCTT 334532 GATTCTAATGATGTTCG----AT-T-A--ATCAGATAT-TT 1 GATTCTAATGATGTTCGATTTATCTGATTATCAGAT-TCTT * * * * * 334564 GATTCTGATGATGTTAGATTTATTTCATTATCAGATACTT 1 GATTCTAATGATGTTCGATTTATCTGATTATCAGATTCTT * * 334604 TATTTTAATGATGTTCGATTTATCTGATTATCAGAT 1 GATTCTAATGATGTTCGATTTATCTGATTATCAGAT 334640 ACCTTGTTGC Statistics Matches: 89, Mismatches: 9, Indels: 20 0.75 0.08 0.17 Matches are distributed among these distances: 32 24 0.27 33 1 0.01 34 1 0.01 35 1 0.01 36 4 0.04 37 1 0.01 38 1 0.01 40 56 0.63 ACGTcount: A:0.28, C:0.10, G:0.15, T:0.47 Consensus pattern (40 bp): GATTCTAATGATGTTCGATTTATCTGATTATCAGATTCTT Found at i:334558 original size:32 final size:31 Alignment explanation

Indices: 334517--334583 Score: 91 Period size: 32 Copynumber: 2.1 Consensus size: 31 334507 CGATTTATCT * 334517 GATTATCAGAT-TCTTGATTCTAATGATGTTC 1 GATTATCAGATAT-TTGATTCTAATGATGTTA * 334548 GATTAATCAGATATTTGATTCTGATGATGTTA 1 GATT-ATCAGATATTTGATTCTAATGATGTTA 334580 GATT 1 GATT 334584 TATTTCATTA Statistics Matches: 32, Mismatches: 2, Indels: 3 0.86 0.05 0.08 Matches are distributed among these distances: 31 4 0.12 32 27 0.84 33 1 0.03 ACGTcount: A:0.28, C:0.09, G:0.18, T:0.45 Consensus pattern (31 bp): GATTATCAGATATTTGATTCTAATGATGTTA Found at i:334640 original size:40 final size:41 Alignment explanation

Indices: 334548--334663 Score: 130 Period size: 40 Copynumber: 2.9 Consensus size: 41 334538 AATGATGTTC * * 334548 GATTAATCAGATA-TTTGATTCTGATGATGTTAGATTTATTT 1 GATT-ATCAGATACTTTGATTCTAATGATGTTAGATTTATCT * * * 334589 CATTATCAGATACTTT-ATTTTAATGATGTTCGATTTATCT 1 GATTATCAGATACTTTGATTCTAATGATGTTAGATTTATCT * * 334629 GATTATCAGATACCTTG-TTGCTAACGATGTTAGAT 1 GATTATCAGATACTTTGATT-CTAATGATGTTAGAT 334664 ATATATAATA Statistics Matches: 62, Mismatches: 10, Indels: 6 0.79 0.13 0.08 Matches are distributed among these distances: 40 44 0.71 41 18 0.29 ACGTcount: A:0.28, C:0.10, G:0.16, T:0.46 Consensus pattern (41 bp): GATTATCAGATACTTTGATTCTAATGATGTTAGATTTATCT Found at i:335451 original size:62 final size:62 Alignment explanation

Indices: 335375--335498 Score: 212 Period size: 62 Copynumber: 2.0 Consensus size: 62 335365 GGTTCTTAAC * * 335375 AACTTAACAATGAAATTACTACACTGAACTATACTAGAACTATTGAAATGAACAATACTCAA 1 AACTTAACAATGAAATTACTACACTGAACTATACTAAAACTACTGAAATGAACAATACTCAA * * 335437 AACTTAACAATGAAATTACTACATTTAACTATACTAAAACTACTGAAATGAACAATACTCAA 1 AACTTAACAATGAAATTACTACACTGAACTATACTAAAACTACTGAAATGAACAATACTCAA 335499 TCTACTTAAC Statistics Matches: 58, Mismatches: 4, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 62 58 1.00 ACGTcount: A:0.49, C:0.18, G:0.06, T:0.27 Consensus pattern (62 bp): AACTTAACAATGAAATTACTACACTGAACTATACTAAAACTACTGAAATGAACAATACTCAA Found at i:335494 original size:24 final size:24 Alignment explanation

Indices: 335467--335513 Score: 58 Period size: 24 Copynumber: 2.0 Consensus size: 24 335457 ACATTTAACT 335467 ATACTAAAACTACTGAAATGAACA 1 ATACTAAAACTACTGAAATGAACA * * * * 335491 ATACTCAATCTACTTAACTGAAC 1 ATACTAAAACTACTGAAATGAAC 335514 TGCGATACTT Statistics Matches: 19, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 24 19 1.00 ACGTcount: A:0.47, C:0.21, G:0.06, T:0.26 Consensus pattern (24 bp): ATACTAAAACTACTGAAATGAACA Found at i:335562 original size:24 final size:24 Alignment explanation

Indices: 335535--335601 Score: 89 Period size: 24 Copynumber: 2.8 Consensus size: 24 335525 TGATCTAAAG * * 335535 AATACTGAAACTGCTGAACTGAAC 1 AATACTAAAACTACTGAACTGAAC * 335559 AATAGTAAAACTACTGAACTGAAC 1 AATACTAAAACTACTGAACTGAAC * * 335583 AATGCTAAGACTACTGAAC 1 AATACTAAAACTACTGAAC 335602 AATGAAACTT Statistics Matches: 37, Mismatches: 6, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 24 37 1.00 ACGTcount: A:0.45, C:0.19, G:0.15, T:0.21 Consensus pattern (24 bp): AATACTAAAACTACTGAACTGAAC Found at i:336007 original size:16 final size:16 Alignment explanation

Indices: 335986--336017 Score: 55 Period size: 16 Copynumber: 2.0 Consensus size: 16 335976 TTTCATGTCA * 335986 TTCAGGTCTTTGGTAT 1 TTCAGGTCTTTAGTAT 336002 TTCAGGTCTTTAGTAT 1 TTCAGGTCTTTAGTAT 336018 GTCCCATATA Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 15 1.00 ACGTcount: A:0.16, C:0.12, G:0.22, T:0.50 Consensus pattern (16 bp): TTCAGGTCTTTAGTAT Found at i:346579 original size:102 final size:103 Alignment explanation

Indices: 346397--346644 Score: 372 Period size: 104 Copynumber: 2.4 Consensus size: 103 346387 TTTTAGAAAA * ** * 346397 AAAGTTGGTTAAACATTGTGTATATCAAACAGACCTGTTTTGCAACAGTTGAGAATAAATCTGTA 1 AAAGTTGGTTAAACATTGTG--TATCAAACATACCTGTTTTGCAACAGTAAAAAATAAATCTGTA * * 346462 AAAATATTGTTTACTTTACATGTACAT-AAAAAAGAACAT 64 AAAATATTGTGTACTTCACATGTACATAAAAAAAGAACAT * * 346501 TAAGTTGGTTAAACATTGTGTATCAAACATACTTGTTTTGCAACAGTAAAAAATAAATCTGTAAA 1 AAAGTTGGTTAAACATTGTGTATCAAACATACCTGTTTTGCAACAGTAAAAAATAAATCTGTAAA * 346566 GATATTGTGTACTTCACATGTACATAAAAAAAAGAACAT 66 AATATTGTGTACTTCACATGTACAT-AAAAAAAGAACAT * 346605 AAAGTGGGTTAAACATTGTGTATCAAACATACCTGTTTTG 1 AAAGTTGGTTAAACATTGTGTATCAAACATACCTGTTTTG 346645 TAAAGATATT Statistics Matches: 130, Mismatches: 12, Indels: 4 0.89 0.08 0.03 Matches are distributed among these distances: 102 62 0.48 104 68 0.52 ACGTcount: A:0.41, C:0.12, G:0.15, T:0.33 Consensus pattern (103 bp): AAAGTTGGTTAAACATTGTGTATCAAACATACCTGTTTTGCAACAGTAAAAAATAAATCTGTAAA AATATTGTGTACTTCACATGTACATAAAAAAAGAACAT Found at i:346812 original size:178 final size:176 Alignment explanation

Indices: 346521--347136 Score: 905 Period size: 176 Copynumber: 3.5 Consensus size: 176 346511 AAACATTGTG * * * * * 346521 TATCAAACATACTTGTTTTGCAACAGT--AAAAAATAAATCTG-----TAAAGATATTGTGTACT 1 TATCAAACATTCCTGTTTTGCAGCAGTAAAAAAAATAAATCTGAAAATTACAGATACTGTGTACT 346579 TCACATGTACATAAAAAAAAGAACATAAAGTGGGTTAAACATTGTGTATCAAACATACCTGTTTT 66 TCACATGTACAT---AAAAA-AACATAAAGTGGGTTAAACATTGTGTATCAAACATACCTGTTTT 346644 GTAAAGATATTGTGTACTTCAATGTACATAAAAAAAACCCATAAAGTTGGT 127 GTAAAGATATTGTGTACTTCAATGTACAT-AAAAAAACCCATAAAGTTGGT * 346695 TATCAAACATTCCTGTTTTGCACCAGTAAAAAAAATAAATCTGAAAAGTTACAGATACTGTGTAC 1 TATCAAACATTCCTGTTTTGCAGCAGTAAAAAAAATAAATCTGAAAA-TTACAGATACTGTGTAC * * 346760 TTCACATGTACATAAAAAACCATTAAGTGGGTTAAACATTGTGTATCAAACATACCTGTTTTGTA 65 TTCACATGTACATAAAAAAACATAAAGTGGGTTAAACATTGTGTATCAAACATACCTGTTTTGTA 346825 AAGATATTGTGTACTTCAATGTACATAAAAAAACCCATAAAGTTGGT 130 AAGATATTGTGTACTTCAATGTACATAAAAAAACCCATAAAGTTGGT * * * 346872 AATCAAACATTCCTGTTTTGCAGCAGTAAAAAAAAAAAAT-TACAAAATTACAGATACTGTGTAC 1 TATCAAACATTCCTGTTTTGCAGCAGTAAAAAAAATAAATCT-GAAAATTACAGATACTGTGTAC * * 346936 TTCACATGTTCATAAAAAAACATAAAGTGGGTTAAACATTGTTTATCAAACATACCTGTTTTGTA 65 TTCACATGTACATAAAAAAACATAAAGTGGGTTAAACATTGTGTATCAAACATACCTGTTTTGTA 347001 AAGATATTGTGTACTTC-ATGTACATAAAAAAA-CCATAAAGTTGGT 130 AAGATATTGTGTACTTCAATGTACATAAAAAAACCCATAAAGTTGGT * * * * 347046 TATCAAACATACATGTTTTGCAGCAGT--AAAATATAAATCTGCAAAATTACAGATACTGTGAAC 1 TATCAAACATTCCTGTTTTGCAGCAGTAAAAAAAATAAATCTG-AAAATTACAGATACTGTGTAC * * 347109 TTCACATGTACATGAAAAACCATAAAGT 65 TTCACATGTACATAAAAAAACATAAAGT 347137 TTAATATTCA Statistics Matches: 406, Mismatches: 25, Indels: 23 0.89 0.06 0.05 Matches are distributed among these distances: 172 9 0.02 173 46 0.11 174 61 0.15 175 15 0.04 176 110 0.27 177 62 0.15 178 71 0.17 179 5 0.01 182 27 0.07 ACGTcount: A:0.42, C:0.14, G:0.13, T:0.31 Consensus pattern (176 bp): TATCAAACATTCCTGTTTTGCAGCAGTAAAAAAAATAAATCTGAAAATTACAGATACTGTGTACT TCACATGTACATAAAAAAACATAAAGTGGGTTAAACATTGTGTATCAAACATACCTGTTTTGTAA AGATATTGTGTACTTCAATGTACATAAAAAAACCCATAAAGTTGGT Found at i:354101 original size:2 final size:2 Alignment explanation

Indices: 354094--354126 Score: 66 Period size: 2 Copynumber: 16.5 Consensus size: 2 354084 ATTTGTATTC 354094 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 A 354127 TTCATTCATC Statistics Matches: 31, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 31 1.00 ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00 Consensus pattern (2 bp): AG Found at i:367631 original size:2 final size:2 Alignment explanation

Indices: 367624--367655 Score: 64 Period size: 2 Copynumber: 16.0 Consensus size: 2 367614 AGACTGAAAA 367624 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 367656 ATGCTTTTAA Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 30 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:370655 original size:16 final size:16 Alignment explanation

Indices: 370616--370657 Score: 59 Period size: 16 Copynumber: 2.6 Consensus size: 16 370606 TGGAGTGCAC 370616 ACACACACACATACAT 1 ACACACACACATACAT * 370632 ACATACACACATACGA- 1 ACACACACACATAC-AT 370648 ACACACACAC 1 ACACACACAC 370658 GCACGGAAGC Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 16 22 0.96 17 1 0.04 ACGTcount: A:0.50, C:0.38, G:0.02, T:0.10 Consensus pattern (16 bp): ACACACACACATACAT Found at i:377650 original size:27 final size:27 Alignment explanation

Indices: 377598--377651 Score: 90 Period size: 27 Copynumber: 2.0 Consensus size: 27 377588 CTTGATTATC ** 377598 GCTCAACCAAAACACAATTACCCACTG 1 GCTCAACCAAAACACAATTAAACACTG 377625 GCTCAACCAAAACACAATTAAACACTG 1 GCTCAACCAAAACACAATTAAACACTG 377652 CAGTTTATTC Statistics Matches: 25, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 27 25 1.00 ACGTcount: A:0.44, C:0.33, G:0.07, T:0.15 Consensus pattern (27 bp): GCTCAACCAAAACACAATTAAACACTG Found at i:389623 original size:14 final size:15 Alignment explanation

Indices: 389604--389641 Score: 55 Period size: 14 Copynumber: 2.7 Consensus size: 15 389594 AAAATATAAC 389604 TAATATGTAAA-CTG 1 TAATATGTAAATCTG 389618 TAATATGTAAATCTG 1 TAATATGTAAATCTG 389633 --ATATGTAAA 1 TAATATGTAAA 389642 ACATTGAATT Statistics Matches: 23, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 13 9 0.39 14 11 0.48 15 3 0.13 ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37 Consensus pattern (15 bp): TAATATGTAAATCTG Found at i:402136 original size:4 final size:4 Alignment explanation

Indices: 402127--402183 Score: 114 Period size: 4 Copynumber: 14.2 Consensus size: 4 402117 CTATGTAACA 402127 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT 1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT 402175 AGAT AGAT A 1 AGAT AGAT A 402184 CGAAGAAACA Statistics Matches: 53, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 53 1.00 ACGTcount: A:0.51, C:0.00, G:0.25, T:0.25 Consensus pattern (4 bp): AGAT Found at i:404213 original size:2 final size:2 Alignment explanation

Indices: 404208--404261 Score: 108 Period size: 2 Copynumber: 27.0 Consensus size: 2 404198 TATTATGTGT 404208 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 404250 GA GA GA GA GA GA 1 GA GA GA GA GA GA 404262 NNNNNNNNNN Statistics Matches: 52, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 52 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:409468 original size:2 final size:2 Alignment explanation

Indices: 409461--409494 Score: 68 Period size: 2 Copynumber: 17.0 Consensus size: 2 409451 TTATAAATAA 409461 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 409495 GACCTGTAGC Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 32 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:410582 original size:17 final size:17 Alignment explanation

Indices: 410560--410592 Score: 66 Period size: 17 Copynumber: 1.9 Consensus size: 17 410550 AACTCTCAGT 410560 TTAGCCGATAACTGGTC 1 TTAGCCGATAACTGGTC 410577 TTAGCCGATAACTGGT 1 TTAGCCGATAACTGGT 410593 ACAGTACCAG Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 16 1.00 ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30 Consensus pattern (17 bp): TTAGCCGATAACTGGTC Found at i:416671 original size:18 final size:18 Alignment explanation

Indices: 416649--416689 Score: 68 Period size: 16 Copynumber: 2.4 Consensus size: 18 416639 ACAATATATT 416649 CTCTCTCTTTTTCTCT-A 1 CTCTCTCTTTTTCTCTCA 416666 -TCTCTCTTTTTCTCTCA 1 CTCTCTCTTTTTCTCTCA 416683 CTCTCTC 1 CTCTCTC 416690 CCGCTCTGTA Statistics Matches: 22, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 16 15 0.68 17 1 0.05 18 6 0.27 ACGTcount: A:0.05, C:0.39, G:0.00, T:0.56 Consensus pattern (18 bp): CTCTCTCTTTTTCTCTCA Found at i:420096 original size:2 final size:2 Alignment explanation

Indices: 420091--420125 Score: 70 Period size: 2 Copynumber: 17.5 Consensus size: 2 420081 AAATAAGACA 420091 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 420126 GCCAGCTTAC 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:423018 original size:22 final size:22 Alignment explanation

Indices: 422986--423122 Score: 177 Period size: 22 Copynumber: 6.2 Consensus size: 22 422976 ACGCTACATG * 422986 TCTCTACCCATGATGCCATGTT 1 TCTCTACCCATCATGCCATGTT * * * 423008 TCTTTTCCCATGATGCCATGTT 1 TCTCTACCCATCATGCCATGTT * * 423030 TGTCTACCCATCATGTCATGTT 1 TCTCTACCCATCATGCCATGTT * 423052 TCTCTTCCCATCATGCCATGTT 1 TCTCTACCCATCATGCCATGTT * 423074 TCTCTACCCATCATGCAATGTT 1 TCTCTACCCATCATGCCATGTT * 423096 TCAT-TACCCATCATGCCGTGTT 1 TC-TCTACCCATCATGCCATGTT 423118 TCTCT 1 TCTCT 423123 TCTTATTAGT Statistics Matches: 99, Mismatches: 14, Indels: 4 0.85 0.12 0.03 Matches are distributed among these distances: 21 1 0.01 22 97 0.98 23 1 0.01 ACGTcount: A:0.17, C:0.31, G:0.12, T:0.40 Consensus pattern (22 bp): TCTCTACCCATCATGCCATGTT Found at i:427237 original size:2 final size:2 Alignment explanation

Indices: 427230--427265 Score: 72 Period size: 2 Copynumber: 18.0 Consensus size: 2 427220 ATGGAAATAT 427230 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 427266 AGTAAGTTAA 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:433429 original size:21 final size:21 Alignment explanation

Indices: 433405--433449 Score: 63 Period size: 21 Copynumber: 2.1 Consensus size: 21 433395 AACAGGAAGA * 433405 TGAAATAACACACACCATTTC 1 TGAAATAACACACACCATTGC * * 433426 TGAAATCACACAGACCATTGC 1 TGAAATAACACACACCATTGC 433447 TGA 1 TGA 433450 TCTGAAGAAG Statistics Matches: 21, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 21 21 1.00 ACGTcount: A:0.40, C:0.27, G:0.11, T:0.22 Consensus pattern (21 bp): TGAAATAACACACACCATTGC Found at i:434559 original size:15 final size:15 Alignment explanation

Indices: 434535--434581 Score: 76 Period size: 15 Copynumber: 3.1 Consensus size: 15 434525 GATGTGTAAT 434535 TACATATTTTAGATA 1 TACATATTTTAGATA * 434550 TACATGTTTTAGATA 1 TACATATTTTAGATA * 434565 TACATATTTTACATA 1 TACATATTTTAGATA 434580 TA 1 TA 434582 TTAGATAGAC Statistics Matches: 29, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 15 29 1.00 ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47 Consensus pattern (15 bp): TACATATTTTAGATA Found at i:435128 original size:13 final size:13 Alignment explanation

Indices: 435110--435134 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 435100 GCATTTTTCA 435110 AATTTTCAAATTT 1 AATTTTCAAATTT 435123 AATTTTCAAATT 1 AATTTTCAAATT 435135 CATTTTGATT 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:0.40, C:0.08, G:0.00, T:0.52 Consensus pattern (13 bp): AATTTTCAAATTT Found at i:439512 original size:22 final size:22 Alignment explanation

Indices: 439484--439526 Score: 68 Period size: 22 Copynumber: 2.0 Consensus size: 22 439474 ACTAGAAGTG 439484 TGCCTACCATTCTGTCAACCAC 1 TGCCTACCATTCTGTCAACCAC * * 439506 TGCCTACCATTTTGTCTACCA 1 TGCCTACCATTCTGTCAACCA 439527 TTCTGTCAAC Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 22 19 1.00 ACGTcount: A:0.21, C:0.37, G:0.09, T:0.33 Consensus pattern (22 bp): TGCCTACCATTCTGTCAACCAC Found at i:439526 original size:12 final size:12 Alignment explanation

Indices: 439509--439561 Score: 65 Period size: 12 Copynumber: 4.6 Consensus size: 12 439499 CAACCACTGC 439509 CTACCATTTTGT 1 CTACCATTTTGT * 439521 CTACCATTCTGT 1 CTACCATTTTGT * * 439533 CAACCA--TTGC 1 CTACCATTTTGT 439543 CTACCATTTTGT 1 CTACCATTTTGT 439555 CTACCAT 1 CTACCAT 439562 GGTCTTCCAT Statistics Matches: 33, Mismatches: 6, Indels: 4 0.77 0.14 0.09 Matches are distributed among these distances: 10 7 0.21 12 26 0.79 ACGTcount: A:0.21, C:0.32, G:0.08, T:0.40 Consensus pattern (12 bp): CTACCATTTTGT Found at i:439527 original size:34 final size:34 Alignment explanation

Indices: 439487--439561 Score: 141 Period size: 34 Copynumber: 2.2 Consensus size: 34 439477 AGAAGTGTGC 439487 CTACCATTCTGTCAACCACTGCCTACCATTTTGT 1 CTACCATTCTGTCAACCACTGCCTACCATTTTGT * 439521 CTACCATTCTGTCAACCATTGCCTACCATTTTGT 1 CTACCATTCTGTCAACCACTGCCTACCATTTTGT 439555 CTACCAT 1 CTACCAT 439562 GGTCTTCCAT Statistics Matches: 40, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 34 40 1.00 ACGTcount: A:0.21, C:0.35, G:0.08, T:0.36 Consensus pattern (34 bp): CTACCATTCTGTCAACCACTGCCTACCATTTTGT Found at i:439788 original size:36 final size:36 Alignment explanation

Indices: 439748--440005 Score: 141 Period size: 36 Copynumber: 7.2 Consensus size: 36 439738 TCTACCATTG 439748 TATCAACTGATCTGTTACTAACTATATGTATCAGTT 1 TATCAACTGATCTGTTACTAACTATATGTATCAGTT * * * * * 439784 TATCAA-TCAATC---TACCAGTCTATCTATCTACCA-TT 1 TATCAACT-GATCTGTTACTA-ACTA--TATGTATCAGTT 439819 GTATCAACTGATCTGTTACTAACTATATGTATCAGTT 1 -TATCAACTGATCTGTTACTAACTATATGTATCAGTT * * * * * 439856 TATCAA-TCAATC---TACCAGTCTATCTATCTACCA-TT 1 TATCAACT-GATCTGTTACTA-ACTA--TATGTATCAGTT 439891 GTATCAACTGATCTGTTACTAACTATATGTATCAGTT 1 -TATCAACTGATCTGTTACTAACTATATGTATCAGTT * * * * * 439928 TATCAA-TCAATC---TACCAGTCTATCTATCTACCA-TT 1 TATCAACT-GATCTGTTACTA-ACTA--TATGTATCAGTT 439963 GTATCAACTGATCTGTTACTAACTATATGTATCAGTT 1 -TATCAACTGATCTGTTACTAACTATATGTATCAGTT 440000 TATCAA 1 TATCAA 440006 TCAATCTACC Statistics Matches: 162, Mismatches: 30, Indels: 60 0.64 0.12 0.24 Matches are distributed among these distances: 33 12 0.07 34 9 0.06 35 9 0.06 36 102 0.63 37 9 0.06 38 9 0.06 39 12 0.07 ACGTcount: A:0.31, C:0.21, G:0.09, T:0.39 Consensus pattern (36 bp): TATCAACTGATCTGTTACTAACTATATGTATCAGTT Found at i:439798 original size:72 final size:72 Alignment explanation

Indices: 439681--440194 Score: 913 Period size: 72 Copynumber: 7.1 Consensus size: 72 439671 CAATGTAACG * 439681 ACTGATCTGTGACTAACTATATGTATCAGTTTATCAATCAATCTACCAGTCTATCTATCTACCAT 1 ACTGATCTGTTACTAACTATATGTATCAGTTTATCAATCAATCTACCAGTCTATCTATCTACCAT 439746 TGTATCA 66 TGTATCA 439753 ACTGATCTGTTACTAACTATATGTATCAGTTTATCAATCAATCTACCAGTCTATCTATCTACCAT 1 ACTGATCTGTTACTAACTATATGTATCAGTTTATCAATCAATCTACCAGTCTATCTATCTACCAT 439818 TGTATCA 66 TGTATCA 439825 ACTGATCTGTTACTAACTATATGTATCAGTTTATCAATCAATCTACCAGTCTATCTATCTACCAT 1 ACTGATCTGTTACTAACTATATGTATCAGTTTATCAATCAATCTACCAGTCTATCTATCTACCAT 439890 TGTATCA 66 TGTATCA 439897 ACTGATCTGTTACTAACTATATGTATCAGTTTATCAATCAATCTACCAGTCTATCTATCTACCAT 1 ACTGATCTGTTACTAACTATATGTATCAGTTTATCAATCAATCTACCAGTCTATCTATCTACCAT 439962 TGTATCA 66 TGTATCA * 439969 ACTGATCTGTTACTAACTATATGTATCAGTTTATCAATCAATCTACCAGTCTATCTATCTACCGT 1 ACTGATCTGTTACTAACTATATGTATCAGTTTATCAATCAATCTACCAGTCTATCTATCTACCAT 440034 TGTATCA 66 TGTATCA * * * 440041 ACT-AGTCTGTGACTAACTATATGTATCAGCTTATCAATCAATCTACCATTCTATCTATCTACCA 1 ACTGA-TCTGTTACTAACTATATGTATCAGTTTATCAATCAATCTACCAGTCTATCTATCTACCA 440105 TTGTATCA 65 TTGTATCA * * * * 440113 ACTGGTCTGTGACTAACTATATGTATCAGTTTATCAATCAATCTACCAGTGTATCTATCTACCGT 1 ACTGATCTGTTACTAACTATATGTATCAGTTTATCAATCAATCTACCAGTCTATCTATCTACCAT * 440178 TGTAACA 66 TGTATCA * 440185 ACTGGTCTGT 1 ACTGATCTGT 440195 GANNNNNNNN Statistics Matches: 428, Mismatches: 12, Indels: 4 0.96 0.03 0.01 Matches are distributed among these distances: 71 1 0.00 72 427 1.00 ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38 Consensus pattern (72 bp): ACTGATCTGTTACTAACTATATGTATCAGTTTATCAATCAATCTACCAGTCTATCTATCTACCAT TGTATCA Found at i:440102 original size:16 final size:16 Alignment explanation

Indices: 440081--440111 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 440071 TTATCAATCA 440081 ATCTACCATTCTATCT 1 ATCTACCATTCTATCT * 440097 ATCTACCATTGTATC 1 ATCTACCATTCTATC 440112 AACTGGTCTG Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 16 14 1.00 ACGTcount: A:0.26, C:0.29, G:0.03, T:0.42 Consensus pattern (16 bp): ATCTACCATTCTATCT Found at i:447692 original size:8 final size:8 Alignment explanation

Indices: 447666--447708 Score: 59 Period size: 8 Copynumber: 5.4 Consensus size: 8 447656 CACCTTGTCC * 447666 GTCCGTCC 1 GTCCGTCT 447674 GTCCGTCT 1 GTCCGTCT * 447682 GTCCGTAT 1 GTCCGTCT * 447690 GTCTGTCT 1 GTCCGTCT 447698 GTCCGTCT 1 GTCCGTCT 447706 GTC 1 GTC 447709 TGTGCAATCA Statistics Matches: 30, Mismatches: 5, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 8 30 1.00 ACGTcount: A:0.02, C:0.35, G:0.26, T:0.37 Consensus pattern (8 bp): GTCCGTCT Found at i:447705 original size:12 final size:12 Alignment explanation

Indices: 447661--447711 Score: 57 Period size: 12 Copynumber: 4.2 Consensus size: 12 447651 GGAATCACCT * 447661 TGTCCGTCCGTC 1 TGTCCGTCTGTC * 447673 CGTCCGTCTGTC 1 TGTCCGTCTGTC * ** 447685 CGTATGTCTGTC 1 TGTCCGTCTGTC 447697 TGTCCGTCTGTC 1 TGTCCGTCTGTC 447709 TGT 1 TGT 447712 GCAATCATGT Statistics Matches: 32, Mismatches: 7, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 12 32 1.00 ACGTcount: A:0.02, C:0.33, G:0.25, T:0.39 Consensus pattern (12 bp): TGTCCGTCTGTC Found at i:447983 original size:146 final size:146 Alignment explanation

Indices: 447719--447986 Score: 414 Period size: 146 Copynumber: 1.8 Consensus size: 146 447709 TGTGCAATCA * 447719 TGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGATCTTACTTCACACAAAGATTGCTTA 1 TGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGATCTTACTTCACACAAAGATTGATTA * * * * 447784 TGACCTAAGGGTGTGTCATGACCTTGACGCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGCAGA 66 TGACCTAAGGATGTGTCATGACCTTGACCCAAGGTCATTCGAGAAAGGTCAAGGTCACTGGCAGA 447849 AAAAGTGCAAAATTTG 131 AAAAGTGCAAAATTTG * * * 447865 TGTCCGGTCCATATCTTTCTTATGGGGAAACATTGGAAGTTCTTAGTTCACACAAAGATTGATTA 1 TGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGATCTTACTTCACACAAAGATTGATTA * * 447930 TGA-TTAAAGGATGTGTCATGACCTTGACCCAAGGTCAATT-GAGAAAGTTCAAGGTCA 66 TGACCT-AAGGATGTGTCATGACCTTGACCCAAGGTC-ATTCGAGAAAGGTCAAGGTCA 447987 TTGTTTCAAA Statistics Matches: 110, Mismatches: 10, Indels: 4 0.89 0.08 0.03 Matches are distributed among these distances: 145 1 0.01 146 106 0.96 147 3 0.03 ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29 Consensus pattern (146 bp): TGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGATCTTACTTCACACAAAGATTGATTA TGACCTAAGGATGTGTCATGACCTTGACCCAAGGTCATTCGAGAAAGGTCAAGGTCACTGGCAGA AAAAGTGCAAAATTTG Found at i:477736 original size:15 final size:15 Alignment explanation

Indices: 477716--477745 Score: 51 Period size: 15 Copynumber: 2.0 Consensus size: 15 477706 TGATACAATG 477716 TTGTATCAAATGATA 1 TTGTATCAAATGATA * 477731 TTGTATCATATGATA 1 TTGTATCAAATGATA 477746 CAATATCATA Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43 Consensus pattern (15 bp): TTGTATCAAATGATA Done.