Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr11 124536837 

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33

Warning! 312 characters in sequence are not A, C, G, or T


File 134 of 427

Found at i:36098401 original size:51 final size:51

Alignment explanation

Indices: 36098194--36098411 Score: 179 Period size: 51 Copynumber: 4.3 Consensus size: 51 36098184 GTTGTGAGAA * * * * 36098194 CACATGTGTAGTACTATGTGCAAGCTACTTTGTGTTTAAA-ATGGTTTTAGGT 1 CACATGTGTAGTACTAAGTGCAAGCTACTATGTG-TAAAAGATAGTTTT-GGT * * * * ** * * 36098246 CACGTTTGTAGTACTAAGTGCATGCTACTACGTGTACTAGAT-GGTTAGGT 1 CACATGTGTAGTACTAAGTGCAAGCTACTATGTGTAAAAGATAGTTTTGGT * * * *** * *** 36098296 CGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAGCTTCCAT 1 CACATGTGTAGTACTAAGTGCAAGCTACTATGTGTAAAAGATAGTTTTGGT * 36098347 CACATGTGTGGTACTAAGTGCAAGCTACTATGTGTAAAAGATAGTTTTGGT 1 CACATGTGTAGTACTAAGTGCAAGCTACTATGTGTAAAAGATAGTTTTGGT * * 36098398 CACAAGTGTGGTAC 1 CACATGTGTAGTAC 36098412 CATGTGAAGG Statistics Matches: 129, Mismatches: 35, Indels: 5 0.76 0.21 0.03 Matches are distributed among these distances: 50 37 0.29 51 62 0.48 52 30 0.23 ACGTcount: A:0.26, C:0.17, G:0.25, T:0.33 Consensus pattern (51 bp): CACATGTGTAGTACTAAGTGCAAGCTACTATGTGTAAAAGATAGTTTTGGT Found at i:36102381 original size:46 final size:46 Alignment explanation

Indices: 36102329--36102419 Score: 166 Period size: 46 Copynumber: 2.0 Consensus size: 46 36102319 AGTAGCTACA 36102329 TAGGAATCAAATT-GCTAAAAGATAATATCTAATAATAATATCCTAT 1 TAGGAATCAAATTCG-TAAAAGATAATATCTAATAATAATATCCTAT 36102375 TAGGAATCAAATTCGTAAAAGATAATATCTAATAATAATATCCTA 1 TAGGAATCAAATTCGTAAAAGATAATATCTAATAATAATATCCTA 36102420 ACATTATTTT Statistics Matches: 44, Mismatches: 0, Indels: 2 0.96 0.00 0.04 Matches are distributed among these distances: 46 43 0.98 47 1 0.02 ACGTcount: A:0.48, C:0.11, G:0.09, T:0.32 Consensus pattern (46 bp): TAGGAATCAAATTCGTAAAAGATAATATCTAATAATAATATCCTAT Found at i:36103761 original size:16 final size:16 Alignment explanation

Indices: 36103728--36103761 Score: 50 Period size: 16 Copynumber: 2.1 Consensus size: 16 36103718 TAGTTGTTAT ** 36103728 TTGAGAACAACTCTTG 1 TTGAGAACAACTAATG 36103744 TTGAGAACAACTAATG 1 TTGAGAACAACTAATG 36103760 TT 1 TT 36103762 TAAAACGACT Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 16 16 1.00 ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32 Consensus pattern (16 bp): TTGAGAACAACTAATG Found at i:36105980 original size:24 final size:24 Alignment explanation

Indices: 36105948--36105998 Score: 93 Period size: 24 Copynumber: 2.1 Consensus size: 24 36105938 AGTTCTAGAC 36105948 ATTGTGTCAAAAAGAGCATATATA 1 ATTGTGTCAAAAAGAGCATATATA * 36105972 ATTGTGTCAAAAAGAGTATATATA 1 ATTGTGTCAAAAAGAGCATATATA 36105996 ATT 1 ATT 36105999 AGAACCTATA Statistics Matches: 26, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 24 26 1.00 ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33 Consensus pattern (24 bp): ATTGTGTCAAAAAGAGCATATATA Found at i:36106074 original size:25 final size:27 Alignment explanation

Indices: 36106018--36106088 Score: 89 Period size: 25 Copynumber: 2.8 Consensus size: 27 36106008 AATGAGATTG * 36106018 TTTAAAAAAAT-ATT-TTTTTAAATTT 1 TTTAAAAATATAATTATTTTTAAATTT 36106043 TTATAAAAATATAATTATTTTT-AA-TT 1 TT-TAAAAATATAATTATTTTTAAATTT 36106069 TTTAAAAATATAA-TATTTTT 1 TTTAAAAATATAATTATTTTT 36106089 CGTAATTCTT Statistics Matches: 42, Mismatches: 1, Indels: 7 0.84 0.02 0.14 Matches are distributed among these distances: 24 7 0.17 25 13 0.31 26 12 0.29 27 5 0.12 28 5 0.12 ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55 Consensus pattern (27 bp): TTTAAAAATATAATTATTTTTAAATTT Found at i:36106115 original size:11 final size:11 Alignment explanation

Indices: 36106099--36106136 Score: 53 Period size: 11 Copynumber: 3.5 Consensus size: 11 36106089 CGTAATTCTT 36106099 AATTTTTTTGA 1 AATTTTTTTGA 36106110 AATTTTTTT-A 1 AATTTTTTTGA 36106120 TAA-TTTTTTGA 1 -AATTTTTTTGA 36106131 AATTTT 1 AATTTT 36106137 ATAAAAATCT Statistics Matches: 24, Mismatches: 0, Indels: 6 0.80 0.00 0.20 Matches are distributed among these distances: 10 9 0.38 11 15 0.62 ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66 Consensus pattern (11 bp): AATTTTTTTGA Found at i:36106117 original size:10 final size:10 Alignment explanation

Indices: 36106102--36106136 Score: 52 Period size: 10 Copynumber: 3.4 Consensus size: 10 36106092 AATTCTTAAT 36106102 TTTTTTGAAA 1 TTTTTTGAAA * 36106112 TTTTTTTATAA 1 TTTTTTGA-AA 36106123 TTTTTTGAAA 1 TTTTTTGAAA 36106133 TTTT 1 TTTT 36106137 ATAAAAATCT Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 10 13 0.59 11 9 0.41 ACGTcount: A:0.26, C:0.00, G:0.06, T:0.69 Consensus pattern (10 bp): TTTTTTGAAA Found at i:36117709 original size:22 final size:22 Alignment explanation

Indices: 36117681--36117803 Score: 65 Period size: 22 Copynumber: 5.3 Consensus size: 22 36117671 ATGTGTATAT 36117681 ATGTGATAAGGCCGAATGGCCA 1 ATGTGATAAGGCCGAATGGCCA * * * 36117703 ATGTGATGAATG-TGAACAT-GCATA 1 ATGTGAT-AAGGCCG-A-ATGGC-CA * 36117727 TATGTGATAAGGCCGAATGGCCT 1 -ATGTGATAAGGCCGAATGGCCA * * * 36117750 ATGTGATGAATG-TGAACAT-GCATA 1 ATGTGAT-AAGGCCG-A-ATGGC-CA 36117774 TATGTGATAAGGCCGAATGGCCA 1 -ATGTGATAAGGCCGAATGGCCA 36117797 ATGTGAT 1 ATGTGAT 36117804 GAACGTGAGC Statistics Matches: 73, Mismatches: 14, Indels: 28 0.63 0.12 0.24 Matches are distributed among these distances: 22 23 0.32 23 17 0.23 24 17 0.23 25 16 0.22 ACGTcount: A:0.33, C:0.13, G:0.28, T:0.26 Consensus pattern (22 bp): ATGTGATAAGGCCGAATGGCCA Found at i:36117710 original size:47 final size:47 Alignment explanation

Indices: 36117656--36117887 Score: 358 Period size: 47 Copynumber: 5.0 Consensus size: 47 36117646 TTAGGATTTT ** * 36117656 ATGTGATGAATGTGAATGTGTATATATGTGATAAGGCCGAATGGCCA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA * 36117703 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCT 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA 36117750 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA * * * 36117797 ATGTGATGAACGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA * * * * 36117844 ATGTGGTGAATATGAACATGCATATATGTGGTAAAG-CGAATGGC 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGC 36117888 TAGTGTGAAA Statistics Matches: 170, Mismatches: 15, Indels: 1 0.91 0.08 0.01 Matches are distributed among these distances: 46 8 0.05 47 162 0.95 ACGTcount: A:0.32, C:0.12, G:0.29, T:0.27 Consensus pattern (47 bp): ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA Found at i:36117852 original size:25 final size:25 Alignment explanation

Indices: 36117777--36117852 Score: 63 Period size: 23 Copynumber: 3.2 Consensus size: 25 36117767 ATGCATATAT 36117777 GTGATAAGGCCGAATGGCCAATGTG 1 GTGATAAGGCCGAATGGCCAATGTG * * * * 36117802 ATGA-ACGTG-AGCAT-G-CATATGT- 1 GTGATAAG-GCCGAATGGCCA-ATGTG 36117824 GTGATAAGGCCGAATGGCCAATGTG 1 GTGATAAGGCCGAATGGCCAATGTG 36117849 GTGA 1 GTGA 36117853 ATATGAACAT Statistics Matches: 36, Mismatches: 8, Indels: 14 0.62 0.14 0.24 Matches are distributed among these distances: 22 6 0.17 23 10 0.28 24 10 0.28 25 10 0.28 ACGTcount: A:0.29, C:0.14, G:0.34, T:0.22 Consensus pattern (25 bp): GTGATAAGGCCGAATGGCCAATGTG Found at i:36118194 original size:37 final size:37 Alignment explanation

Indices: 36118049--36118193 Score: 236 Period size: 37 Copynumber: 3.9 Consensus size: 37 36118039 GGAAATATAT * 36118049 TCCGGGTGAGACCCGATGACTACGTGTGGAGATTATG 1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG * * 36118086 TCCGGGTAAGACCCGATGACTATGTGTGGAGAGTATG 1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG * 36118123 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG 1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG * * 36118160 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATT 1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT 36118194 TCGTCTGAGC Statistics Matches: 100, Mismatches: 8, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 37 100 1.00 ACGTcount: A:0.23, C:0.19, G:0.33, T:0.26 Consensus pattern (37 bp): TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG Found at i:36119535 original size:40 final size:40 Alignment explanation

Indices: 36119480--36119674 Score: 286 Period size: 40 Copynumber: 4.9 Consensus size: 40 36119470 GAGAATTGAG * 36119480 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTTCT 1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT * 36119520 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT 1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT * * * * 36119560 AGTGATGTATCCGGACTAAGTCTCGAAGAGCATTCGTGCT 1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT * * 36119600 AGTGATATATCCGGGCT-AATACCGAAGTGCATTCGTGCT 1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT * * 36119639 AGTGATATATCTGGACTAAAT-CCGAAGAGCATTCGT 1 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGT 36119675 CGGGCTAAGT Statistics Matches: 140, Mismatches: 14, Indels: 3 0.89 0.09 0.02 Matches are distributed among these distances: 39 47 0.34 40 93 0.66 ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27 Consensus pattern (40 bp): AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT Found at i:36119613 original size:80 final size:78 Alignment explanation

Indices: 36119480--36120175 Score: 720 Period size: 80 Copynumber: 8.9 Consensus size: 78 36119470 GAGAATTGAG * * * 36119480 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTTCTAGTGATATATCCGGGCTAAGTCCCG 1 AGTGATATATCCGGACTAAAT-CCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAA-TACCG 36119545 AAGAGCATTCGTGCT 64 AAGAGCATTCGTGCT * * 36119560 AGTGATGTATCCGGACTAAGTCTCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAATACCGA 1 AGTGATATATCCGGACTAAATC-CGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAATACCGA * 36119625 AGTGCATTCGTGCT 65 AGAGCATTCGTGCT * * * * * * 36119639 AGTGATATATCTGGACTAAATCCGAAGAGCATTCGT-C--GGGCTA-AGTCC---CGAAGAGC-A 1 AGTGATATATCCGGACTAAATCCGAAGAGCATTCGTGCTAGTGATATA-TCCGGGCTAATACCGA * * 36119696 TTAGTGC--TAGTG-- 65 --AGAGCATTCGTGCT * * **** *** * 36119708 A-TG-TAT-CCGGACTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAATCCCGA 1 AGTGATATATCCGGACTAAATCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCT-AATACCGA 36119770 AGAGCATTCGTGCT 65 AGAGCATTCGTGCT * * * * * 36119784 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTCCCG 1 AGTGATATATCCGGACTAAAT-CCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAA-TACCG 36119849 AAGAGCATTCGTGCT 64 AAGAGCATTCGTGCT * * * 36119864 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAATCCCG 1 AGTGATATATCCGGACTAAAT-CCGAAGAGCATTCGTGCTAGTGATATATCCGGGCT-AATACCG 36119929 AAGAGCATTCGTGCT 64 AAGAGCATTCGTGCT * * * * * 36119944 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTCCCG 1 AGTGATATATCCGGACTAAAT-CCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAA-TACCG 36120009 AAGAGCATTCGTGCT 64 AAGAGCATTCGTGCT * * * * * 36120024 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTCCCG 1 AGTGATATATCCGGACTAAAT-CCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAA-TACCG 36120089 AAGAGCATTCGTGCT 64 AAGAGCATTCGTGCT * * * * 36120104 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCG 1 AGTGATATATCCGGACTAAAT-CCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAA-TACCG 36120169 AAGAGCA 64 AAGAGCA 36120176 ATCATGCTGG Statistics Matches: 538, Mismatches: 54, Indels: 48 0.84 0.08 0.08 Matches are distributed among these distances: 66 18 0.03 67 4 0.01 68 2 0.00 69 8 0.01 70 1 0.00 71 5 0.01 72 10 0.02 73 8 0.01 74 6 0.01 75 7 0.01 76 1 0.00 77 3 0.01 78 17 0.03 79 45 0.08 80 401 0.75 81 2 0.00 ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25 Consensus pattern (78 bp): AGTGATATATCCGGACTAAATCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAATACCGAA GAGCATTCGTGCT Found at i:36119720 original size:65 final size:65 Alignment explanation

Indices: 36119611--36119740 Score: 190 Period size: 65 Copynumber: 2.0 Consensus size: 65 36119601 GTGATATATC * * * 36119611 CGGGCTAATACCGAAGTGCATTCGTGCTAGTGATATATCTGGACTAAAT-CCGAAGAGCATTCGT 1 CGGGCTAATACCGAAGAGCATTAGTGCTAGTGATATATCCGGACTAAATCCCGAAGAGCATTCGT * * * 36119675 CGGGCTAAGTCCCGAAGAGCATTAGTGCTAGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCG 1 CGGGCTAA-TACCGAAGAGCATTAGTGCTAGTGATATATCCGGACTAAATCCCGAAGAGCATTCG 36119740 T 65 T 36119741 GCTAGTGATA Statistics Matches: 58, Mismatches: 6, Indels: 2 0.88 0.09 0.03 Matches are distributed among these distances: 64 8 0.14 65 35 0.60 66 15 0.26 ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25 Consensus pattern (65 bp): CGGGCTAATACCGAAGAGCATTAGTGCTAGTGATATATCCGGACTAAATCCCGAAGAGCATTCGT Found at i:36119734 original size:40 final size:40 Alignment explanation

Indices: 36119679--36120175 Score: 886 Period size: 40 Copynumber: 12.4 Consensus size: 40 36119669 ATTCGTCGGG * 36119679 CTAAGTCCCGAAGAGCATTAGTGCTAGTGATGTATCCGGA 1 CTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGA * * 36119719 CTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGG 1 CTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGA * * * 36119759 CTAAATCCCGAAGAGCATTCGTGCTAGTGATATATCCGGG 1 CTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGA 36119799 CTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGA 1 CTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGA 36119839 CTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGA 1 CTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGA * * 36119879 CTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGG 1 CTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGA * * * 36119919 CTAAATCCCGAAGAGCATTCGTGCTAGTGATATATCCGGG 1 CTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGA 36119959 CTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGA 1 CTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGA 36119999 CTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGA 1 CTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGA 36120039 CTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGA 1 CTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGA 36120079 CTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGA 1 CTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGA * 36120119 CTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGG 1 CTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGA 36120159 CTAAGTCCCGAAGAGCA 1 CTAAGTCCCGAAGAGCA 36120176 ATCATGCTGG Statistics Matches: 443, Mismatches: 14, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 40 443 1.00 ACGTcount: A:0.26, C:0.23, G:0.27, T:0.25 Consensus pattern (40 bp): CTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGA Found at i:36123636 original size:47 final size:47 Alignment explanation

Indices: 36123533--36123857 Score: 501 Period size: 47 Copynumber: 7.0 Consensus size: 47 36123523 TTAGGATTTT ** * 36123533 ATGTGATGAATGT-AATGTGTATATATGTGATAAGGCCG-ATGGCCA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA 36123578 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA * 36123625 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGACCA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA * 36123672 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCT 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA ** 36123719 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCTAAATGGCCA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA * * * 36123766 ATGTGATGAACGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA * * * * * 36123813 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGTCGAATGGC 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGC 36123858 TAGTGTGAAA Statistics Matches: 256, Mismatches: 22, Indels: 2 0.91 0.08 0.01 Matches are distributed among these distances: 45 13 0.05 46 22 0.09 47 221 0.86 ACGTcount: A:0.33, C:0.12, G:0.28, T:0.27 Consensus pattern (47 bp): ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA Found at i:36124139 original size:72 final size:73 Alignment explanation

Indices: 36124022--36124162 Score: 239 Period size: 72 Copynumber: 1.9 Consensus size: 73 36124012 AAATATATTC * * 36124022 CGGGTGAGACCCGATGACTACGTGTGGAGATTATGTCCGGGTAAGACCCGATGAC-TAGTGTGGA 1 CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTCCGGGTAAGACCCGATAACTTAGTGTGGA 36124086 GATTATGT 66 GATTATGT * * 36124094 CGGGTAAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGTAAGACCCGATAACTTCGTGTGGA 1 CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTCCGGGTAAGACCCGATAACTTAGTGTGGA 36124159 GATT 66 GATT 36124163 TCGTCTGAGC Statistics Matches: 64, Mismatches: 4, Indels: 1 0.93 0.06 0.01 Matches are distributed among these distances: 72 52 0.81 73 12 0.19 ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26 Consensus pattern (73 bp): CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTCCGGGTAAGACCCGATAACTTAGTGTGGA GATTATGT Found at i:36124163 original size:37 final size:37 Alignment explanation

Indices: 36124020--36124162 Score: 236 Period size: 37 Copynumber: 3.9 Consensus size: 37 36124010 GGAAATATAT * 36124020 TCCGGGTGAGACCCGATGACTACGTGTGGAGATTATG 1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG 36124057 TCCGGGTAAGACCCGATGACTA-GTGTGGAGATTATG 1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG * 36124093 T-CGGGTAAGACCCGATGACTACGTGTGGAGATTTTG 1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG * * 36124129 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATT 1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT 36124163 TCGTCTGAGC Statistics Matches: 100, Mismatches: 4, Indels: 4 0.93 0.04 0.04 Matches are distributed among these distances: 35 20 0.20 36 29 0.29 37 51 0.51 ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26 Consensus pattern (37 bp): TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG Found at i:36129412 original size:28 final size:29 Alignment explanation

Indices: 36129372--36129441 Score: 108 Period size: 29 Copynumber: 2.4 Consensus size: 29 36129362 AATTGTACAA * 36129372 CACTAAGTGTGCGAGTTTG-AT-TATATAG 1 CACTAAGTGTGCGAG-CTGAATGTATATAG 36129400 CACTAAGTGTGCGAGCTGAATGTATATAG 1 CACTAAGTGTGCGAGCTGAATGTATATAG 36129429 CACTAAGTGTGCG 1 CACTAAGTGTGCG 36129442 GATTCACTAT Statistics Matches: 39, Mismatches: 1, Indels: 3 0.91 0.02 0.07 Matches are distributed among these distances: 27 2 0.05 28 17 0.44 29 20 0.51 ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30 Consensus pattern (29 bp): CACTAAGTGTGCGAGCTGAATGTATATAG Found at i:36133633 original size:40 final size:40 Alignment explanation

Indices: 36133588--36133755 Score: 158 Period size: 40 Copynumber: 4.2 Consensus size: 40 36133578 CGGAATATAA 36133588 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TAGCACAAATGCCTTCGGGTCTTAGC * *** * * 36133628 CCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC * * * * 36133668 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC *** * * * * * 36133708 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC 1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC 36133748 CCGGATAT 1 CCGGATAT 36133756 CATTCAATTT Statistics Matches: 102, Mismatches: 25, Indels: 2 0.79 0.19 0.02 Matches are distributed among these distances: 39 1 0.01 40 101 0.99 ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26 Consensus pattern (40 bp): CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC Found at i:36133738 original size:80 final size:80 Alignment explanation

Indices: 36133604--36133753 Score: 205 Period size: 80 Copynumber: 1.9 Consensus size: 80 36133594 ATAACCACGT * * 36133604 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGCC 1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGGCTTAGCC 36133669 CGGATGTAGCCACTA 66 CGGATGTAGCCACTA * * * * * 36133684 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGGCTTAG 1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTC-GCACGAA-TGCCTTCGGGGCTTAG 36133747 CCCGGAT 64 CCCGGAT 36133754 ATCATTCAAT Statistics Matches: 61, Mismatches: 7, Indels: 4 0.85 0.10 0.06 Matches are distributed among these distances: 79 3 0.05 80 58 0.95 ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27 Consensus pattern (80 bp): GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGGCTTAGCC CGGATGTAGCCACTA Found at i:36141630 original size:40 final size:40 Alignment explanation

Indices: 36141585--36141752 Score: 158 Period size: 40 Copynumber: 4.2 Consensus size: 40 36141575 CGGAATATAA 36141585 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TAGCACAAATGCCTTCGGGTCTTAGC * *** * * 36141625 CCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC * * * * 36141665 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC *** * * * * * 36141705 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC 1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC 36141745 CCGGATAT 1 CCGGATAT 36141753 CATTCAATTT Statistics Matches: 102, Mismatches: 25, Indels: 2 0.79 0.19 0.02 Matches are distributed among these distances: 39 1 0.01 40 101 0.99 ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26 Consensus pattern (40 bp): CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC Found at i:36141735 original size:80 final size:80 Alignment explanation

Indices: 36141601--36141750 Score: 205 Period size: 80 Copynumber: 1.9 Consensus size: 80 36141591 ATAACCACGT * * 36141601 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGCC 1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGGCTTAGCC 36141666 CGGATGTAGCCACTA 66 CGGATGTAGCCACTA * * * * * 36141681 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGGCTTAG 1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTC-GCACGAA-TGCCTTCGGGGCTTAG 36141744 CCCGGAT 64 CCCGGAT 36141751 ATCATTCAAT Statistics Matches: 61, Mismatches: 7, Indels: 4 0.85 0.10 0.06 Matches are distributed among these distances: 79 3 0.05 80 58 0.95 ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27 Consensus pattern (80 bp): GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGGCTTAGCC CGGATGTAGCCACTA Found at i:36147781 original size:48 final size:48 Alignment explanation

Indices: 36147706--36147933 Score: 263 Period size: 48 Copynumber: 4.9 Consensus size: 48 36147696 CACATTGTAG * * * * * 36147706 GATGCCAATGCCATATCCCGGATATGGTCCTACATGAGATCACATATC 1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC * 36147754 GATGCCAATGCCATGTCCTAGACATGGTCTTACATGGGATCACATATC 1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC * * 36147802 GATTCCAATGCCATGTCCCAGACATGATCTTACATGGGATCACATATC 1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC * ** * 36147850 GATGCCAAT---A-G-CCCAG-CTATGGTCTTACACGAAATTACATATC 1 GATGCCAATGCCATGTCCCAGAC-ATGGTCTTACATGGGATCACATATC * * 36147893 GATGCCTAA-GCCATGTCCTAGATATGGTCTTACATGGGATC 1 GATGCC-AATGCCATGTCCCAGACATGGTCTTACATGGGATC 36147934 GCACATAACC Statistics Matches: 151, Mismatches: 21, Indels: 16 0.80 0.11 0.09 Matches are distributed among these distances: 42 1 0.01 43 31 0.21 44 3 0.02 45 1 0.01 46 1 0.01 47 1 0.01 48 113 0.75 ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27 Consensus pattern (48 bp): GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC Found at i:36147924 original size:91 final size:94 Alignment explanation

Indices: 36147706--36147933 Score: 268 Period size: 91 Copynumber: 2.4 Consensus size: 94 36147696 CACATTGTAG * * * * 36147706 GATGCCAATGCCATATCCCGGATATGGTCCTACATGAGATCACATATCGATGCCAATGCCATGTC 1 GATGCCAATGCCATGTCCCAGATATGGTCTTACATGGGATCACATATCGATGCCAAT--CATGTC * * ** 36147771 CTAGACATGGTCTTACATGGGATCACATATC 64 CCAGACATGGTCTTACACGAAATCACATATC * * * 36147802 GATTCCAATGCCATGTCCCAGACATGATCTTACATGGGATCACATATCGATGCCAAT-A-G-CCC 1 GATGCCAATGCCATGTCCCAGATATGGTCTTACATGGGATCACATATCGATGCCAATCATGTCCC * 36147864 AG-CTATGGTCTTACACGAAATTACATATC 66 AGAC-ATGGTCTTACACGAAATCACATATC * 36147893 GATGCCTAA-GCCATGTCCTAGATATGGTCTTACATGGGATC 1 GATGCC-AATGCCATGTCCCAGATATGGTCTTACATGGGATC 36147934 GCACATAACC Statistics Matches: 114, Mismatches: 16, Indels: 9 0.82 0.12 0.06 Matches are distributed among these distances: 90 1 0.01 91 59 0.52 92 3 0.03 93 1 0.01 96 50 0.44 ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27 Consensus pattern (94 bp): GATGCCAATGCCATGTCCCAGATATGGTCTTACATGGGATCACATATCGATGCCAATCATGTCCC AGACATGGTCTTACACGAAATCACATATC Found at i:36153525 original size:39 final size:39 Alignment explanation

Indices: 36153425--36153609 Score: 196 Period size: 40 Copynumber: 4.7 Consensus size: 39 36153415 TCGAATGATG * * * * 36153425 TCCGAGCTAAGTCCCAAAGGC-TTTGTGCTAAGTGACTATA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-A * * 36153465 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTGCTAA 1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA * 36153504 TCCCGGGCTAAG-CCCGAAGGCATTTGTGCGGGTTACTAAA 1 T-CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AA * * 36153544 TCCGGGTTAAGTCCCGAAGGCATTTATGCGAGTTACTATA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-A * * 36153584 ACCGGGCTATGTCCCGAAGGCATTTG 1 TCCGGGCTAAGTCCCGAAGGCATTTG 36153610 AATGAGTAGC Statistics Matches: 122, Mismatches: 16, Indels: 14 0.80 0.11 0.09 Matches are distributed among these distances: 39 34 0.28 40 80 0.66 41 8 0.07 ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26 Consensus pattern (39 bp): TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA Found at i:36153631 original size:79 final size:77 Alignment explanation

Indices: 36153459--36153642 Score: 183 Period size: 79 Copynumber: 2.3 Consensus size: 77 36153449 GTGCTAAGTG * * * * 36153459 ACTATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTGCTAATCCCGGGCTAAGCCCGAAGG 1 ACTATATCCGG-TTAAG-TCCGAAGGCATTTATGCGAGTTACTAATACCGGGCTAAGCCCGAAGG ** * 36153524 CATTTGTGCGGGTT 64 CATTTGAACGAGTT * * 36153538 ACTAAATCCGGGTTAAGTCCCGAAGGCATTTATGCGAGTTACT-ATAACCGGGCTATGTCCCGAA 1 ACTATATCC-GGTTAAGT-CCGAAGGCATTTATGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAA * 36153602 GGCATTTGAATGAG-T 62 GGCATTTGAACGAGTT * 36153617 AGCTATATCCGGTTAAATTCCGAAGG 1 A-CTATATCCGGTT-AAGTCCGAAGG 36153643 TACGTGATTT Statistics Matches: 87, Mismatches: 12, Indels: 12 0.78 0.11 0.11 Matches are distributed among these distances: 78 3 0.03 79 56 0.64 80 28 0.32 ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26 Consensus pattern (77 bp): ACTATATCCGGTTAAGTCCGAAGGCATTTATGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCA TTTGAACGAGTT Found at i:36156692 original size:46 final size:46 Alignment explanation

Indices: 36156637--36156817 Score: 242 Period size: 46 Copynumber: 3.9 Consensus size: 46 36156627 TAGGATGGTT 36156637 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC 1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC * * * 36156683 GAGCGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAAC 1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---C * 36156729 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC 1 GA-GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC * * * 36156776 GAACACCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG 1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG 36156818 GCGGGTTACA Statistics Matches: 117, Mismatches: 11, Indels: 14 0.82 0.08 0.10 Matches are distributed among these distances: 43 4 0.03 45 2 0.02 46 72 0.62 47 33 0.28 48 2 0.02 50 4 0.03 ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28 Consensus pattern (46 bp): GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC Found at i:36156798 original size:93 final size:93 Alignment explanation

Indices: 36156639--36156809 Score: 306 Period size: 93 Copynumber: 1.8 Consensus size: 93 36156629 GGATGGTTGA * ** 36156639 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAGT 1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT 36156704 TGAGTCCGAGTTCGTGAGATGTAACTAG 66 TGAGTCCGAGTTCGTGAGATGTAACTAG * 36156732 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAGCTCGTTGAGT 1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT 36156797 TGAGTCCGAGTTC 66 TGAGTCCGAGTTC 36156810 ACTTATGGGC Statistics Matches: 74, Mismatches: 4, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 93 74 1.00 ACGTcount: A:0.21, C:0.22, G:0.29, T:0.27 Consensus pattern (93 bp): GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT TGAGTCCGAGTTCGTGAGATGTAACTAG Found at i:36159787 original size:15 final size:15 Alignment explanation

Indices: 36159767--36159835 Score: 84 Period size: 15 Copynumber: 4.6 Consensus size: 15 36159757 GTATCTTGGG 36159767 TTTCTTTATCCTGGA 1 TTTCTTTATCCTGGA * * 36159782 TCTCTTTATTCTGGA 1 TTTCTTTATCCTGGA * * 36159797 TTTCTTTATTCTGGG 1 TTTCTTTATCCTGGA * * 36159812 TTTCTCTATCTTGGA 1 TTTCTTTATCCTGGA 36159827 TTTCTTTAT 1 TTTCTTTAT 36159836 TCGGTTTTCT Statistics Matches: 45, Mismatches: 9, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 15 45 1.00 ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58 Consensus pattern (15 bp): TTTCTTTATCCTGGA Found at i:36159836 original size:30 final size:30 Alignment explanation

Indices: 36159758--36159845 Score: 99 Period size: 30 Copynumber: 3.0 Consensus size: 30 36159748 CATAGTATCG * * * * 36159758 TATCTTGGGTTTCTTTATCCTGGATCTCTT 1 TATCTTGGATTTCTTTATTCTGGATTTCTC * 36159788 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC 1 TATCT-TGGATTTCTTTATTCTGGATTTCTC * 36159818 TATCTTGGATTTCTTTATTC-GGTTTTCT 1 TATCTTGGATTTCTTTATTCTGGATTTCT 36159846 TGTTATCTTT Statistics Matches: 50, Mismatches: 6, Indels: 5 0.82 0.10 0.08 Matches are distributed among these distances: 29 8 0.16 30 41 0.82 31 1 0.02 ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57 Consensus pattern (30 bp): TATCTTGGATTTCTTTATTCTGGATTTCTC Found at i:36162268 original size:46 final size:46 Alignment explanation

Indices: 36162213--36162393 Score: 233 Period size: 46 Copynumber: 3.9 Consensus size: 46 36162203 TAGGATGGTT 36162213 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC 1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC * * * 36162259 GAGCGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAAC 1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---C * 36162305 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC 1 GA-GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC * ** * 36162352 GAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG 1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG 36162394 GCGGGTTACA Statistics Matches: 116, Mismatches: 12, Indels: 14 0.82 0.08 0.10 Matches are distributed among these distances: 43 4 0.03 45 2 0.02 46 71 0.61 47 33 0.28 48 2 0.02 50 4 0.03 ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28 Consensus pattern (46 bp): GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC Found at i:36162374 original size:93 final size:93 Alignment explanation

Indices: 36162215--36162385 Score: 315 Period size: 93 Copynumber: 1.8 Consensus size: 93 36162205 GGATGGTTGA * * 36162215 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAGT 1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT 36162280 TGAGTCCGAGTTCGTGAGATGTAACTAG 66 TGAGTCCGAGTTCGTGAGATGTAACTAG * 36162308 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT 1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT 36162373 TGAGTCCGAGTTC 66 TGAGTCCGAGTTC 36162386 ACTTATGGGC Statistics Matches: 75, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 93 75 1.00 ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27 Consensus pattern (93 bp): GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT TGAGTCCGAGTTCGTGAGATGTAACTAG Found at i:36171866 original size:40 final size:40 Alignment explanation

Indices: 36171782--36171966 Score: 227 Period size: 40 Copynumber: 4.7 Consensus size: 40 36171772 TCGAATGATG * * 36171782 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT * 36171821 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT 1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT * * 36171862 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT * 36171901 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT * * 36171940 AACCGGGCTATGTCCCGAAGGCATTTG 1 -TCCGGGCTAAGTCCCGAAGGCATTTG 36171967 AACGAGTAGC Statistics Matches: 127, Mismatches: 12, Indels: 12 0.84 0.08 0.08 Matches are distributed among these distances: 39 36 0.28 40 81 0.64 41 10 0.08 ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26 Consensus pattern (40 bp): TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT Found at i:36171918 original size:79 final size:81 Alignment explanation

Indices: 36171782--36171964 Score: 241 Period size: 79 Copynumber: 2.3 Consensus size: 81 36171772 TCGAATGATG * * 36171782 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT 1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATT 36171846 TGTGCGAGTTACTA-A 66 TGTGCGAGTTACTATA * * ** 36171861 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA 1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGAT-CCGAAGGCA 36171923 TTTGTGCGAGTTACTATA 64 TTTGTGCGAGTTACTATA * * 36171941 ACCGGGCTATGTCCCGAAGGCATT 1 TCCGGGCTAAGTCCCGAAGGCATT 36171965 TGAACGAGTA Statistics Matches: 91, Mismatches: 8, Indels: 8 0.85 0.07 0.07 Matches are distributed among these distances: 78 1 0.01 79 60 0.66 80 30 0.33 ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26 Consensus pattern (81 bp): TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATT TGTGCGAGTTACTATA Found at i:36171988 original size:79 final size:79 Alignment explanation

Indices: 36171783--36171998 Score: 239 Period size: 79 Copynumber: 2.7 Consensus size: 79 36171773 CGAATGATGT * * 36171783 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGT-GACTATATCCGGACTAAGATCCGAAGGCATT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTAG-CTATATCCGG-TTAAGATCCGAAGGCATT * 36171846 TGTGCGAGTTACTAATT 63 TGTGCGAGTTACTAATA * * 36171863 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTA-CTAAATCCGGGTTAAG-TCCCGAAGGCATT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TAGCTATATCC-GGTTAAGAT-CCGAAGGCATT 36171925 TGTGCGAGTTACT-ATAA 63 TGTGCGAGTTACTAAT-A * ** * 36171942 CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATATCCGGTTAA-ATTCGAAGG 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGTTAAGATCCGAAGG 36171999 TACGTGATTC Statistics Matches: 116, Mismatches: 11, Indels: 20 0.79 0.07 0.14 Matches are distributed among these distances: 78 9 0.08 79 64 0.55 80 43 0.37 ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25 Consensus pattern (79 bp): CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGTTAAGATCCGAAGGCATTTGT GCGAGTTACTAATA Found at i:36177275 original size:41 final size:41 Alignment explanation

Indices: 36177230--36177347 Score: 107 Period size: 41 Copynumber: 3.1 Consensus size: 41 36177220 TGAAAGATAA 36177230 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC 1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC * * * * 36177271 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGACA-A 1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC 36177301 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC 1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC 36177342 ATGTAG 1 ATGTAG 36177348 ACAAGAGAGC Statistics Matches: 56, Mismatches: 8, Indels: 26 0.62 0.09 0.29 Matches are distributed among these distances: 29 1 0.02 30 8 0.14 31 10 0.18 32 1 0.02 33 3 0.05 34 1 0.02 35 1 0.02 36 1 0.02 37 1 0.02 38 3 0.05 39 1 0.02 40 10 0.18 41 14 0.25 42 1 0.02 ACGTcount: A:0.32, C:0.19, G:0.29, T:0.20 Consensus pattern (41 bp): ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC Found at i:36177286 original size:71 final size:71 Alignment explanation

Indices: 36177198--36177361 Score: 319 Period size: 71 Copynumber: 2.3 Consensus size: 71 36177188 GAGATGTATC * 36177198 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 1 CCATGTAGACAAGAGAGCTACGTGAAAGACAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 36177263 AGGACA 66 AGGACA 36177269 CCATGTAGACAAGAGAGCTACGTGAAAGACAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 1 CCATGTAGACAAGAGAGCTACGTGAAAGACAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 36177334 AGGACA 66 AGGACA 36177340 CCATGTAGACAAGAGAGCTACG 1 CCATGTAGACAAGAGAGCTACG 36177362 AGACAAATCG Statistics Matches: 92, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 71 92 1.00 ACGTcount: A:0.35, C:0.18, G:0.28, T:0.18 Consensus pattern (71 bp): CCATGTAGACAAGAGAGCTACGTGAAAGACAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA AGGACA Found at i:36182221 original size:40 final size:39 Alignment explanation

Indices: 36182135--36182315 Score: 154 Period size: 40 Copynumber: 4.5 Consensus size: 39 36182125 ATGATGTCCG * * * 36182135 GGCTAAGTCCTGAAGGC-TTTGTGCTAAGTGT-CTATATCC- 1 GGCTAAGTCC-AAAGGCATTTGTGC-GAGT-TACTAAATCCA * * 36182174 GGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAATTCCA 1 GG-CTAAG-TCCAAAGGCATTTGTGCGAGTTACTAAATCCA * * * 36182215 GGCTAAGCCCAAAGGCATTGGTGCGAGTTACTAAATCCG 1 GGCTAAGTCCAAAGGCATTTGTGCGAGTTACTAAATCCA * * 36182254 GGTTAAGTCCCAAAGGCATTTGTGCGAGTTACTATAA-CCG 1 GGCTAAGT-CCAAAGGCATTTGTGCGAGTTACTA-AATCCA * * 36182294 GGCTATGTCCCGAAGGCATTTG 1 GGCTAAGT-CCAAAGGCATTTG 36182316 AATGAGTAGC Statistics Matches: 121, Mismatches: 14, Indels: 13 0.82 0.09 0.09 Matches are distributed among these distances: 39 36 0.30 40 71 0.59 41 14 0.12 ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27 Consensus pattern (39 bp): GGCTAAGTCCAAAGGCATTTGTGCGAGTTACTAAATCCA Found at i:36182232 original size:39 final size:40 Alignment explanation

Indices: 36182187--36182315 Score: 172 Period size: 40 Copynumber: 3.2 Consensus size: 40 36182177 CTAAGATCCG * 36182187 AAGGCATTTGTGCGAGTTACTAATTCCAGGCTAAG-CCCA 1 AAGGCATTTGTGCGAGTTACTAAATCCAGGCTAAGTCCCA * * * 36182226 AAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCA 1 AAGGCATTTGTGCGAGTTACTAAATCCAGGCTAAGTCCCA * * * 36182266 AAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCG 1 AAGGCATTTGTGCGAGTTACTA-AATCCAGGCTAAGTCCCA 36182306 AAGGCATTTG 1 AAGGCATTTG 36182316 AATGAGTAGC Statistics Matches: 80, Mismatches: 8, Indels: 3 0.88 0.09 0.03 Matches are distributed among these distances: 39 31 0.39 40 47 0.59 41 2 0.03 ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26 Consensus pattern (40 bp): AAGGCATTTGTGCGAGTTACTAAATCCAGGCTAAGTCCCA Found at i:36182337 original size:79 final size:79 Alignment explanation

Indices: 36182187--36182338 Score: 175 Period size: 79 Copynumber: 1.9 Consensus size: 79 36182177 CTAAGATCCG * ** 36182187 AAGGCATTTGTGCGAGTTACTAATTCCAGGCTAAGCCCAAAGGCATTGGTGCGAGTTACTAAATC 1 AAGGCATTTGTGCGAGTTACTAATACCAGGCTAAGCCCAAAGGCATTGGAACGAGTTACTAAATC 36182252 CGGGTTAAGTCCCA 66 CGGGTTAAGTCCCA * * * * * * 36182266 AAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAATGAG-TAGCTAT 1 AAGGCATTTGTGCGAGTTACTAAT-ACCAGGCTAAG-CCCAAAGGCATTGGAACGAGTTA-CTAA 36182329 ATCC-GGTTAA 63 ATCCGGGTTAA 36182339 ATTCTGAAGG Statistics Matches: 61, Mismatches: 9, Indels: 6 0.80 0.12 0.08 Matches are distributed among these distances: 78 2 0.03 79 37 0.61 80 22 0.36 ACGTcount: A:0.28, C:0.20, G:0.26, T:0.27 Consensus pattern (79 bp): AAGGCATTTGTGCGAGTTACTAATACCAGGCTAAGCCCAAAGGCATTGGAACGAGTTACTAAATC CGGGTTAAGTCCCA Found at i:36186664 original size:18 final size:15 Alignment explanation

Indices: 36186625--36186656 Score: 64 Period size: 15 Copynumber: 2.1 Consensus size: 15 36186615 AATTAAACTA 36186625 AATGCAATGATCCCT 1 AATGCAATGATCCCT 36186640 AATGCAATGATCCCT 1 AATGCAATGATCCCT 36186655 AA 1 AA 36186657 GTATGCAAAC Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 17 1.00 ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25 Consensus pattern (15 bp): AATGCAATGATCCCT Found at i:36188693 original size:12 final size:12 Alignment explanation

Indices: 36188676--36188700 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 36188666 CATAAGCGTA 36188676 AATGGAAGGAGG 1 AATGGAAGGAGG 36188688 AATGGAAGGAGG 1 AATGGAAGGAGG 36188700 A 1 A 36188701 TCTTGTGCTT 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:0.44, C:0.00, G:0.48, T:0.08 Consensus pattern (12 bp): AATGGAAGGAGG Found at i:36191589 original size:26 final size:26 Alignment explanation

Indices: 36191542--36191592 Score: 68 Period size: 26 Copynumber: 2.0 Consensus size: 26 36191532 CTCGCTGCAA * 36191542 TCTGGTGGCTCGCCACATATATCTGT 1 TCTGGTGACTCGCCACATATATCTGT * 36191568 TCTGGTGACTTCGTCACA-ATATCTG 1 TCTGGTGAC-TCGCCACATATATCTG 36191593 GCAGCCTCGC Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 26 15 0.68 27 7 0.32 ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35 Consensus pattern (26 bp): TCTGGTGACTCGCCACATATATCTGT Found at i:36192936 original size:26 final size:25 Alignment explanation

Indices: 36192907--36192955 Score: 71 Period size: 26 Copynumber: 1.9 Consensus size: 25 36192897 ACATTCTCTC * 36192907 GAGCCATATATCAGGAATGCTTATAA 1 GAGCCATATAACAGGAA-GCTTATAA * 36192933 GAGCCATGTAACAGGAAGCTTAT 1 GAGCCATATAACAGGAAGCTTAT 36192956 CCGAGCTAAA Statistics Matches: 21, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 25 6 0.29 26 15 0.71 ACGTcount: A:0.37, C:0.16, G:0.22, T:0.24 Consensus pattern (25 bp): GAGCCATATAACAGGAAGCTTATAA Found at i:36192961 original size:25 final size:26 Alignment explanation

Indices: 36192906--36192961 Score: 69 Period size: 26 Copynumber: 2.2 Consensus size: 26 36192896 AACATTCTCT * 36192906 CGAGCCATATATCAGGAATGCTTATA 1 CGAGCCATATAACAGGAATGCTTATA * * * 36192932 AGAGCCATGTAACAGGAA-GCTTATC 1 CGAGCCATATAACAGGAATGCTTATA 36192957 CGAGC 1 CGAGC 36192962 TAAATCAGGA Statistics Matches: 25, Mismatches: 5, Indels: 1 0.81 0.16 0.03 Matches are distributed among these distances: 25 10 0.40 26 15 0.60 ACGTcount: A:0.34, C:0.21, G:0.23, T:0.21 Consensus pattern (26 bp): CGAGCCATATAACAGGAATGCTTATA Found at i:36193205 original size:65 final size:65 Alignment explanation

Indices: 36193114--36193263 Score: 185 Period size: 65 Copynumber: 2.3 Consensus size: 65 36193104 TGAGCCATAT * * * * * * 36193114 CAGGACACTCATAAAGAGCTATGTTTGTGTCCACAATATATGTAGGATCACAACCGATC-GCATA 1 CAGGACGCTCACAAAGAGCTACGTTTGTGTCCACAACATATATAGGATCACAACCGATCAACA-A 36193178 A 65 A * * ** 36193179 CAGGATGCTCACAAAGAGTTACGTTTGTGTCTGCAACATATATAGGATCACAACCGATCAACAAA 1 CAGGACGCTCACAAAGAGCTACGTTTGTGTCCACAACATATATAGGATCACAACCGATCAACAAA * 36193244 CAGGACGCTTACAAAGAGCT 1 CAGGACGCTCACAAAGAGCT 36193264 GCACTAGTCA Statistics Matches: 71, Mismatches: 13, Indels: 2 0.83 0.15 0.02 Matches are distributed among these distances: 65 69 0.97 66 2 0.03 ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23 Consensus pattern (65 bp): CAGGACGCTCACAAAGAGCTACGTTTGTGTCCACAACATATATAGGATCACAACCGATCAACAAA Found at i:36202892 original size:39 final size:40 Alignment explanation

Indices: 36202779--36202934 Score: 181 Period size: 39 Copynumber: 4.0 Consensus size: 40 36202769 CTCGTTCAAA * * ** * * 36202779 TGCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAA 1 TGCCTTCGGGACTTAGCCCGGATATCATAACTCGCACAAT * * * 36202819 TGCCTTCGGGACTTAACCTGGATATCACAACTCGCACAAT 1 TGCCTTCGGGACTTAGCCCGGATATCATAACTCGCACAAT * * 36202859 TGCCTTCGGG-CTTAGCCCGGATATCATAGCTCGCACCAT 1 TGCCTTCGGGACTTAGCCCGGATATCATAACTCGCACAAT * * 36202898 TGCCTTCGGG-CTTAGCCCGGATATCACAATTCGCACA 1 TGCCTTCGGGACTTAGCCCGGATATCATAACTCGCACA 36202935 TTCATACACA Statistics Matches: 98, Mismatches: 18, Indels: 1 0.84 0.15 0.01 Matches are distributed among these distances: 39 57 0.58 40 41 0.42 ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24 Consensus pattern (40 bp): TGCCTTCGGGACTTAGCCCGGATATCATAACTCGCACAAT Found at i:36202894 original size:79 final size:79 Alignment explanation

Indices: 36202779--36202934 Score: 197 Period size: 79 Copynumber: 2.0 Consensus size: 79 36202769 CTCGTTCAAA * ** * 36202779 TGCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATGCCTTCGGGACTTAACCTGGATAT 1 TGCCTTCGGGACATAGCCCGGATATCATAACCCGCACAAATGCCTTCGGG-CTTAACCCGGATAT 36202844 CACAACTCGCACAAT 65 CACAACTCGCACAAT * * * * * * 36202859 TGCCTTCGGG-CTTAGCCCGGATATCATAGCTCGCACCATTGCCTTCGGGCTTAGCCCGGATATC 1 TGCCTTCGGGACATAGCCCGGATATCATAACCCGCACAAATGCCTTCGGGCTTAACCCGGATATC * 36202923 ACAATTCGCACA 66 ACAACTCGCACA 36202935 TTCATACACA Statistics Matches: 65, Mismatches: 11, Indels: 2 0.83 0.14 0.03 Matches are distributed among these distances: 78 24 0.37 79 31 0.48 80 10 0.15 ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24 Consensus pattern (79 bp): TGCCTTCGGGACATAGCCCGGATATCATAACCCGCACAAATGCCTTCGGGCTTAACCCGGATATC ACAACTCGCACAAT Found at i:36208807 original size:47 final size:46 Alignment explanation

Indices: 36208607--36208876 Score: 156 Period size: 47 Copynumber: 5.8 Consensus size: 46 36208597 GGAAAAGTTA * * * * 36208607 CCGATGCCATGTCCCAGACATGGTCTTATACTAGCTCTCGTATATACGT-G 1 CCGATG-CATGTCCCAGACAT-GTCTTACACTAGCACCCATA-AT-C-TCG * * * * * 36208657 CTGATGCATGACCTAGACATGTCTTACACTAGCA--CA-ACTCTTAG 1 CCGATGCATGTCCCAGACATGTCTTACACTAGCACCCATAATC-TCG * * * * * * ** 36208701 CCGATGCGTGTCCCAGACACGTTTTACACTGGCTA-TCATCATCGAGG 1 CCGATGCATGTCCCAGACATGTCTTACACTAGC-ACCCATAATC-TCG * ** * 36208748 CTGATGTGTGTCCCAGACATGTCTTACACTAGCACCCAT-CTCTCCG 1 CCGATGCATGTCCCAGACATGTCTTACACTAGCACCCATAATCT-CG * * * * * * 36208794 CCGATGCCATGTCCCAAACATGGTCTTATACTGGCACTCATAATGTGG 1 CCGATG-CATGTCCCAGACAT-GTCTTACACTAGCACCCATAATCTCG 36208842 CCGATGCATGTCCCAGACATGTCTTACACTAGCAC 1 CCGATGCATGTCCCAGACATGTCTTACACTAGCAC 36208877 ACAAGAAATT Statistics Matches: 169, Mismatches: 42, Indels: 22 0.73 0.18 0.09 Matches are distributed among these distances: 43 2 0.01 44 28 0.17 45 2 0.01 46 25 0.15 47 58 0.34 48 35 0.21 49 14 0.08 50 5 0.03 ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27 Consensus pattern (46 bp): CCGATGCATGTCCCAGACATGTCTTACACTAGCACCCATAATCTCG Found at i:36208863 original size:94 final size:93 Alignment explanation

Indices: 36208607--36208876 Score: 289 Period size: 94 Copynumber: 2.9 Consensus size: 93 36208597 GGAAAAGTTA * * * * * 36208607 CCGATGCCATGTCCCAGACATGGTCTTATACTAGCTCTCGTATATACGT-GCTGATGCATGACCT 1 CCGATGCCATGTCCCAGACATGGTCTTATACTGGCACTC--ATA-ATGTGGCTGATGCATGTCCC * 36208671 AGACATGTCTTACACTAGCA-CAACTCTTAG 63 AGACATGTCTTACACTAGCACCAACTCTCAG * * * * * * ** 36208701 CCGATG-CGTGTCCCAGACA-CGTTTTACACTGGCTA-TCATCATCGAGGCTGATGTGTGTCCCA 1 CCGATGCCATGTCCCAGACATGGTCTTATACTGGC-ACTCATAAT-GTGGCTGATGCATGTCCCA * * 36208763 GACATGTCTTACACTAGCACCCATCTCTCCG 64 GACATGTCTTACACTAGCA-CCAACTCTCAG * * 36208794 CCGATGCCATGTCCCAAACATGGTCTTATACTGGCACTCATAATGTGGCCGATGCATGTCCCAGA 1 CCGATGCCATGTCCCAGACATGGTCTTATACTGGCACTCATAATGTGGCTGATGCATGTCCCAGA 36208859 CATGTCTTACACTAGCAC 66 CATGTCTTACACTAGCAC 36208877 ACAAGAAATT Statistics Matches: 142, Mismatches: 26, Indels: 17 0.77 0.14 0.09 Matches are distributed among these distances: 89 1 0.01 90 3 0.02 91 31 0.22 92 12 0.08 93 26 0.18 94 52 0.37 95 17 0.12 ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27 Consensus pattern (93 bp): CCGATGCCATGTCCCAGACATGGTCTTATACTGGCACTCATAATGTGGCTGATGCATGTCCCAGA CATGTCTTACACTAGCACCAACTCTCAG Found at i:36210654 original size:33 final size:33 Alignment explanation

Indices: 36210617--36210693 Score: 145 Period size: 33 Copynumber: 2.3 Consensus size: 33 36210607 GATTGGTAGA * 36210617 TGAAATTCTTATTGTACGAACTTACTAAGCATT 1 TGAAATGCTTATTGTACGAACTTACTAAGCATT 36210650 TGAAATGCTTATTGTACGAACTTACTAAGCATT 1 TGAAATGCTTATTGTACGAACTTACTAAGCATT 36210683 TGAAATGCTTA 1 TGAAATGCTTA 36210694 CTCAATTTTC Statistics Matches: 43, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 33 43 1.00 ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38 Consensus pattern (33 bp): TGAAATGCTTATTGTACGAACTTACTAAGCATT Found at i:36219979 original size:40 final size:39 Alignment explanation

Indices: 36219814--36219997 Score: 138 Period size: 40 Copynumber: 4.6 Consensus size: 39 36219804 AAATTGAATG * * * 36219814 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T 1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT * * * * * * 36219854 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T * * * * * 36219894 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT * 36219934 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT * * * 36219973 GATATCCGGGTTAAGTCCCGTAGGC 1 -ATATCCGGGCTAAGACCCGAAGGC 36219998 CTTGGTGCGG Statistics Matches: 113, Mismatches: 26, Indels: 10 0.76 0.17 0.07 Matches are distributed among these distances: 37 4 0.04 38 2 0.02 39 3 0.03 40 104 0.92 ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22 Consensus pattern (39 bp): ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT Found at i:36220022 original size:80 final size:81 Alignment explanation

Indices: 36219854--36220042 Score: 186 Period size: 80 Copynumber: 2.4 Consensus size: 81 36219844 GCTGGAAATT * * * * 36219854 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA 1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA * 36219919 TTCGTGCGAGTCATTC 66 TTCGTGCGAGTCATCC * * * * * * 36219935 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC 1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC * * * * 36219998 CTTGGTGCGGGTTA-CC 65 ATTCGTGCGAGTCATCC * * * 36220014 ATAACCGGGCTATGTCCCGAAGGCGATTG 1 ATAACCGGGCTAAGACCCGAAGGCAATTG 36220043 ATCGAGTAGC Statistics Matches: 86, Mismatches: 20, Indels: 5 0.77 0.18 0.05 Matches are distributed among these distances: 79 2 0.02 80 84 0.98 ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23 Consensus pattern (81 bp): ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA TTCGTGCGAGTCATCC Found at i:36224640 original size:40 final size:39 Alignment explanation

Indices: 36224475--36224658 Score: 138 Period size: 40 Copynumber: 4.6 Consensus size: 39 36224465 AAATTGAATG * * * 36224475 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T 1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT * * * * * 36224515 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAATGGCT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T * * * * * 36224555 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT * * 36224595 CTATCCGGGCTAAGACCCAAAGGCATTTGTGCAAATCGT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT * * * 36224634 GATATCCGGGTTAAGTCCCGTAGGC 1 -ATATCCGGGCTAAGACCCGAAGGC 36224659 CTTGGTGCGG Statistics Matches: 111, Mismatches: 28, Indels: 10 0.74 0.19 0.07 Matches are distributed among these distances: 37 5 0.05 38 2 0.02 39 3 0.03 40 101 0.91 ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22 Consensus pattern (39 bp): ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT Found at i:36224641 original size:80 final size:80 Alignment explanation

Indices: 36224519--36224667 Score: 183 Period size: 80 Copynumber: 1.9 Consensus size: 80 36224509 GAAATTATAA * * * * 36224519 CCGGGTTAAGACCCGAAGGCAATTGTGCTAATGGCTACATCCGGGCTAAGACCCGAAGGCATTCG 1 CCGGGCTAAGACCCAAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCATTCG 36224584 TGCGAGTCATTCTAT 66 TGCGAGTCATTCTAT * * * * * * * 36224599 CCGGGCTAAGACCCAAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGCCTTG 1 CCGGGCTAAGACCCAAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGCATTC 36224663 GTGCG 65 GTGCG 36224668 GGTTACCATA Statistics Matches: 57, Mismatches: 11, Indels: 2 0.81 0.16 0.03 Matches are distributed among these distances: 79 1 0.02 80 56 0.98 ACGTcount: A:0.23, C:0.25, G:0.29, T:0.23 Consensus pattern (80 bp): CCGGGCTAAGACCCAAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCATTCG TGCGAGTCATTCTAT Found at i:36224683 original size:80 final size:81 Alignment explanation

Indices: 36224515--36224686 Score: 179 Period size: 80 Copynumber: 2.1 Consensus size: 81 36224505 GCTGGAAATT * * * * 36224515 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAATGGCTACATCCGGGCTAAGACCCGAAGGCA 1 ATAACCGGGCTAAGACCCAAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA * 36224580 TTCGTGCGAGTCATTC 66 TTCGTGCGAGTCATCC * * * * * * 36224596 -TATCCGGGCTAAGACCCAAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC 1 ATAACCGGGCTAAGACCCAAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC * * * * 36224659 CTTGGTGCGGGTTA-CC 65 ATTCGTGCGAGTCATCC 36224675 ATAACCGGGCTA 1 ATAACCGGGCTA 36224687 TGTCCCGAAG Statistics Matches: 73, Mismatches: 16, Indels: 5 0.78 0.17 0.05 Matches are distributed among these distances: 79 2 0.03 80 71 0.97 ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23 Consensus pattern (81 bp): ATAACCGGGCTAAGACCCAAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA TTCGTGCGAGTCATCC Found at i:36231934 original size:42 final size:40 Alignment explanation

Indices: 36231865--36231966 Score: 123 Period size: 42 Copynumber: 2.5 Consensus size: 40 36231855 AGCTTGGTCT * 36231865 CGAAGGGCTTTTGAGCCAGTCTAATAACCGAACTTAGTTT 1 CGAAGGGCTTTTGAGCCAGTCTAATAACCGAACTTAGTTC * * * * 36231905 TGAAGGGCTTTTTAGAGCCAGTGTCATAACCGGACTTAGTTC 1 CGAAGGGC-TTTT-GAGCCAGTCTAATAACCGAACTTAGTTC * * 36231947 CGAAGGGCCTTCGAGCCAGT 1 CGAAGGGCTTTTGAGCCAGT 36231967 AGTCTAATCC Statistics Matches: 52, Mismatches: 8, Indels: 4 0.81 0.12 0.06 Matches are distributed among these distances: 40 15 0.29 41 6 0.12 42 31 0.60 ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27 Consensus pattern (40 bp): CGAAGGGCTTTTGAGCCAGTCTAATAACCGAACTTAGTTC Found at i:36235366 original size:70 final size:71 Alignment explanation

Indices: 36235281--36235443 Score: 319 Period size: 70 Copynumber: 2.3 Consensus size: 71 36235271 CGATTTGTCT 36235281 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACA-TTAT 1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 36235345 CTTTCA 66 CTTTCA 36235351 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 36235416 CTTTCA 66 CTTTCA 36235422 CGTAGCTCTCTTGTCTACATGG 1 CGTAGCTCTCTTGTCTACATGG 36235444 GATACATCTC Statistics Matches: 92, Mismatches: 0, Indels: 1 0.99 0.00 0.01 Matches are distributed among these distances: 70 60 0.65 71 32 0.35 ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35 Consensus pattern (71 bp): CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT CTTTCA Found at i:36235481 original size:71 final size:69 Alignment explanation

Indices: 36235281--36235477 Score: 247 Period size: 70 Copynumber: 2.8 Consensus size: 69 36235271 CGATTTGTCT * * * * 36235281 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTATC 1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTATC 36235346 TTTCA 65 TTTCA * * * * 36235351 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACA-TTAT 36235416 CTTTCA 64 CTTTCA * * 36235422 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC 1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC 36235478 TACAGGGTGT Statistics Matches: 119, Mismatches: 6, Indels: 6 0.91 0.05 0.05 Matches are distributed among these distances: 68 22 0.18 69 1 0.01 70 61 0.51 71 35 0.29 ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34 Consensus pattern (69 bp): CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTATCT TTCA Found at i:36242472 original size:71 final size:71 Alignment explanation

Indices: 36242386--36242549 Score: 328 Period size: 71 Copynumber: 2.3 Consensus size: 71 36242376 CGATTTGTCT 36242386 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 36242451 CTTTCA 66 CTTTCA 36242457 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 36242522 CTTTCA 66 CTTTCA 36242528 CGTAGCTCTCTTGTCTACATGG 1 CGTAGCTCTCTTGTCTACATGG 36242550 GATACATCTC Statistics Matches: 93, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 71 93 1.00 ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35 Consensus pattern (71 bp): CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT CTTTCA Found at i:36242587 original size:71 final size:70 Alignment explanation

Indices: 36242386--36242583 Score: 258 Period size: 71 Copynumber: 2.8 Consensus size: 70 36242376 CGATTTGTCT * * * * 36242386 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT 36242451 CTTTCA 65 CTTTCA * * * * 36242457 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT 36242522 CTTTCA 65 CTTTCA * * 36242528 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC 1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC 36242584 TACAGGGTGT Statistics Matches: 120, Mismatches: 6, Indels: 5 0.92 0.05 0.04 Matches are distributed among these distances: 68 22 0.18 69 1 0.01 70 1 0.01 71 96 0.80 ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34 Consensus pattern (70 bp): CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC TTTCA Found at i:36249675 original size:41 final size:40 Alignment explanation

Indices: 36249605--36249752 Score: 158 Period size: 41 Copynumber: 3.6 Consensus size: 40 36249595 GAGCTTGGTC 36249605 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT 1 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAG-T ** * * 36249646 TCGAAGGTTTTTTAGAGCCAGTG-TCATAACCGGACTTAGT 1 TCGAAGGGCTTTT-GAGCCAGTGCTAATAACCGAACTTAGT * * * * 36249686 TCGAAGGGCCTTCGAGCCAGTAGTCTAAT--CCGAGCTTGGT 1 TCGAAGGGCTTTTGAGCCAGT-G-CTAATAACCGAACTTAGT 36249726 CTCGAAGGGCTTTTGAGCCAGTGCTAA 1 -TCGAAGGGCTTTTGAGCCAGTGCTAA 36249753 GAGTCAGACT Statistics Matches: 88, Mismatches: 14, Indels: 12 0.77 0.12 0.11 Matches are distributed among these distances: 39 12 0.14 40 20 0.23 41 44 0.50 42 12 0.14 ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28 Consensus pattern (40 bp): TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT Found at i:36251059 original size:17 final size:19 Alignment explanation

Indices: 36250982--36251052 Score: 114 Period size: 17 Copynumber: 3.9 Consensus size: 19 36250972 ATAATCTTCA 36250982 ATGATATGCAATCTTAGAT 1 ATGATATGCAATCTTAGAT 36251001 ATGATA--CAATCTTAGAT 1 ATGATATGCAATCTTAGAT 36251018 ATGAT-T-CAATCTTAGAT 1 ATGATATGCAATCTTAGAT 36251035 ATGATATGCAATCTTAGA 1 ATGATATGCAATCTTAGA 36251053 AGATATGATT Statistics Matches: 49, Mismatches: 0, Indels: 6 0.89 0.00 0.11 Matches are distributed among these distances: 17 32 0.65 18 1 0.02 19 16 0.33 ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37 Consensus pattern (19 bp): ATGATATGCAATCTTAGAT Found at i:36251078 original size:22 final size:22 Alignment explanation

Indices: 36250982--36251075 Score: 70 Period size: 17 Copynumber: 4.8 Consensus size: 22 36250972 ATAATCTTCA 36250982 ATGATATGCAATCTT---AGAT 1 ATGATATGCAATCTTAGAAGAT 36251001 ATGATA--CAATCTT---AGAT 1 ATGATATGCAATCTTAGAAGAT 36251018 ATGAT-T-CAATCTT---AGAT 1 ATGATATGCAATCTTAGAAGAT 36251035 ATGATATGCAATCTTAGAAGAT 1 ATGATATGCAATCTTAGAAGAT * * 36251057 ATGATTTTGTAATCTTAGA 1 ATGA-TATGCAATCTTAGA 36251076 GATTTAATTT Statistics Matches: 66, Mismatches: 2, Indels: 10 0.85 0.03 0.13 Matches are distributed among these distances: 17 32 0.48 18 1 0.02 19 13 0.20 22 8 0.12 23 12 0.18 ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38 Consensus pattern (22 bp): ATGATATGCAATCTTAGAAGAT Found at i:36251363 original size:17 final size:17 Alignment explanation

Indices: 36251339--36251373 Score: 52 Period size: 18 Copynumber: 2.0 Consensus size: 17 36251329 TGTTTCCCTG * 36251339 ATTTTTTTATATATTTTA 1 ATTTTTTAATA-ATTTTA 36251357 ATTTTTTAATAATTTTA 1 ATTTTTTAATAATTTTA 36251374 GTATCATATC Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 17 6 0.38 18 10 0.62 ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69 Consensus pattern (17 bp): ATTTTTTAATAATTTTA Found at i:36259584 original size:44 final size:44 Alignment explanation

Indices: 36259461--36259631 Score: 175 Period size: 44 Copynumber: 3.9 Consensus size: 44 36259451 ACTCTAAGAT * 36259461 GATTTGGCGTCTCTGTATTGTCAGAGAGTAGATCAAAGATAGTA 1 GATTTGGCGTCTCTGTATTGTCAGAGAGTAGATCGAAGATAGTA * * * 36259505 GATTTGACATCTCTGTATTGTCAGAGAGCAGATCGAAGATAGTA 1 GATTTGGCGTCTCTGTATTGTCAGAGAGTAGATCGAAGATAGTA * * * * * ** 36259549 GATTTGGTGTCTTTGTACTGTCAGAGAATAAATCGAAGA-AACA 1 GATTTGGCGTCTCTGTATTGTCAGAGAGTAGATCGAAGATAGTA * ** * 36259592 GATTTGGCATCTCCATATTCGAT-AGAGAGCAGATCGAAGA 1 GATTTGGCGTCTCTGTATT-G-TCAGAGAGTAGATCGAAGA 36259632 CATAGCAGAT Statistics Matches: 102, Mismatches: 23, Indels: 4 0.79 0.18 0.03 Matches are distributed among these distances: 43 15 0.15 44 86 0.84 45 1 0.01 ACGTcount: A:0.32, C:0.13, G:0.25, T:0.29 Consensus pattern (44 bp): GATTTGGCGTCTCTGTATTGTCAGAGAGTAGATCGAAGATAGTA Found at i:36259619 original size:88 final size:88 Alignment explanation

Indices: 36259461--36259631 Score: 211 Period size: 88 Copynumber: 1.9 Consensus size: 88 36259451 ACTCTAAGAT * * * ** ** 36259461 GATTTGGCGTCTCTGTATTGTCAGAGAGTAGATCAAAGATAGTAGATTTGACATCTCTGTATTGT 1 GATTTGGCGTCTCTGTACTGTCAGAGAATAAATCAAAGATAACAGATTTGACATCTCCATATTGT 36259526 CAGAGAGCAGATCGAAGATAGTA 66 CAGAGAGCAGATCGAAGATAGTA * * * * 36259549 GATTTGGTGTCTTTGTACTGTCAGAGAATAAATCGAAGA-AACAGATTTGGCATCTCCATATTCG 1 GATTTGGCGTCTCTGTACTGTCAGAGAATAAATCAAAGATAACAGATTTGACATCTCCATATT-G 36259613 AT-AGAGAGCAGATCGAAGA 65 -TCAGAGAGCAGATCGAAGA 36259632 CATAGCAGAT Statistics Matches: 70, Mismatches: 11, Indels: 4 0.82 0.13 0.05 Matches are distributed among these distances: 87 18 0.26 88 51 0.73 89 1 0.01 ACGTcount: A:0.32, C:0.13, G:0.25, T:0.29 Consensus pattern (88 bp): GATTTGGCGTCTCTGTACTGTCAGAGAATAAATCAAAGATAACAGATTTGACATCTCCATATTGT CAGAGAGCAGATCGAAGATAGTA Found at i:36259823 original size:44 final size:44 Alignment explanation

Indices: 36259769--36259912 Score: 164 Period size: 44 Copynumber: 3.3 Consensus size: 44 36259759 AATCTAAGAT * * 36259769 GATTTGGCGTCTCTGTATTGTTAGAGAGCAGATTAAAGATAGCA 1 GATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCAAAGATAGCA * * 36259813 GATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAGTA 1 GATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCAAAGATAGCA * * * * * * * * 36259857 AATTTGGTGTCTCTGTACTATCAGAGAACAAATCGAAGA-AACA 1 GATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCAAAGATAGCA * 36259900 GATTTGGCATCTC 1 GATTTGGCGTCTC 36259913 CATATTTGAC Statistics Matches: 85, Mismatches: 15, Indels: 1 0.84 0.15 0.01 Matches are distributed among these distances: 43 12 0.14 44 73 0.86 ACGTcount: A:0.31, C:0.15, G:0.25, T:0.30 Consensus pattern (44 bp): GATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCAAAGATAGCA Found at i:36259883 original size:308 final size:308 Alignment explanation

Indices: 36259319--36260123 Score: 1333 Period size: 308 Copynumber: 2.6 Consensus size: 308 36259309 GTAACAGGCT * * 36259319 GAAGACATAGCAGATCTAACCTTCGAATGTTTTTGCATCGAACCAGATCCT-AGATGATTTGGCA 1 GAAGACATAGCAGATCTAACCTTCGGATGTTTTTGCATCGAAGCAGAT-CTAAGATGATTTGGCA * * * 36259383 TCCTTGCATTTACAAGGAGCAGATTGAAGACATAGCATATTTGGCTTTCACGTGTTTACGCTGAA 65 TCCTTGCGTTTACAAGGAGCAGATCGAAGACATAGCAGATTTGGCTTTCACGTGTTTACGCTGAA * * * 36259448 GCAACTCTAAGATGATTTGGCGTCTCTGTATTGTCAGAGAGTAGATCAAAGATAGTAGATTTGAC 130 GCAAATCTAAGATGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCAAAGATAGCAGATTTGAC * * * * 36259513 ATCTCTGTATTGTCAGAGAGCAGATCGAAGATAGTAGATTTGGTGTCTTTGTACTGTCAGAGAAT 195 ATCTCTGTATTGTCAGAGAGCAGATCGAAGATAGTAAATTTGGTGTCTCTGTACTATCAGAGAAC * 36259578 AAATCGAAGAAACAGATTTGGCATCTCCATATTCGATAGAGAGCAGATC 260 AAATCGAAGAAACAGATTTGGCATCTCCATATTCGACAGAGAGCAGATC * 36259627 GAAGACATAGCAGATCTAACCTTCGGATGTTTTTGCATCAAAGCAGATCTAAGATGATTTGGCAT 1 GAAGACATAGCAGATCTAACCTTCGGATGTTTTTGCATCGAAGCAGATCTAAGATGATTTGGCAT * * * 36259692 CCTTGCGTTTACAAGGAGCAGATCGAAGACATAGCAGGTTTGGCTTTCACATGTTTACACTGAAG 66 CCTTGCGTTTACAAGGAGCAGATCGAAGACATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAG * * * * 36259757 CAAATCTAAGATGATTTGGCGTCTCTGTATTGTTAGAGAGCAGATTAAAGATAGCAGATTTGGCG 131 CAAATCTAAGATGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCAAAGATAGCAGATTTGACA 36259822 TCTCTGTATTGTCAGAGAGCAGATCGAAGATAGTAAATTTGGTGTCTCTGTACTATCAGAGAACA 196 TCTCTGTATTGTCAGAGAGCAGATCGAAGATAGTAAATTTGGTGTCTCTGTACTATCAGAGAACA * * * 36259887 AATCGAAGAAACAGATTTGGCATCTCCATATTTGACGGAGAGTAGATC 261 AATCGAAGAAACAGATTTGGCATCTCCATATTCGACAGAGAGCAGATC * 36259935 GAAGACATAGCAGATCTAACCTTCGGATGTTTTTGCATCGAAGCAGATCCAAGATGATTTGGCAT 1 GAAGACATAGCAGATCTAACCTTCGGATGTTTTTGCATCGAAGCAGATCTAAGATGATTTGGCAT * * 36260000 CCTTGCGTTTACAAGGAGCAGATCAAAGATATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAG 66 CCTTGCGTTTACAAGGAGCAGATCGAAGACATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAG * * 36260065 CAAATCTAAGATGATTTGGCGTCTCTATATTGTCAGAGAGCAGATCAAAAATAGCAGAT 131 CAAATCTAAGATGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCAAAGATAGCAGAT 36260124 CGAAAATAGT Statistics Matches: 461, Mismatches: 35, Indels: 2 0.93 0.07 0.00 Matches are distributed among these distances: 307 2 0.00 308 459 1.00 ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29 Consensus pattern (308 bp): GAAGACATAGCAGATCTAACCTTCGGATGTTTTTGCATCGAAGCAGATCTAAGATGATTTGGCAT CCTTGCGTTTACAAGGAGCAGATCGAAGACATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAG CAAATCTAAGATGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCAAAGATAGCAGATTTGACA TCTCTGTATTGTCAGAGAGCAGATCGAAGATAGTAAATTTGGTGTCTCTGTACTATCAGAGAACA AATCGAAGAAACAGATTTGGCATCTCCATATTCGACAGAGAGCAGATC Found at i:36260122 original size:14 final size:14 Alignment explanation

Indices: 36260103--36260137 Score: 52 Period size: 14 Copynumber: 2.5 Consensus size: 14 36260093 ATTGTCAGAG 36260103 AGCAGATCAAAAAT 1 AGCAGATCAAAAAT * 36260117 AGCAGATCGAAAAT 1 AGCAGATCAAAAAT * 36260131 AGTAGAT 1 AGCAGAT 36260138 TTGGTGTCTC Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 14 19 1.00 ACGTcount: A:0.51, C:0.11, G:0.20, T:0.17 Consensus pattern (14 bp): AGCAGATCAAAAAT Found at i:36260336 original size:278 final size:278 Alignment explanation

Indices: 36259839--36260391 Score: 935 Period size: 278 Copynumber: 2.0 Consensus size: 278 36259829 ATTGTCAGAG * * 36259839 AGCAGATCGAAGATAGTAAATTTGGTGTCTCTGTACTATCAGAGAACAAATCGAAGAAACAGATT 1 AGCAGATCGAAAATAGTAAATTTGGTGTCTCTGTACTATCAGAGAACAAATCAAAGAAACAGATT * * * 36259904 TGGCATCTCCATATTTGACGGAGAGTAGATCGAAGACATAGCAGATCTAACCTTCGGATGTTTTT 66 TGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTAACCTTCGGATGTTTTC * * * 36259969 GCATCGAAGCAGATCCAAGATGATTTGGCATCCTTGCGTTTACAAGGAGCAGATCAAAGATATAG 131 ACATCGAAGCAGATCCAAGATGATTTGGAATCCTTGCGTTTACAAGGAGCAGATCAAAGACATAG * * 36260034 CAGATTTGGCTTTCACGTGTTTACGCTGAAGCAAATCTAAGATGATTTGGCGTCTCTATATTGTC 196 CAGATTTGGCTTTCACGTGTTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTATACTGTC * * 36260099 AGAGAGCAGATCAAAAAT 261 AGAGAACAAATCAAAAAT * * 36260117 AGCAGATCGAAAATAGTAGATTTGGTGTCTCTGTACTGTCAGAGAACAAATCAAAGAAACAGATT 1 AGCAGATCGAAAATAGTAAATTTGGTGTCTCTGTACTATCAGAGAACAAATCAAAGAAACAGATT 36260182 TGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTAACCTTCGGATGTTTTC 66 TGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTAACCTTCGGATGTTTTC * * * 36260247 ACATCGAAGTAGATCCAAGATGATTTGGAATCCTTGCGTTTATAAGGAGCAGATCGAAGACATAG 131 ACATCGAAGCAGATCCAAGATGATTTGGAATCCTTGCGTTTACAAGGAGCAGATCAAAGACATAG * * 36260312 CAGATTTGGCTTTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCTCTGTACTGTC 196 CAGATTTGGCTTTCACGTGTTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTATACTGTC 36260377 AGAGAACAAATCAAA 261 AGAGAACAAATCAAA 36260392 GAAACAGATT Statistics Matches: 256, Mismatches: 19, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 278 256 1.00 ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27 Consensus pattern (278 bp): AGCAGATCGAAAATAGTAAATTTGGTGTCTCTGTACTATCAGAGAACAAATCAAAGAAACAGATT TGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTAACCTTCGGATGTTTTC ACATCGAAGCAGATCCAAGATGATTTGGAATCCTTGCGTTTACAAGGAGCAGATCAAAGACATAG CAGATTTGGCTTTCACGTGTTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTATACTGTC AGAGAACAAATCAAAAAT Found at i:36260506 original size:78 final size:78 Alignment explanation

Indices: 36260398--36260614 Score: 326 Period size: 78 Copynumber: 2.8 Consensus size: 78 36260388 CAAAGAAACA * ** * * 36260398 GATTTGGTATCTCCATATTCGACGGAGAGCAGATCAAAGACATAGCAGATCAGACCTTCATTGAA 1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGACATAGCAGATCAGACCTTCATTGAA 36260463 GCAGATCCAAGAT 66 GCAGATCCAAGAT * ** 36260476 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGACATAACAGATTGGACCTTCATTGAA 1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGACATAGCAGATCAGACCTTCATTGAA * 36260541 GCAGATCTAAGAT 66 GCAGATCCAAGAT * * * 36260554 GATTTGGCATCTCTGTATTAGATGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCAT 1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGACATAGCAGATCAGACCTTCAT 36260615 GTGTTTACAT Statistics Matches: 125, Mismatches: 14, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 78 125 1.00 ACGTcount: A:0.32, C:0.18, G:0.24, T:0.25 Consensus pattern (78 bp): GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGACATAGCAGATCAGACCTTCATTGAA GCAGATCCAAGAT Found at i:36260707 original size:45 final size:45 Alignment explanation

Indices: 36260637--36260827 Score: 260 Period size: 45 Copynumber: 4.3 Consensus size: 45 36260627 AAGTAGATCC * 36260637 AAGATGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCG 1 AAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCG * * * * 36260682 GAGATAACAGATTTGGCATCTCTGTATTAGACAGGGAGCAGATTG 1 AAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCG * 36260727 AAGA-AGCAGATTTGGCATCTCTGTATTAGACGGGGAG-AAGATCG 1 AAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAGCAA-ATCG * * * * 36260771 AAGATAACAGATTTGGGATCTCTGTATTAGACGGTGAGCAGATCA 1 AAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCG * 36260816 AAGATAGCAGAT 1 AAGATAACAGAT 36260828 ATTGCCTTCC Statistics Matches: 127, Mismatches: 16, Indels: 6 0.85 0.11 0.04 Matches are distributed among these distances: 43 1 0.01 44 38 0.30 45 87 0.69 46 1 0.01 ACGTcount: A:0.33, C:0.14, G:0.29, T:0.25 Consensus pattern (45 bp): AAGATAACAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCG Found at i:36260795 original size:89 final size:90 Alignment explanation

Indices: 36260631--36260827 Score: 294 Period size: 89 Copynumber: 2.2 Consensus size: 90 36260621 ACATCGAAGT * * 36260631 AGATCCAAGAT-GACAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGGAGATAACAGATT 1 AGATCAAAGATAG-CAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGATAACAGATT 36260695 TGGCATCTCTGTATTAGACAGG-GAGC 65 TGGCATCTCTGTATTAGAC-GGTGAGC ** 36260721 AGATTGAAGA-AGCAGATTTGGCATCTCTGTATTAGACGGGGAG-AAGATCGAAGATAACAGATT 1 AGATCAAAGATAGCAGATTTGGCATCTCTGTATTAGACGGGGAGCAA-ATCGAAGATAACAGATT * 36260784 TGGGATCTCTGTATTAGACGGTGAGC 65 TGGCATCTCTGTATTAGACGGTGAGC 36260810 AGATCAAAGATAGCAGAT 1 AGATCAAAGATAGCAGAT 36260828 ATTGCCTTCC Statistics Matches: 97, Mismatches: 6, Indels: 8 0.87 0.05 0.07 Matches are distributed among these distances: 88 4 0.04 89 77 0.79 90 16 0.16 ACGTcount: A:0.33, C:0.14, G:0.28, T:0.24 Consensus pattern (90 bp): AGATCAAAGATAGCAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGATAACAGATTT GGCATCTCTGTATTAGACGGTGAGC Found at i:36261274 original size:17 final size:19 Alignment explanation

Indices: 36261177--36261267 Score: 152 Period size: 19 Copynumber: 4.9 Consensus size: 19 36261167 ATAATCTTCA 36261177 ATGATATGCAATCTTAGAT 1 ATGATATGCAATCTTAGAT 36261196 ATGATATGCAATCTTAGAT 1 ATGATATGCAATCTTAGAT 36261215 ATGATA--CAATCTTAGAT 1 ATGATATGCAATCTTAGAT * 36261232 ATGAT-TGCAATGTTAGAT 1 ATGATATGCAATCTTAGAT 36261250 ATGATATGCAATCTTAGA 1 ATGATATGCAATCTTAGA 36261268 AGATATGATT Statistics Matches: 67, Mismatches: 2, Indels: 6 0.89 0.03 0.08 Matches are distributed among these distances: 17 16 0.24 18 15 0.22 19 36 0.54 ACGTcount: A:0.37, C:0.10, G:0.16, T:0.36 Consensus pattern (19 bp): ATGATATGCAATCTTAGAT Found at i:36261293 original size:22 final size:22 Alignment explanation

Indices: 36261177--36261290 Score: 87 Period size: 19 Copynumber: 5.8 Consensus size: 22 36261167 ATAATCTTCA 36261177 ATGATATGCAATCTT---AGAT 1 ATGATATGCAATCTTAGAAGAT 36261196 ATGATATGCAATCTT---AGAT 1 ATGATATGCAATCTTAGAAGAT 36261215 ATGATA--CAATCTT---AGAT 1 ATGATATGCAATCTTAGAAGAT * 36261232 ATGAT-TGCAATGTT---AGAT 1 ATGATATGCAATCTTAGAAGAT 36261250 ATGATATGCAATCTTAGAAGAT 1 ATGATATGCAATCTTAGAAGAT * * 36261272 ATGATTTTGTAATCTTAGA 1 ATGA-TATGCAATCTTAGA 36261291 GATTTAATTT Statistics Matches: 84, Mismatches: 4, Indels: 10 0.86 0.04 0.10 Matches are distributed among these distances: 17 16 0.19 18 15 0.18 19 33 0.39 22 8 0.10 23 12 0.14 ACGTcount: A:0.37, C:0.09, G:0.17, T:0.38 Consensus pattern (22 bp): ATGATATGCAATCTTAGAAGAT Found at i:36261592 original size:17 final size:19 Alignment explanation

Indices: 36261558--36261594 Score: 51 Period size: 19 Copynumber: 2.1 Consensus size: 19 36261548 TGTTTCCCTG * 36261558 ATTTTTTTGTATATATTTT 1 ATTTTTTTGAATATATTTT 36261577 ATTTTTTT-AATA-ATTTT 1 ATTTTTTTGAATATATTTT 36261594 A 1 A 36261595 GTATCATATC Statistics Matches: 17, Mismatches: 1, Indels: 2 0.85 0.05 0.10 Matches are distributed among these distances: 17 6 0.35 18 3 0.18 19 8 0.47 ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70 Consensus pattern (19 bp): ATTTTTTTGAATATATTTT Found at i:36264164 original size:42 final size:43 Alignment explanation

Indices: 36264069--36264223 Score: 178 Period size: 41 Copynumber: 3.7 Consensus size: 43 36264059 TATTTGAAAA * * * 36264069 AAACGCTGCTAAAGAACA-TGACCTTTAGCAGCACTTTTCCCAC 1 AAACGCCGCTAAAGATCAGTGACCTTTAGC-GCGCTTTTCCCAC ** 36264112 AAACATCGCTAAAGATCAGT-ACCTTTAGCGGCGC-TTTCCCAC 1 AAACGCCGCTAAAGATCAGTGACCTTTAGC-GCGCTTTTCCCAC * * 36264154 AAACGCCGCTAAAGAT-AATGACCTTTAAC-CGCTTTTCCCAC 1 AAACGCCGCTAAAGATCAGTGACCTTTAGCGCGCTTTTCCCAC * 36264195 AAACGCCGCTAAAGATCA-AGACCTTTAGC 1 AAACGCCGCTAAAGATCAGTGACCTTTAGC 36264224 AGGATCACGA Statistics Matches: 96, Mismatches: 12, Indels: 10 0.81 0.10 0.08 Matches are distributed among these distances: 40 3 0.03 41 35 0.36 42 31 0.32 43 26 0.27 44 1 0.01 ACGTcount: A:0.32, C:0.30, G:0.15, T:0.23 Consensus pattern (43 bp): AAACGCCGCTAAAGATCAGTGACCTTTAGCGCGCTTTTCCCAC Found at i:36264203 original size:41 final size:40 Alignment explanation

Indices: 36264102--36264221 Score: 152 Period size: 42 Copynumber: 2.9 Consensus size: 40 36264092 TTTAGCAGCA ** * * 36264102 CTTTTCCCACAAACATCGCTAAAGATCAGTACCTTTAGCGGCG 1 CTTTTCCCACAAACGCCGCTAAAGATAAG-ACCTTTAAC--CG 36264145 C-TTTCCCACAAACGCCGCTAAAGATAATGACCTTTAACCG 1 CTTTTCCCACAAACGCCGCTAAAGATAA-GACCTTTAACCG 36264185 CTTTTCCCACAAACGCCGCTAAAGATCAAGACCTTTA 1 CTTTTCCCACAAACGCCGCTAAAGAT-AAGACCTTTA 36264222 GCAGGATCAC Statistics Matches: 70, Mismatches: 4, Indels: 8 0.85 0.05 0.10 Matches are distributed among these distances: 40 3 0.04 41 32 0.46 42 33 0.47 43 2 0.03 ACGTcount: A:0.31, C:0.32, G:0.13, T:0.24 Consensus pattern (40 bp): CTTTTCCCACAAACGCCGCTAAAGATAAGACCTTTAACCG Found at i:36264210 original size:83 final size:84 Alignment explanation

Indices: 36264069--36264223 Score: 217 Period size: 83 Copynumber: 1.8 Consensus size: 84 36264059 TATTTGAAAA * * * 36264069 AAACGCTGCTAAAGAACATGACCTTTAGCAGCACTTTTCCCACAAACATCGCTAAAGATC-AGTA 1 AAACGCCGCTAAAGAACATGACCTTTA-CACCACTTTTCCCACAAACACCGCTAAAGATCAAG-A 36264133 CCTTTAGCGGCGCTTTCCCAC 64 CCTTTAGCGGCGCTTTCCCAC * * 36264154 AAACGCCGCTAAAGATA-ATGACCTTTA-ACCGCTTTTCCCACAAACGCCGCTAAAGATCAAGAC 1 AAACGCCGCTAAAGA-ACATGACCTTTACACCACTTTTCCCACAAACACCGCTAAAGATCAAGAC 36264217 CTTTAGC 65 CTTTAGC 36264224 AGGATCACGA Statistics Matches: 63, Mismatches: 5, Indels: 6 0.85 0.07 0.08 Matches are distributed among these distances: 83 36 0.57 84 2 0.03 85 24 0.38 86 1 0.02 ACGTcount: A:0.32, C:0.30, G:0.15, T:0.23 Consensus pattern (84 bp): AAACGCCGCTAAAGAACATGACCTTTACACCACTTTTCCCACAAACACCGCTAAAGATCAAGACC TTTAGCGGCGCTTTCCCAC Found at i:36265766 original size:15 final size:16 Alignment explanation

Indices: 36265740--36265770 Score: 55 Period size: 15 Copynumber: 2.0 Consensus size: 16 36265730 TCTCTCTTGC 36265740 TTTTAGATCATATATA 1 TTTTAGATCATATATA 36265756 TTTTA-ATCATATATA 1 TTTTAGATCATATATA 36265771 AGACAAAAAC Statistics Matches: 15, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 15 10 0.67 16 5 0.33 ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52 Consensus pattern (16 bp): TTTTAGATCATATATA Found at i:36269471 original size:19 final size:18 Alignment explanation

Indices: 36269431--36269470 Score: 55 Period size: 18 Copynumber: 2.2 Consensus size: 18 36269421 TATTACTTAA * 36269431 TTTTAAATTTTTTTTCAT 1 TTTTAAATATTTTTTCAT 36269449 TTTTAACATATTTTTT-AT 1 TTTTAA-ATATTTTTTCAT 36269467 TTTT 1 TTTT 36269471 TCTTTCAAAA Statistics Matches: 20, Mismatches: 1, Indels: 2 0.87 0.04 0.09 Matches are distributed among these distances: 18 12 0.60 19 8 0.40 ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72 Consensus pattern (18 bp): TTTTAAATATTTTTTCAT Found at i:36269589 original size:8 final size:8 Alignment explanation

Indices: 36269578--36269662 Score: 70 Period size: 7 Copynumber: 10.6 Consensus size: 8 36269568 ATATTTAATA 36269578 TTTAATTT 1 TTTAATTT 36269586 TTTAATTT 1 TTTAATTT 36269594 TTTAA-TT 1 TTTAATTT 36269601 TTT-ATTT 1 TTTAATTT 36269608 TTT-ATTT 1 TTTAATTT 36269615 TTT-ATTT 1 TTTAATTT * 36269622 TTAAATTT 1 TTTAATTT ** 36269630 TAAAAATTT 1 T-TTAATTT 36269639 TTTGAATATT 1 TTT-AAT-TT * 36269649 TTTATAATT 1 TTTA-ATTT 36269658 TTTAA 1 TTTAA 36269663 ATTAACATAT Statistics Matches: 66, Mismatches: 5, Indels: 12 0.80 0.06 0.14 Matches are distributed among these distances: 6 1 0.02 7 23 0.35 8 19 0.29 9 17 0.26 10 6 0.09 ACGTcount: A:0.29, C:0.00, G:0.01, T:0.69 Consensus pattern (8 bp): TTTAATTT Found at i:36269589 original size:15 final size:16 Alignment explanation

Indices: 36269571--36269630 Score: 51 Period size: 15 Copynumber: 4.1 Consensus size: 16 36269561 ATATTAAATA 36269571 TTTAA-TATTTAATTT 1 TTTAATTATTTAATTT * 36269586 TTTAATTTTTTAA-TT 1 TTTAATTATTTAATTT * 36269601 TTT-ATT-TTTTATTT 1 TTTAATTATTTAATTT 36269615 TTT-ATT-TTTAAATTT 1 TTTAATTATTT-AATTT 36269630 T 1 T 36269631 AAAAATTTTT Statistics Matches: 39, Mismatches: 3, Indels: 6 0.81 0.06 0.12 Matches are distributed among these distances: 13 4 0.10 14 14 0.36 15 15 0.38 16 6 0.15 ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75 Consensus pattern (16 bp): TTTAATTATTTAATTT Found at i:36269594 original size:7 final size:7 Alignment explanation

Indices: 36269571--36269632 Score: 63 Period size: 7 Copynumber: 8.7 Consensus size: 7 36269561 ATATTAAATA * 36269571 TTTAATA 1 TTTAATT 36269578 TTTAATTT 1 TTTAA-TT 36269586 TTTAATTT 1 TTTAA-TT 36269594 TTTAATT 1 TTTAATT 36269601 TTT-ATT 1 TTTAATT * 36269607 TTTTATT 1 TTTAATT * 36269614 TTTTATT 1 TTTAATT * 36269621 TTTAAAT 1 TTTAATT 36269628 TTTAA 1 TTTAA 36269633 AAATTTTTTG Statistics Matches: 50, Mismatches: 3, Indels: 4 0.88 0.05 0.07 Matches are distributed among these distances: 6 6 0.12 7 30 0.60 8 14 0.28 ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73 Consensus pattern (7 bp): TTTAATT Found at i:36269665 original size:8 final size:8 Alignment explanation

Indices: 36269564--36269665 Score: 54 Period size: 7 Copynumber: 12.9 Consensus size: 8 36269554 AACTAAAATA * 36269564 TTAAATAT 1 TTAAATTT * 36269572 TT-AATAT 1 TTAAATTT 36269579 TT-AATTT 1 TTAAATTT * 36269586 TTTAATTT 1 TTAAATTT * 36269594 TTTAATTT 1 TTAAATTT 36269602 TT--ATTT 1 TTAAATTT * 36269608 TT-TATTT 1 TTAAATTT * 36269615 TT-TATTT 1 TTAAATTT 36269622 TTAAATTT 1 TTAAATTT * 36269630 TAAAAATTTT 1 T-TAAA-TTT 36269640 TTGAATATTT 1 TT-AA-ATTT 36269650 TTATAATTT 1 TTA-AATTT 36269659 TTAAATT 1 TTAAATT 36269666 AACATATAAA Statistics Matches: 82, Mismatches: 4, Indels: 16 0.80 0.04 0.16 Matches are distributed among these distances: 6 6 0.07 7 26 0.32 8 26 0.32 9 11 0.13 10 12 0.15 11 1 0.01 ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67 Consensus pattern (8 bp): TTAAATTT Found at i:36270407 original size:14 final size:14 Alignment explanation

Indices: 36270372--36270424 Score: 61 Period size: 14 Copynumber: 3.8 Consensus size: 14 36270362 ATAATCTCTA * * 36270372 AACCCTAAAAACCT 1 AACCCTTAAACCCT * * 36270386 AACTCTTAACCCCT 1 AACCCTTAAACCCT * 36270400 AAGCCTTAAACCCT 1 AACCCTTAAACCCT 36270414 AACCCTTAAAC 1 AACCCTTAAAC 36270425 AATAAACCAT Statistics Matches: 31, Mismatches: 8, Indels: 0 0.79 0.21 0.00 Matches are distributed among these distances: 14 31 1.00 ACGTcount: A:0.40, C:0.38, G:0.02, T:0.21 Consensus pattern (14 bp): AACCCTTAAACCCT Found at i:36270497 original size:7 final size:7 Alignment explanation

Indices: 36270485--36270510 Score: 52 Period size: 7 Copynumber: 3.7 Consensus size: 7 36270475 TCATACACTT 36270485 TAAACCC 1 TAAACCC 36270492 TAAACCC 1 TAAACCC 36270499 TAAACCC 1 TAAACCC 36270506 TAAAC 1 TAAAC 36270511 TATAATGATA Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 19 1.00 ACGTcount: A:0.46, C:0.38, G:0.00, T:0.15 Consensus pattern (7 bp): TAAACCC Found at i:36270637 original size:15 final size:14 Alignment explanation

Indices: 36270634--36270762 Score: 54 Period size: 14 Copynumber: 9.3 Consensus size: 14 36270624 TCATAATCCC * 36270634 TAAACCCTAAACCC 1 TAAACCCTAAACCA * * * 36270648 TAAATCTTAAAACA 1 TAAACCCTAAACCA * 36270662 TAAACCCTGAACCA 1 TAAACCCTAAACCA * 36270676 TGAACCCCTAACACC- 1 T-AAACCCTAA-ACCA * 36270691 TAAACCTTAAACC- 1 TAAACCCTAAACCA ** 36270704 CCAACCCTTAAACC- 1 TAAACCC-TAAACCA 36270718 ---ACCCGTAAACCA 1 TAAACCC-TAAACCA * 36270730 TAATCCCTAAACCCA 1 TAAACCCTAAA-CCA * * * 36270745 TAATCCATAAACCT 1 TAAACCCTAAACCA 36270759 TAAA 1 TAAA 36270763 ATAGTAACTC Statistics Matches: 87, Mismatches: 20, Indels: 16 0.71 0.16 0.13 Matches are distributed among these distances: 11 10 0.11 13 7 0.08 14 43 0.49 15 24 0.28 16 3 0.03 ACGTcount: A:0.43, C:0.36, G:0.02, T:0.19 Consensus pattern (14 bp): TAAACCCTAAACCA Found at i:36270643 original size:7 final size:7 Alignment explanation

Indices: 36270610--36270717 Score: 58 Period size: 7 Copynumber: 15.0 Consensus size: 7 36270600 ATTAATTAAT 36270610 CTAAACAC 1 CTAAAC-C 36270618 CTAAACTC 1 CTAAAC-C * * 36270626 ATAATCC 1 CTAAACC 36270633 CTAAACC 1 CTAAACC 36270640 CTAAACC 1 CTAAACC * 36270647 CTAAATC 1 CTAAACC * * 36270654 TTAAAAC 1 CTAAACC * 36270661 ATAAACC 1 CTAAACC * 36270668 CTGAACC 1 CTAAACC * * 36270675 ATGAACCC 1 CT-AAACC 36270683 CT-AACAC 1 CTAAAC-C 36270690 CTAAACC 1 CTAAACC * 36270697 TTAAACC 1 CTAAACC * 36270704 C-CAACC 1 CTAAACC 36270710 CTTAAACC 1 C-TAAACC 36270718 ACCCGTAAAC Statistics Matches: 74, Mismatches: 21, Indels: 10 0.70 0.20 0.10 Matches are distributed among these distances: 6 7 0.09 7 45 0.61 8 22 0.30 ACGTcount: A:0.43, C:0.37, G:0.02, T:0.19 Consensus pattern (7 bp): CTAAACC Found at i:36270762 original size:22 final size:22 Alignment explanation

Indices: 36270718--36270762 Score: 54 Period size: 22 Copynumber: 2.0 Consensus size: 22 36270708 CCCTTAAACC * * 36270718 ACCCGTAAACCATAATCCCTAA 1 ACCCATAAACCATAAACCCTAA * * 36270740 ACCCATAATCCATAAACCTTAA 1 ACCCATAAACCATAAACCCTAA 36270762 A 1 A 36270763 ATAGTAACTC Statistics Matches: 19, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 22 19 1.00 ACGTcount: A:0.44, C:0.33, G:0.02, T:0.20 Consensus pattern (22 bp): ACCCATAAACCATAAACCCTAA Found at i:36271108 original size:40 final size:40 Alignment explanation

Indices: 36271064--36271152 Score: 110 Period size: 40 Copynumber: 2.2 Consensus size: 40 36271054 TTTCATTAAA * 36271064 CGCCGCTAAAGATCG-AGCAT-TAGTGGCATTTCTCAAAAAG 1 CGCCGCTAAAGAT-GTA-CATATAGCGGCATTTCTCAAAAAG * * * 36271104 CGCCGCTAAAGGTGTACATATAGCGGCGTTTCTTAAAAAG 1 CGCCGCTAAAGATGTACATATAGCGGCATTTCTCAAAAAG 36271144 CGCCGCTAA 1 CGCCGCTAA 36271153 TACTTGATCT Statistics Matches: 43, Mismatches: 4, Indels: 4 0.84 0.08 0.08 Matches are distributed among these distances: 39 4 0.09 40 39 0.91 ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22 Consensus pattern (40 bp): CGCCGCTAAAGATGTACATATAGCGGCATTTCTCAAAAAG Found at i:36271306 original size:40 final size:40 Alignment explanation

Indices: 36271247--36271349 Score: 113 Period size: 40 Copynumber: 2.6 Consensus size: 40 36271237 TTTTGCAGTA * * * 36271247 TTTTTCAAAAAGCGTCGCTAAAGGTGTA-CTTATAGCGGCG 1 TTTTTTAAAAAGCGCCGCTAAAGCTGTATCTT-TAGCGGCG * * * 36271287 TTTTTTAAAAAGAGCCGCTAATA-CTTTATCTTTAGTGGCG 1 TTTTTTAAAAAGCGCCGCTAA-AGCTGTATCTTTAGCGGCG 36271327 -TTTTTAAAAAGCGCCGCTAAAGC 1 TTTTTTAAAAAGCGCCGCTAAAGC 36271350 CACTAAAAGT Statistics Matches: 53, Mismatches: 7, Indels: 7 0.79 0.10 0.10 Matches are distributed among these distances: 38 1 0.02 39 20 0.38 40 28 0.53 41 4 0.08 ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33 Consensus pattern (40 bp): TTTTTTAAAAAGCGCCGCTAAAGCTGTATCTTTAGCGGCG Found at i:36271396 original size:155 final size:155 Alignment explanation

Indices: 36271090--36271486 Score: 523 Period size: 155 Copynumber: 2.6 Consensus size: 155 36271080 GCATTAGTGG * * * * * 36271090 CATTTCTCAAAAAGCGCCGCTAAAGGTGTACATATAGCGGCGTTTCTTAAAAAGCGCCGCTAATA 1 CATTTTTCAAAAAGCGACGCTAAAGGTGTACTTATAGCGGCGTTTTTTAAAAAGAGCCGCTAATA * 36271155 CTTGATCTTTAGCGGTGTTTTTAAAAAGTGCCGCTAAAGCCACTAAAAGCTCAATACAAAAACAA 66 CTTGATCTTTAGCGGTGTTTTTAAAAAGCGCCGCTAAAGCCACTAAAAGCTCAATACAAAAACAA * * 36271220 TGGAGTTTTGCAAAAAATTTTGCAG 131 CGGAGTTTTGCAAAAAATTTTGCAA * * 36271245 TATTTTTCAAAAAGCGTCGCTAAAGGTGTACTTATAGCGGCGTTTTTTAAAAAGAGCCGCTAATA 1 CATTTTTCAAAAAGCGACGCTAAAGGTGTACTTATAGCGGCGTTTTTTAAAAAGAGCCGCTAATA * * * * ** 36271310 CTTTATCTTTAGTGGCGTTTTTAAAAAGCGCCGCTAAAGCCACTAAAAGTTCAATAC-AAAATGA 66 CTTGATCTTTAGCGGTGTTTTTAAAAAGCGCCGCTAAAGCCACTAAAAGCTCAATACAAAAACAA ** 36271374 CGGAGTTTTGCAAAATTCTTTTGCAA 131 CGGAGTTTTGCAAAA-AATTTTGCAA * * * * * 36271400 CGTTTTTCAAAAAAC-ACTGCTAAAGGTGTA-TATATAGAGGCATTTTTAAAAAAGCA-CCGCTA 1 CATTTTTCAAAAAGCGAC-GCTAAAGGTGTACT-TATAGCGGCGTTTTTTAAAAAG-AGCCGCTA 36271462 ATACTTGATCTTTAGCGGTGTTTTT 63 ATACTTGATCTTTAGCGGTGTTTTT 36271487 TGTAAAACGC Statistics Matches: 211, Mismatches: 27, Indels: 8 0.86 0.11 0.03 Matches are distributed among these distances: 154 21 0.10 155 189 0.90 156 1 0.00 ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31 Consensus pattern (155 bp): CATTTTTCAAAAAGCGACGCTAAAGGTGTACTTATAGCGGCGTTTTTTAAAAAGAGCCGCTAATA CTTGATCTTTAGCGGTGTTTTTAAAAAGCGCCGCTAAAGCCACTAAAAGCTCAATACAAAAACAA CGGAGTTTTGCAAAAAATTTTGCAA Found at i:36274546 original size:60 final size:60 Alignment explanation

Indices: 36274446--36274584 Score: 176 Period size: 60 Copynumber: 2.3 Consensus size: 60 36274436 AACTGTGTTA * * 36274446 ATATGGGCAAGGCCCAATATATCTCGACTTGTAATAGGGCTACGGCCTAGATTAATACTG 1 ATATGGGCTAGGCCCAATATATCTCGACTTGTAATAGGGCTACGGCCCAGATTAATACTG * * * 36274506 ATATGGGCTAGGCCCAATATA-CTCTGA-TACTGTAA-GGGGCTATGGCCCAGATTAATATTG 1 ATATGGGCTAGGCCCAATATATCTC-GACT--TGTAATAGGGCTACGGCCCAGATTAATACTG 36274566 ATATGGGCTAGGGCCCAAT 1 ATATGGGCTA-GGCCCAAT 36274585 TAACACTAAT Statistics Matches: 70, Mismatches: 5, Indels: 7 0.85 0.06 0.09 Matches are distributed among these distances: 59 4 0.06 60 53 0.76 61 13 0.19 ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27 Consensus pattern (60 bp): ATATGGGCTAGGCCCAATATATCTCGACTTGTAATAGGGCTACGGCCCAGATTAATACTG Found at i:36275927 original size:26 final size:26 Alignment explanation

Indices: 36275880--36275930 Score: 77 Period size: 26 Copynumber: 2.0 Consensus size: 26 36275870 CCGTTTGGCC * 36275880 CCTAGCCCAAAACTCATTTTCTAACG 1 CCTAGCCCAAAACTCATCTTCTAACG 36275906 CCTAGCCCAAAAC-CTATCTTCTAAC 1 CCTAGCCCAAAACTC-ATCTTCTAAC 36275931 CCACAAAGCC Statistics Matches: 23, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 25 1 0.04 26 22 0.96 ACGTcount: A:0.31, C:0.37, G:0.06, T:0.25 Consensus pattern (26 bp): CCTAGCCCAAAACTCATCTTCTAACG Found at i:36277284 original size:2 final size:2 Alignment explanation

Indices: 36277277--36277317 Score: 55 Period size: 2 Copynumber: 20.0 Consensus size: 2 36277267 ACATTATACC * * 36277277 AT AT AT AT AT AT TT AT AA AT AT CAT 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 36277318 TTAATACATT Statistics Matches: 34, Mismatches: 4, Indels: 2 0.85 0.10 0.05 Matches are distributed among these distances: 2 32 0.94 3 2 0.06 ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49 Consensus pattern (2 bp): AT Found at i:36278981 original size:27 final size:27 Alignment explanation

Indices: 36278941--36279227 Score: 355 Period size: 27 Copynumber: 10.6 Consensus size: 27 36278931 ATCTCATATT * 36278941 TGTAGGCTAGAATTACCGAAATACCCC 1 TGTAGGGTAGAATTACCGAAATACCCC * * 36278968 TATAGGGTAGAATTACCGAAATACCCT 1 TGTAGGGTAGAATTACCGAAATACCCC * * * * 36278995 TATAAGGTAGAATTACTGAAATATCCC 1 TGTAGGGTAGAATTACCGAAATACCCC * 36279022 TGTAAGGTAGAATTACCGAAATACCCC 1 TGTAGGGTAGAATTACCGAAATACCCC 36279049 TGTAGGGTAGAATTACCGAAATACCCC 1 TGTAGGGTAGAATTACCGAAATACCCC * 36279076 -GTTTGGGTAGAATTACCGAAATACCCC 1 TG-TAGGGTAGAATTACCGAAATACCCC * 36279103 TCTAGGGTAGAATTACCGAAATACCTCC 1 TGTAGGGTAGAATTACCGAAATACC-CC * * 36279131 T-TTGGGTAG-ATTACTGAAATACCCC 1 TGTAGGGTAGAATTACCGAAATACCCC * * 36279156 TCTAGGGTAGAATTACTGAAATACCCC 1 TGTAGGGTAGAATTACCGAAATACCCC * * * 36279183 TGTAGGGTAGAGTTACCGAGATACCCT 1 TGTAGGGTAGAATTACCGAAATACCCC * * 36279210 TGTGGGGTAAAAATTACC 1 TGTAGGGT-AGAATTACC 36279228 ATTTTTCCCC Statistics Matches: 229, Mismatches: 25, Indels: 11 0.86 0.09 0.04 Matches are distributed among these distances: 25 3 0.01 26 21 0.09 27 195 0.85 28 10 0.04 ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26 Consensus pattern (27 bp): TGTAGGGTAGAATTACCGAAATACCCC Found at i:36279498 original size:28 final size:27 Alignment explanation

Indices: 36279451--36279540 Score: 119 Period size: 28 Copynumber: 3.3 Consensus size: 27 36279441 TGGAGGAAGC * 36279451 GTTCCGGTGGCTATGCCACAAATATCT 1 GTTCTGGTGGCTATGCCACAAATATCT * 36279478 GTTTCTGTTGGCTATGCCACAAATATCT 1 G-TTCTGGTGGCTATGCCACAAATATCT * * 36279506 GTTCTGGTGGCTCTGCCAC-AATATTT 1 GTTCTGGTGGCTATGCCACAAATATCT 36279532 GTATCTGGT 1 GT-TCTGGT 36279541 AACTCTGTCA Statistics Matches: 56, Mismatches: 5, Indels: 4 0.86 0.08 0.06 Matches are distributed among these distances: 26 8 0.14 27 23 0.41 28 25 0.45 ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37 Consensus pattern (27 bp): GTTCTGGTGGCTATGCCACAAATATCT Found at i:36279522 original size:27 final size:26 Alignment explanation

Indices: 36279451--36279561 Score: 114 Period size: 27 Copynumber: 4.1 Consensus size: 26 36279441 TGGAGGAAGC * 36279451 GTTCCGGTGGCTATGCCACAAATATCT 1 GTTCTGGTGGCTATGCCAC-AATATCT * 36279478 GTTTCTGTTGGCTATGCCACAAATATCT 1 G-TTCTGGTGGCTATGCCAC-AATATCT * * 36279506 GTTCTGGTGGCTCTGCCACAATATTT 1 GTTCTGGTGGCTATGCCACAATATCT ** * * 36279532 GTATCTGGTAACTCTGTCACAATATCT 1 GT-TCTGGTGGCTATGCCACAATATCT 36279559 GTT 1 GTT 36279562 GACCGATCGA Statistics Matches: 73, Mismatches: 9, Indels: 5 0.84 0.10 0.06 Matches are distributed among these distances: 26 9 0.12 27 39 0.53 28 25 0.34 ACGTcount: A:0.21, C:0.23, G:0.20, T:0.37 Consensus pattern (26 bp): GTTCTGGTGGCTATGCCACAATATCT Found at i:36279739 original size:78 final size:78 Alignment explanation

Indices: 36279567--36279732 Score: 251 Period size: 78 Copynumber: 2.1 Consensus size: 78 36279557 CTGTTGACCG * * * 36279567 ATCGATGGCTGAGTGCCGATCATGTTACCGAAGGCTGTGTGCCATTATTATGGGCTTCGTACCGA 1 ATCGATGGCTGAGTGCCGATCATGTTACCAAAGGCTGTGTACCATTATTATAGGCTTCGTACCGA 36279632 TTATAGACCCGTT 66 TTATAGACCCGTT * * * * * 36279645 ATCGATGGCTGAGTGCCGATCATGTTATCAAAGGCTGTGTACCGTTATTGTAGGCTTCGTGCTGA 1 ATCGATGGCTGAGTGCCGATCATGTTACCAAAGGCTGTGTACCATTATTATAGGCTTCGTACCGA * 36279710 TTATAGACCTGTT 66 TTATAGACCCGTT 36279723 ATCGATGGCT 1 ATCGATGGCT 36279733 TTGTGCCACG Statistics Matches: 79, Mismatches: 9, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 78 79 1.00 ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33 Consensus pattern (78 bp): ATCGATGGCTGAGTGCCGATCATGTTACCAAAGGCTGTGTACCATTATTATAGGCTTCGTACCGA TTATAGACCCGTT Found at i:36279810 original size:27 final size:28 Alignment explanation

Indices: 36279754--36279829 Score: 93 Period size: 27 Copynumber: 2.8 Consensus size: 28 36279744 ATTCTGTTAA * * * 36279754 GTGGCTTTGCCACATTATCTG-ATTCTG 1 GTGGCTCTGCCACAATATCTGTATTCAG 36279781 GTGGCTCTGCCACAATATCTGTA-TCAG 1 GTGGCTCTGCCACAATATCTGTATTCAG * * 36279808 GTGACTCTGTCACAATATCTGT 1 GTGGCTCTGCCACAATATCTGT 36279830 TTTGGCAGCC Statistics Matches: 43, Mismatches: 5, Indels: 2 0.86 0.10 0.04 Matches are distributed among these distances: 27 42 0.98 28 1 0.02 ACGTcount: A:0.20, C:0.24, G:0.21, T:0.36 Consensus pattern (28 bp): GTGGCTCTGCCACAATATCTGTATTCAG Found at i:36279961 original size:6 final size:6 Alignment explanation

Indices: 36279952--36280064 Score: 79 Period size: 6 Copynumber: 18.3 Consensus size: 6 36279942 TTGCATTCAC * * * * * 36279952 ATTCTG ATTCTG ATTCTG TTTCCTG ATACTG ATTCCG ATTCTG CCA-CCTA 1 ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG ATTCTG --ATTCTG * * * 36280002 ATTCTG ATTCTG ATTCT- ATCACTGG ATTCTG ATTCTG ATTCTC ATTTTG 1 ATTCTG ATTCTG ATTCTG AT-TCT-G ATTCTG ATTCTG ATTCTG ATTCTG 36280051 ATTCT- AGTTCTG AT 1 ATTCTG A-TTCTG AT 36280065 AATGTTTCTT Statistics Matches: 82, Mismatches: 16, Indels: 18 0.71 0.14 0.16 Matches are distributed among these distances: 5 4 0.05 6 66 0.80 7 9 0.11 8 3 0.04 ACGTcount: A:0.19, C:0.21, G:0.14, T:0.46 Consensus pattern (6 bp): ATTCTG Found at i:36279983 original size:25 final size:25 Alignment explanation

Indices: 36279952--36280043 Score: 91 Period size: 25 Copynumber: 3.7 Consensus size: 25 36279942 TTGCATTCAC * 36279952 ATTCTGATTCTGATTCTGTTTCCTG 1 ATTCTGATTCTGATTCTGTATCCTG * * * * 36279977 ATACTGATTCCGATTCTGCCA-CCTA 1 ATTCTGATTCTGATTCTG-TATCCTG 36280002 ATTCTGATTCTGATTC--TATCACTGG 1 ATTCTGATTCTGATTCTGTATC-CT-G 36280027 ATTCTGATTCTGATTCT 1 ATTCTGATTCTGATTCT 36280044 CATTTTGATT Statistics Matches: 53, Mismatches: 9, Indels: 9 0.75 0.13 0.13 Matches are distributed among these distances: 22 1 0.02 23 1 0.02 24 2 0.04 25 49 0.92 ACGTcount: A:0.18, C:0.23, G:0.14, T:0.45 Consensus pattern (25 bp): ATTCTGATTCTGATTCTGTATCCTG Found at i:36281740 original size:16 final size:15 Alignment explanation

Indices: 36281713--36281745 Score: 57 Period size: 16 Copynumber: 2.1 Consensus size: 15 36281703 TTTGTAATAA 36281713 AATATATAAATAAAT 1 AATATATAAATAAAT 36281728 AATATAGTAAATAAAT 1 AATATA-TAAATAAAT 36281744 AA 1 AA 36281746 GCAAAATTAA Statistics Matches: 17, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 15 6 0.35 16 11 0.65 ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30 Consensus pattern (15 bp): AATATATAAATAAAT Found at i:36282349 original size:3 final size:3 Alignment explanation

Indices: 36282337--36282372 Score: 65 Period size: 3 Copynumber: 12.3 Consensus size: 3 36282327 GAGTGAAAGT 36282337 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A 1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A 36282373 ACTAATTAAT Statistics Matches: 32, Mismatches: 0, Indels: 2 0.94 0.00 0.06 Matches are distributed among these distances: 2 2 0.06 3 30 0.94 ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31 Consensus pattern (3 bp): ATA Found at i:36286833 original size:41 final size:42 Alignment explanation

Indices: 36286733--36286870 Score: 131 Period size: 42 Copynumber: 3.3 Consensus size: 42 36286723 TGAGTTTACA * * * * * 36286733 TGTAAGACCATATCTGAGATATGGCATC-ATTATTAGATTTCG 1 TGTAAGACCATAGCTGGGACATGGCATCGA-TATGAGATATCG 36286775 TGTAAGACCAT-GTCTGGGACATGGCATCGATATGAGA-ATCG 1 TGTAAGACCATAG-CTGGGACATGGCATCGATATGAGATATCG * ** * 36286816 TGTAAGACCATAGCTGGG-CTATAGGCATCGATATGTGATCCCA 1 TGTAAGACCATAGCTGGGAC-AT-GGCATCGATATGAGATATCG 36286859 TGTAAGACCATA 1 TGTAAGACCATA 36286871 TTTGGGTATG Statistics Matches: 81, Mismatches: 9, Indels: 11 0.80 0.09 0.11 Matches are distributed among these distances: 40 1 0.01 41 21 0.26 42 45 0.56 43 14 0.17 ACGTcount: A:0.30, C:0.17, G:0.24, T:0.28 Consensus pattern (42 bp): TGTAAGACCATAGCTGGGACATGGCATCGATATGAGATATCG Found at i:36290266 original size:15 final size:15 Alignment explanation

Indices: 36290246--36290278 Score: 66 Period size: 15 Copynumber: 2.2 Consensus size: 15 36290236 ATGAAGGATG 36290246 AGGGATAATGGATAA 1 AGGGATAATGGATAA 36290261 AGGGATAATGGATAA 1 AGGGATAATGGATAA 36290276 AGG 1 AGG 36290279 AATGAGGGGG Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 18 1.00 ACGTcount: A:0.45, C:0.00, G:0.36, T:0.18 Consensus pattern (15 bp): AGGGATAATGGATAA Found at i:36293356 original size:18 final size:17 Alignment explanation

Indices: 36293333--36293366 Score: 59 Period size: 18 Copynumber: 1.9 Consensus size: 17 36293323 TAGCTGTGCC 36293333 GTTTTCTCTTCTGTATTA 1 GTTTTCTCTTCT-TATTA 36293351 GTTTTCTCTTCTTATT 1 GTTTTCTCTTCTTATT 36293367 TTCTTCCTTA Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 17 4 0.25 18 12 0.75 ACGTcount: A:0.09, C:0.18, G:0.09, T:0.65 Consensus pattern (17 bp): GTTTTCTCTTCTTATTA Found at i:36294595 original size:20 final size:20 Alignment explanation

Indices: 36294570--36294620 Score: 84 Period size: 20 Copynumber: 2.5 Consensus size: 20 36294560 ATTTTGATAA * 36294570 ACATGATATGTATGATATGC 1 ACATGACATGTATGATATGC 36294590 ACATGACATGTATGATATGC 1 ACATGACATGTATGATATGC * 36294610 ACATGAGATGT 1 ACATGACATGT 36294621 TCATAAATGC Statistics Matches: 29, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 20 29 1.00 ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31 Consensus pattern (20 bp): ACATGACATGTATGATATGC Found at i:36294833 original size:23 final size:24 Alignment explanation

Indices: 36294666--36294853 Score: 269 Period size: 23 Copynumber: 8.0 Consensus size: 24 36294656 GAGGAAGTGC 36294666 AAAAGGGCTTATGCCCCAGTTATT 1 AAAAGGGCTTATGCCCCAGTTATT 36294690 -AAAGGGCTTATGCCCCAGTTATT 1 AAAAGGGCTTATGCCCCAGTTATT 36294713 -AAAGGGCTTATGCCCCAGTTATT 1 AAAAGGGCTTATGCCCCAGTTATT * * * 36294736 -AAAGGGCTCATGCCCTAGTTATC 1 AAAAGGGCTTATGCCCCAGTTATT * 36294759 AAAAGGGCTTATGCCCCAGTTATC 1 AAAAGGGCTTATGCCCCAGTTATT * 36294783 AAAAGGGCTTATGCCCCAGTTATC 1 AAAAGGGCTTATGCCCCAGTTATT 36294807 AAAAGGGCTT-TGCCCCAGTTATT 1 AAAAGGGCTTATGCCCCAGTTATT * 36294830 AAAAGAGGC-TAGGCCTCCAGTTAT 1 AAAAG-GGCTTATGCC-CCAGTTAT 36294854 ATGATAAAGC Statistics Matches: 153, Mismatches: 7, Indels: 7 0.92 0.04 0.04 Matches are distributed among these distances: 23 84 0.55 24 61 0.40 25 8 0.05 ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27 Consensus pattern (24 bp): AAAAGGGCTTATGCCCCAGTTATT Found at i:36295082 original size:31 final size:31 Alignment explanation

Indices: 36295047--36295110 Score: 101 Period size: 31 Copynumber: 2.1 Consensus size: 31 36295037 CGTTTACAGT 36295047 AAAGGCTTCGGCCCAGTAATATGAAATATGA 1 AAAGGCTTCGGCCCAGTAATATGAAATATGA ** * 36295078 AAAGGCTTCGGCCCAGTGTTATGAATTATGA 1 AAAGGCTTCGGCCCAGTAATATGAAATATGA 36295109 AA 1 AA 36295111 TATGAAAAGG Statistics Matches: 30, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 31 30 1.00 ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25 Consensus pattern (31 bp): AAAGGCTTCGGCCCAGTAATATGAAATATGA Found at i:36301473 original size:31 final size:31 Alignment explanation

Indices: 36301450--36301523 Score: 93 Period size: 31 Copynumber: 2.5 Consensus size: 31 36301440 ATAGTGAATC ** 36301450 CGCACACTTAGTGCTATATATATATTCAGCT 1 CGCACACTTAGTGCTATATATATATGAAGCT 36301481 CGCACACTTAGTGCTATATA-ATCA--AA-CT 1 CGCACACTTAGTGCTATATATAT-ATGAAGCT 36301509 CGCACACTTAGTGCT 1 CGCACACTTAGTGCT 36301524 GTACAATTTT Statistics Matches: 41, Mismatches: 1, Indels: 5 0.87 0.02 0.11 Matches are distributed among these distances: 28 17 0.41 29 1 0.02 30 2 0.05 31 21 0.51 ACGTcount: A:0.30, C:0.26, G:0.14, T:0.31 Consensus pattern (31 bp): CGCACACTTAGTGCTATATATATATGAAGCT Found at i:36301545 original size:30 final size:29 Alignment explanation

Indices: 36301449--36301552 Score: 111 Period size: 28 Copynumber: 3.5 Consensus size: 29 36301439 TATAGTGAAT * * 36301449 CCGCACACTTAGTGCTATATATATATTCAGC 1 CCGCACACTTAGTGCTATATA-AT-TTAAAC * * 36301480 TCGCACACTTAGTGCTATATAA-TCAAAC 1 CCGCACACTTAGTGCTATATAATTTAAAC * * * 36301508 TCGCACACTTAGTGCTGTACAATTTTAAAC 1 CCGCACACTTAGTGCTATATAA-TTTAAAC 36301538 CCGCACACTTAGTGC 1 CCGCACACTTAGTGC 36301553 CAATCTTGTC Statistics Matches: 63, Mismatches: 8, Indels: 5 0.83 0.11 0.07 Matches are distributed among these distances: 28 23 0.37 30 20 0.32 31 20 0.32 ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30 Consensus pattern (29 bp): CCGCACACTTAGTGCTATATAATTTAAAC Found at i:36307422 original size:27 final size:29 Alignment explanation

Indices: 36307392--36307507 Score: 110 Period size: 29 Copynumber: 4.0 Consensus size: 29 36307382 AACGCAAGAG * 36307392 TATATA-GTGAATC-CGCACACTTAGTGC 1 TATATATGTGAAGCTCGCACACTTAGTGC * ** 36307419 TATATATTTTCAGCTCGCACACTTAGTGC 1 TATATATGTGAAGCTCGCACACTTAGTGC * ** 36307448 TATATAATTTTCAGCTCGCACACTTAGTGC 1 TATAT-ATGTGAAGCTCGCACACTTAGTGC * ** * 36307478 TATATATTTTCAGTTCGCACACTTAGTGC 1 TATATATGTGAAGCTCGCACACTTAGTGC 36307507 T 1 T 36307508 GTACAATTTT Statistics Matches: 81, Mismatches: 5, Indels: 4 0.90 0.06 0.04 Matches are distributed among these distances: 27 6 0.07 28 3 0.04 29 43 0.53 30 29 0.36 ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37 Consensus pattern (29 bp): TATATATGTGAAGCTCGCACACTTAGTGC Found at i:36307460 original size:30 final size:29 Alignment explanation

Indices: 36307405--36307507 Score: 188 Period size: 29 Copynumber: 3.5 Consensus size: 29 36307395 ATAGTGAATC 36307405 CGCACACTTAGTGCTATATATTTTCAGCT 1 CGCACACTTAGTGCTATATATTTTCAGCT 36307434 CGCACACTTAGTGCTATATAATTTTCAGCT 1 CGCACACTTAGTGCTATAT-ATTTTCAGCT * 36307464 CGCACACTTAGTGCTATATATTTTCAGTT 1 CGCACACTTAGTGCTATATATTTTCAGCT 36307493 CGCACACTTAGTGCT 1 CGCACACTTAGTGCT 36307508 GTACAATTTT Statistics Matches: 72, Mismatches: 1, Indels: 2 0.96 0.01 0.03 Matches are distributed among these distances: 29 43 0.60 30 29 0.40 ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37 Consensus pattern (29 bp): CGCACACTTAGTGCTATATATTTTCAGCT Found at i:36307481 original size:59 final size:60 Alignment explanation

Indices: 36307404--36307537 Score: 207 Period size: 59 Copynumber: 2.2 Consensus size: 60 36307394 TATAGTGAAT * * * 36307404 CCGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAA-TTTTCAGC 1 CCGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATACAATTTTTAAAC * * * 36307463 TCGCACACTTAGTGCTATATATTTTCAGTTCGCACACTTAGTGCTGTACAATTTTTAAAC 1 CCGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATACAATTTTTAAAC 36307523 CCGCACACTTAGTGC 1 CCGCACACTTAGTGC 36307538 CAATCTTGTC Statistics Matches: 67, Mismatches: 7, Indels: 1 0.89 0.09 0.01 Matches are distributed among these distances: 59 47 0.70 60 20 0.30 ACGTcount: A:0.25, C:0.25, G:0.14, T:0.35 Consensus pattern (60 bp): CCGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATACAATTTTTAAAC Found at i:36316550 original size:43 final size:43 Alignment explanation

Indices: 36316486--36316586 Score: 116 Period size: 42 Copynumber: 2.4 Consensus size: 43 36316476 CCCAAATACA * * * 36316486 GTCTTACATGGAAT-TTCATATCAATGCTAATAGCCCAGCTATG 1 GTCTTACACGAAATCTTCATATCAATG-TAATAGCCCAGATATG * * * * 36316529 GTCTTACACGAAATCTT-ATATCGATGTCATATCTCAGATATG 1 GTCTTACACGAAATCTTCATATCAATGTAATAGCCCAGATATG 36316571 GTCTTACACGAAATCT 1 GTCTTACACGAAATCT 36316587 CAACTAACCC Statistics Matches: 50, Mismatches: 7, Indels: 3 0.83 0.12 0.05 Matches are distributed among these distances: 42 28 0.56 43 20 0.40 44 2 0.04 ACGTcount: A:0.31, C:0.21, G:0.15, T:0.34 Consensus pattern (43 bp): GTCTTACACGAAATCTTCATATCAATGTAATAGCCCAGATATG Found at i:36324241 original size:40 final size:40 Alignment explanation

Indices: 36324175--36324318 Score: 130 Period size: 40 Copynumber: 3.6 Consensus size: 40 36324165 AAATTGAATG * * * 36324175 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT 1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCTAGAAACT * * *** 36324214 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT 1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCTAGAAACT * * ** * 36324254 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCATT 1 ATATCCGGGCTAAGACCCGAAGGCAATT-ATGCTAGAAACT * * 36324294 CTATCCAGGCTAAGACCCGAAGGCA 1 ATATCCGGGCTAAGACCCGAAGGCA 36324319 TTTGTGCACA Statistics Matches: 87, Mismatches: 15, Indels: 4 0.82 0.14 0.04 Matches are distributed among these distances: 39 16 0.18 40 71 0.82 ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22 Consensus pattern (40 bp): ATATCCGGGCTAAGACCCGAAGGCAATTATGCTAGAAACT Done.