Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr12 103066607 

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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33

Warning! 238 characters in sequence are not A, C, G, or T


File 39 of 345

Found at i:11571839 original size:40 final size:40

Alignment explanation

Indices: 11571774--11571849 Score: 107 Period size: 40 Copynumber: 1.9 Consensus size: 40 11571764 TACGGTACCT * * * 11571774 TATGGTGTGTAGGGTTGGATGGGTCGATTATATCCCCATA 1 TATGGTGTGCAGGGATGGATAGGTCGATTATATCCCCATA * * 11571814 TATGGTGTGCAGGGATGGGTAGGTCGATTTTATCCC 1 TATGGTGTGCAGGGATGGATAGGTCGATTATATCCC 11571850 TACATAGTGT Statistics Matches: 31, Mismatches: 5, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 40 31 1.00 ACGTcount: A:0.18, C:0.13, G:0.34, T:0.34 Consensus pattern (40 bp): TATGGTGTGCAGGGATGGATAGGTCGATTATATCCCCATA Found at i:11578964 original size:42 final size:42 Alignment explanation

Indices: 11578901--11579076 Score: 185 Period size: 42 Copynumber: 4.0 Consensus size: 42 11578891 CTTCGTTTTC ** * * * 11578901 TCGATGCCATAGTTCAACTATGGTTTTACACATCTTCACATAA 1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A * 11578944 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA 1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA 11578985 TCGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATA 1 TCGATGCCATAGCCCAGCTATGGTCTTACAC---AT---AT-TCACATA * * * 11579034 TCGATACCATAGCCCAACTATGGTCTTACACA-AATCACATA 1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA 11579075 TC 1 TC 11579077 TCACTGATGC Statistics Matches: 115, Mismatches: 10, Indels: 18 0.80 0.07 0.13 Matches are distributed among these distances: 41 11 0.10 42 63 0.55 43 1 0.01 45 2 0.02 46 1 0.01 48 2 0.02 49 35 0.30 ACGTcount: A:0.31, C:0.27, G:0.12, T:0.30 Consensus pattern (42 bp): TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA Found at i:11579044 original size:49 final size:48 Alignment explanation

Indices: 11578971--11579076 Score: 158 Period size: 49 Copynumber: 2.2 Consensus size: 48 11578961 TATGGTCTTA * * * * 11578971 CACATATTCATATATCGATGCCATAGCCCAGCTATGGTCTTACACGTAAT 1 CACATA-TCACATATCGATACCATAGCCCAACTATGGTCTTACAC-AAAT 11579021 CACATATCACATATCGATACCATAGCCCAACTATGGTCTTACACAAAT 1 CACATATCACATATCGATACCATAGCCCAACTATGGTCTTACACAAAT 11579069 CACATATC 1 CACATATC 11579077 TCACTGATGC Statistics Matches: 52, Mismatches: 4, Indels: 2 0.90 0.07 0.03 Matches are distributed among these distances: 48 11 0.21 49 35 0.67 50 6 0.12 ACGTcount: A:0.34, C:0.28, G:0.10, T:0.27 Consensus pattern (48 bp): CACATATCACATATCGATACCATAGCCCAACTATGGTCTTACACAAAT Found at i:11579218 original size:31 final size:31 Alignment explanation

Indices: 11579183--11579329 Score: 233 Period size: 31 Copynumber: 4.7 Consensus size: 31 11579173 CTTGTCACTT * 11579183 GTAGCCGAAGCTACCACTATTCACTGATCAG 1 GTAGCCGAAGCTACCACTTTTCACTGATCAG * 11579214 GTAGCC-AGAGCTACCATTTTTCACTGATCAG 1 GTAGCCGA-AGCTACCACTTTTCACTGATCAG * 11579245 GTAGCCGGAGCTACCACTTTTCACTGATCAG 1 GTAGCCGAAGCTACCACTTTTCACTGATCAG * 11579276 GTAGCAGAAGCTACCACTTTTCACTGATCAG 1 GTAGCCGAAGCTACCACTTTTCACTGATCAG * 11579307 GTAGCCAAAGCTACCACTTTTCA 1 GTAGCCGAAGCTACCACTTTTCA 11579330 GTTGTCATTT Statistics Matches: 106, Mismatches: 8, Indels: 4 0.90 0.07 0.03 Matches are distributed among these distances: 30 1 0.01 31 105 0.99 ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26 Consensus pattern (31 bp): GTAGCCGAAGCTACCACTTTTCACTGATCAG Found at i:11579405 original size:50 final size:50 Alignment explanation

Indices: 11579338--11579433 Score: 156 Period size: 50 Copynumber: 1.9 Consensus size: 50 11579328 CAGTTGTCAT * 11579338 TTGTCATTGATCAGATAAGTGTAGCCGAAGCTATCACTTACCACTTTCAC 1 TTGTCATTGATCAGATAAGTGTAGCCGAACCTATCACTTACCACTTTCAC * * * 11579388 TTGTCCTTGATCAGATAAGTGTAGTCGAACCTATCACTTATCACTT 1 TTGTCATTGATCAGATAAGTGTAGCCGAACCTATCACTTACCACTT 11579434 GTTGCCATAG Statistics Matches: 42, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 50 42 1.00 ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34 Consensus pattern (50 bp): TTGTCATTGATCAGATAAGTGTAGCCGAACCTATCACTTACCACTTTCAC Found at i:11579700 original size:46 final size:47 Alignment explanation

Indices: 11579632--11579751 Score: 134 Period size: 47 Copynumber: 2.6 Consensus size: 47 11579622 CTCAGAAGTT * * * * * 11579632 CGATGCCATAGCCCAGCTATGGTCTTACAC-GAATCACATATCTCAT 1 CGATGCCATATCCCAGATATGGTCTTACACAGAAGCACATATCACAC * * * * * 11579678 TGATGCCATATTCCAGATATGGTCTTATACAGTAGCATATATCACAC 1 CGATGCCATATCCCAGATATGGTCTTACACAGAAGCACATATCACAC * 11579725 CGATGACATATCCCAGATATGGTCTTA 1 CGATGCCATATCCCAGATATGGTCTTA 11579752 TACGGAAATC Statistics Matches: 60, Mismatches: 13, Indels: 1 0.81 0.18 0.01 Matches are distributed among these distances: 46 25 0.42 47 35 0.58 ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29 Consensus pattern (47 bp): CGATGCCATATCCCAGATATGGTCTTACACAGAAGCACATATCACAC Found at i:11579822 original size:31 final size:31 Alignment explanation

Indices: 11579787--11579926 Score: 174 Period size: 31 Copynumber: 4.5 Consensus size: 31 11579777 CTTGTAGTCG * * 11579787 AAGCTACCACTATTCACTAATCAGGTAGCCA 1 AAGCTACCACTTTTCACTGATCAGGTAGCCA * * *** 11579818 AAGCTACCATTTTTCACTGATTAGGTAGTTG 1 AAGCTACCACTTTTCACTGATCAGGTAGCCA * * 11579849 GAGCTACCACTTTTCACTGGTCAGGTAG-CA 1 AAGCTACCACTTTTCACTGATCAGGTAGCCA * 11579879 GAAGCTACCACTTTTCACTGATCAGGTAGCCG 1 -AAGCTACCACTTTTCACTGATCAGGTAGCCA 11579911 AAGCTACCACTTTTCA 1 AAGCTACCACTTTTCA 11579927 GTTGTCATTT Statistics Matches: 91, Mismatches: 16, Indels: 4 0.82 0.14 0.04 Matches are distributed among these distances: 31 90 0.99 32 1 0.01 ACGTcount: A:0.28, C:0.26, G:0.18, T:0.29 Consensus pattern (31 bp): AAGCTACCACTTTTCACTGATCAGGTAGCCA Found at i:11579877 original size:62 final size:62 Alignment explanation

Indices: 11579780--11579926 Score: 197 Period size: 62 Copynumber: 2.4 Consensus size: 62 11579770 CTTGTCACTT * * * * 11579780 GTAGTCGAAGCTACCACTATTCACTAATCAGGTAGCCA-AAGCTACCATTTTTCACTGATTAG 1 GTAGCCGAAGCTACCACTTTTCACTAATCAGGTAG-CAGAAGCTACCACTTTTCACTGATCAG ** * ** 11579842 GTAGTTGGAGCTACCACTTTTCACTGGTCAGGTAGCAGAAGCTACCACTTTTCACTGATCAG 1 GTAGCCGAAGCTACCACTTTTCACTAATCAGGTAGCAGAAGCTACCACTTTTCACTGATCAG 11579904 GTAGCCGAAGCTACCACTTTTCA 1 GTAGCCGAAGCTACCACTTTTCA 11579927 GTTGTCATTT Statistics Matches: 74, Mismatches: 10, Indels: 2 0.86 0.12 0.02 Matches are distributed among these distances: 61 2 0.03 62 72 0.97 ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29 Consensus pattern (62 bp): GTAGCCGAAGCTACCACTTTTCACTAATCAGGTAGCAGAAGCTACCACTTTTCACTGATCAG Found at i:11580006 original size:50 final size:51 Alignment explanation

Indices: 11579904--11580032 Score: 188 Period size: 50 Copynumber: 2.5 Consensus size: 51 11579894 CACTGATCAG * * * * * 11579904 GTAGCCGAAGCTACCACTTTTCAGTTGTCATTTGTCATTGATCAGATAAGT 1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTGTCATTAATCAGATAAGT * 11579955 GTAGCCGAAGCTATCACTTATCACTT-TCACTTGTCCTTAATCAGATAAGT 1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTGTCATTAATCAGATAAGT * 11580005 GTAGCCGAACCTATCACTTATCACTTGT 1 GTAGCCGAAGCTATCACTTATCACTTGT 11580033 TGCCATGGTC Statistics Matches: 70, Mismatches: 7, Indels: 2 0.89 0.09 0.03 Matches are distributed among these distances: 50 46 0.66 51 24 0.34 ACGTcount: A:0.26, C:0.23, G:0.16, T:0.34 Consensus pattern (51 bp): GTAGCCGAAGCTATCACTTATCACTTGTCACTTGTCATTAATCAGATAAGT Found at i:11580173 original size:597 final size:597 Alignment explanation

Indices: 11579034--11580232 Score: 2191 Period size: 597 Copynumber: 2.0 Consensus size: 597 11579024 ATATCACATA 11579034 TCGATACCATAGCCCAACTATGGTCTTACACAAATCACATATCTCACTGATGCCATATTCCAGAT 1 TCGATACCATAGCCCAACTATGGTCTTACACAAATCACATATCTCACTGATGCCATATTCCAGAT * 11579099 ATGGTCTTATACAGTAGCATATATCACACCGATGCCATATCCCAGATATGGTCTTATACGAAAAT 66 ATGGTCTTATACAGTAGCATATATCACACCGATGACATATCCCAGATATGGTCTTATACGAAAAT * * 11579164 CACTTGTCACTTGTCACTTGTAGCCGAAGCTACCACTATTCACTGATCAGGTAGCCAGAGCTACC 131 CACTTGTCACTTGTCACTTGTAGCCGAAGCTACCACTATTCACTAATCAGGTAGCCAAAGCTACC 11579229 ATTTTTCACTGATCAGGTAGCCGGAGCTACCACTTTTCACTGATCAGGTAGCAGAAGCTACCACT 196 ATTTTTCACTGATCAGGTAGCCGGAGCTACCACTTTTCACTGATCAGGTAGCAGAAGCTACCACT 11579294 TTTCACTGATCAGGTAGCCAAAGCTACCACTTTTCAGTTGTCATTTGTCATTGATCAGATAAGTG 261 TTTCACTGATCAGGTAGCCAAAGCTACCACTTTTCAGTTGTCATTTGTCATTGATCAGATAAGTG * * 11579359 TAGCCGAAGCTATCACTTACCACTTTCACTTGTCCTTGATCAGATAAGTGTAGTCGAACCTATCA 326 TAGCCGAAGCTATCACTTACCACTTTCACTTGTCCTTAATCAGATAAGTGTAGCCGAACCTATCA * 11579424 CTTATCACTTGTTGCCATAGTCCAACCAAGGTCTTTTCCTTCAATTCATCTTGTCATTGAACTAA 391 CTTATCACTTGTTGCCATAGTCCAACCAAGGTCTTTTCCTTCAATTCATCTTGTCACTGAACTAA 11579489 AATGCTCAATTTGATCATTTATTCAATTTTCATGCTTTTATATTATTCACGATTTTATCATCAAT 456 AATGCTCAATTTGATCATTTATTCAATTTTCATGCTTTTATATTATTCACGATTTTATCATCAAT 11579554 ACATATGAAATAACACATCATGAAATTCATAAAATTAACAAATAATCACTAAAATTTAGCCATAT 521 ACATATGAAATAACACATCATGAAATTCATAAAATTAACAAATAATCACTAAAATTTAGCCATAT * 11579619 AAACTCAGAAGT 586 AAACTCAAAAGT * * * * 11579631 TCGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCATTGATGCCATATTCCAGAT 1 TCGATACCATAGCCCAACTATGGTCTTACACAAATCACATATCTCACTGATGCCATATTCCAGAT * 11579696 ATGGTCTTATACAGTAGCATATATCACACCGATGACATATCCCAGATATGGTCTTATACGGAAAT 66 ATGGTCTTATACAGTAGCATATATCACACCGATGACATATCCCAGATATGGTCTTATACGAAAAT * 11579761 CACTTGTCACTTGTCACTTGTAGTCGAAGCTACCACTATTCACTAATCAGGTAGCCAAAGCTACC 131 CACTTGTCACTTGTCACTTGTAGCCGAAGCTACCACTATTCACTAATCAGGTAGCCAAAGCTACC * ** * 11579826 ATTTTTCACTGATTAGGTAGTTGGAGCTACCACTTTTCACTGGTCAGGTAGCAGAAGCTACCACT 196 ATTTTTCACTGATCAGGTAGCCGGAGCTACCACTTTTCACTGATCAGGTAGCAGAAGCTACCACT * 11579891 TTTCACTGATCAGGTAGCCGAAGCTACCACTTTTCAGTTGTCATTTGTCATTGATCAGATAAGTG 261 TTTCACTGATCAGGTAGCCAAAGCTACCACTTTTCAGTTGTCATTTGTCATTGATCAGATAAGTG * 11579956 TAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTAATCAGATAAGTGTAGCCGAACCTATCA 326 TAGCCGAAGCTATCACTTACCACTTTCACTTGTCCTTAATCAGATAAGTGTAGCCGAACCTATCA * * 11580021 CTTATCACTTGTTGCCATGGTCCAACCATGGTCTTTTCCTTCAATTCATCTTGTCACTGAACTAA 391 CTTATCACTTGTTGCCATAGTCCAACCAAGGTCTTTTCCTTCAATTCATCTTGTCACTGAACTAA * 11580086 AATGCTCAATTTGATCATTTATTCAATTTTCATGCTTTTATATTGTTCACGATTTTATCATCAAT 456 AATGCTCAATTTGATCATTTATTCAATTTTCATGCTTTTATATTATTCACGATTTTATCATCAAT * 11580151 ACATATGAAATAACACATCATGAAATTCATAAAATTAATAAATAATCACTAAAATTTAGCCATAT 521 ACATATGAAATAACACATCATGAAATTCATAAAATTAACAAATAATCACTAAAATTTAGCCATAT 11580216 AAACTCAAAAGT 586 AAACTCAAAAGT 11580228 TCGAT 1 TCGAT 11580233 TTTGTTATTA Statistics Matches: 579, Mismatches: 23, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 597 579 1.00 ACGTcount: A:0.31, C:0.23, G:0.14, T:0.33 Consensus pattern (597 bp): TCGATACCATAGCCCAACTATGGTCTTACACAAATCACATATCTCACTGATGCCATATTCCAGAT ATGGTCTTATACAGTAGCATATATCACACCGATGACATATCCCAGATATGGTCTTATACGAAAAT CACTTGTCACTTGTCACTTGTAGCCGAAGCTACCACTATTCACTAATCAGGTAGCCAAAGCTACC ATTTTTCACTGATCAGGTAGCCGGAGCTACCACTTTTCACTGATCAGGTAGCAGAAGCTACCACT TTTCACTGATCAGGTAGCCAAAGCTACCACTTTTCAGTTGTCATTTGTCATTGATCAGATAAGTG TAGCCGAAGCTATCACTTACCACTTTCACTTGTCCTTAATCAGATAAGTGTAGCCGAACCTATCA CTTATCACTTGTTGCCATAGTCCAACCAAGGTCTTTTCCTTCAATTCATCTTGTCACTGAACTAA AATGCTCAATTTGATCATTTATTCAATTTTCATGCTTTTATATTATTCACGATTTTATCATCAAT ACATATGAAATAACACATCATGAAATTCATAAAATTAACAAATAATCACTAAAATTTAGCCATAT AAACTCAAAAGT Found at i:11582496 original size:26 final size:26 Alignment explanation

Indices: 11582461--11582631 Score: 115 Period size: 24 Copynumber: 6.8 Consensus size: 26 11582451 GCAGCTCTTA * * 11582461 TGAGCGTCCCGATATATGGCTCTTTG 1 TGAGCTTCCCGTTATATGGCTCTTTG * * * 11582487 TGAGCTTCCCGTT-TAAAGGTTTTTTG 1 TGAGCTTCCCGTTAT-ATGGCTCTTTG ** 11582513 TGAGCTTCCCGTTA-ATGGCTCTCCG 1 TGAGCTTCCCGTTATATGGCTCTTTG * * *** 11582538 -GAGCTTCCTGATAT-TGGCTC-GCA 1 TGAGCTTCCCGTTATATGGCTCTTTG * 11582561 TGAGCTTCCTGTTA-ATGGCTCTTTG 1 TGAGCTTCCCGTTATATGGCTCTTTG * *** 11582586 -GAGCTTCCCGTTACATGGCTC-ACA 1 TGAGCTTCCCGTTATATGGCTCTTTG * 11582610 TGAGCTTTCCGTTATATGGCTC 1 TGAGCTTCCCGTTATATGGCTC 11582632 AAGAGAGAGC Statistics Matches: 113, Mismatches: 24, Indels: 17 0.73 0.16 0.11 Matches are distributed among these distances: 23 1 0.01 24 47 0.42 25 33 0.29 26 32 0.28 ACGTcount: A:0.15, C:0.25, G:0.24, T:0.36 Consensus pattern (26 bp): TGAGCTTCCCGTTATATGGCTCTTTG Found at i:11582569 original size:48 final size:49 Alignment explanation

Indices: 11582513--11582631 Score: 150 Period size: 48 Copynumber: 2.4 Consensus size: 49 11582503 AGGTTTTTTG * * * 11582513 TGAGCTTCCCGTTAATGGCTCTCCGGAGCTTCCTGATA-TTGGCTCGCA 1 TGAGCTTCCCGTTAATGGCTCTCCGGAGCTTCCCGATACATGGCTCACA * ** * 11582561 TGAGCTTCCTGTTAATGGCTCTTTGGAGCTTCCCGTTACATGGCTCACA 1 TGAGCTTCCCGTTAATGGCTCTCCGGAGCTTCCCGATACATGGCTCACA * 11582610 TGAGCTTTCCGTTATATGGCTC 1 TGAGCTTCCCGTTA-ATGGCTC 11582632 AAGAGAGAGC Statistics Matches: 60, Mismatches: 9, Indels: 2 0.85 0.13 0.03 Matches are distributed among these distances: 48 33 0.55 49 20 0.33 50 7 0.12 ACGTcount: A:0.15, C:0.27, G:0.24, T:0.34 Consensus pattern (49 bp): TGAGCTTCCCGTTAATGGCTCTCCGGAGCTTCCCGATACATGGCTCACA Found at i:11582649 original size:27 final size:26 Alignment explanation

Indices: 11582586--11582659 Score: 64 Period size: 25 Copynumber: 2.8 Consensus size: 26 11582576 TGGCTCTTTG * * * 11582586 GAGCTTCCCGTTACATGGCTC-ACAT 1 GAGCTTCTCGTTATATGGCTCAACAA * 11582611 GAGCTT-TCCGTTATATGGCTCAAGAGA 1 GAGCTTCT-CGTTATATGGCTCAACA-A 11582638 GAGCTTCTCGTT-TATGTGCTCA 1 GAGCTTCTCGTTATATG-GCTCA 11582660 TATGAGCATT Statistics Matches: 40, Mismatches: 4, Indels: 8 0.77 0.08 0.15 Matches are distributed among these distances: 25 18 0.45 26 6 0.15 27 15 0.38 28 1 0.03 ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32 Consensus pattern (26 bp): GAGCTTCTCGTTATATGGCTCAACAA Found at i:11585713 original size:26 final size:26 Alignment explanation

Indices: 11585684--11585744 Score: 70 Period size: 26 Copynumber: 2.3 Consensus size: 26 11585674 TCAAAAATAT ** * 11585684 TTTTTAAATTTACTTTTCCACAA-CAC 1 TTTTTAAAAATACTTTT-CAAAAGCAC * 11585710 TTTTTAAAAATACTTTTTAAAAGCAC 1 TTTTTAAAAATACTTTTCAAAAGCAC 11585736 TTTTTAAAA 1 TTTTTAAAA 11585745 GTAATGCTAA Statistics Matches: 30, Mismatches: 4, Indels: 2 0.83 0.11 0.06 Matches are distributed among these distances: 25 3 0.10 26 27 0.90 ACGTcount: A:0.38, C:0.15, G:0.02, T:0.46 Consensus pattern (26 bp): TTTTTAAAAATACTTTTCAAAAGCAC Found at i:11585724 original size:13 final size:13 Alignment explanation

Indices: 11585669--11585744 Score: 62 Period size: 13 Copynumber: 5.8 Consensus size: 13 11585659 CTTAAATCAA * 11585669 ACTTTTCAAAAAT 1 ACTTTTTAAAAAT * ** 11585682 ATTTTTTAAATTT 1 ACTTTTTAAAAAT ** * * 11585695 ACTTTTCCACAAC 1 ACTTTTTAAAAAT 11585708 ACTTTTTAAAAAT 1 ACTTTTTAAAAAT ** 11585721 ACTTTTTAAAAGC 1 ACTTTTTAAAAAT 11585734 ACTTTTTAAAA 1 ACTTTTTAAAA 11585745 GTAATGCTAA Statistics Matches: 46, Mismatches: 17, Indels: 0 0.73 0.27 0.00 Matches are distributed among these distances: 13 46 1.00 ACGTcount: A:0.39, C:0.14, G:0.01, T:0.45 Consensus pattern (13 bp): ACTTTTTAAAAAT Found at i:11599063 original size:2 final size:2 Alignment explanation

Indices: 11599056--11599271 Score: 432 Period size: 2 Copynumber: 108.0 Consensus size: 2 11599046 ACAAAAAGAG 11599056 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 11599098 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 11599140 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 11599182 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 11599224 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 11599266 CT CT CT 1 CT CT CT 11599272 TAATTTGAAT Statistics Matches: 214, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 214 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:11600149 original size:2 final size:2 Alignment explanation

Indices: 11600144--11600180 Score: 74 Period size: 2 Copynumber: 18.5 Consensus size: 2 11600134 AAAAATTATC 11600144 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 11600181 TCTGTAAATT Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 35 1.00 ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51 Consensus pattern (2 bp): TA Found at i:11602586 original size:5 final size:5 Alignment explanation

Indices: 11602576--11602602 Score: 54 Period size: 5 Copynumber: 5.4 Consensus size: 5 11602566 TAAAAAAGAT 11602576 AATAA AATAA AATAA AATAA AATAA AA 1 AATAA AATAA AATAA AATAA AATAA AA 11602603 CTTCATGCTT Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 22 1.00 ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19 Consensus pattern (5 bp): AATAA Found at i:11604302 original size:13 final size:13 Alignment explanation

Indices: 11604284--11604310 Score: 54 Period size: 13 Copynumber: 2.1 Consensus size: 13 11604274 AACAAAAAAC 11604284 TAAATGAATCACA 1 TAAATGAATCACA 11604297 TAAATGAATCACA 1 TAAATGAATCACA 11604310 T 1 T 11604311 GAAACAAAAC Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 14 1.00 ACGTcount: A:0.52, C:0.15, G:0.07, T:0.26 Consensus pattern (13 bp): TAAATGAATCACA Found at i:11605559 original size:17 final size:17 Alignment explanation

Indices: 11605537--11605572 Score: 54 Period size: 17 Copynumber: 2.1 Consensus size: 17 11605527 TAATAAAAAA 11605537 TATTAAATTAATTTTTT 1 TATTAAATTAATTTTTT * * 11605554 TATTAATTTTATTTTTT 1 TATTAAATTAATTTTTT 11605571 TA 1 TA 11605573 AATTTTATTT Statistics Matches: 17, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 17 17 1.00 ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69 Consensus pattern (17 bp): TATTAAATTAATTTTTT Found at i:11605576 original size:15 final size:16 Alignment explanation

Indices: 11605547--11605587 Score: 57 Period size: 15 Copynumber: 2.5 Consensus size: 16 11605537 TATTAAATTA 11605547 ATTTTTTTATTAATTTT 1 ATTTTTTTA-TAATTTT 11605564 ATTTTTTTA-AATTTT 1 ATTTTTTTATAATTTT 11605579 ATTTATTTT 1 ATTT-TTTT 11605588 TATTGTTAAG Statistics Matches: 23, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 15 10 0.43 16 4 0.17 17 9 0.39 ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76 Consensus pattern (16 bp): ATTTTTTTATAATTTT Found at i:11617468 original size:30 final size:29 Alignment explanation

Indices: 11617412--11617470 Score: 75 Period size: 30 Copynumber: 2.0 Consensus size: 29 11617402 AATTAAGCTT * 11617412 AAAATTTAAAATTTAAATTCTTAAAAATA 1 AAAATTTAAAATTTAAATTCTCAAAAATA * 11617441 AAAATATTAAACTTTAAATT-TACAAAAATA 1 AAAAT-TTAAAATTTAAATTCT-CAAAAATA 11617471 CTAAACATAT Statistics Matches: 26, Mismatches: 2, Indels: 3 0.84 0.06 0.10 Matches are distributed among these distances: 29 6 0.23 30 20 0.77 ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36 Consensus pattern (29 bp): AAAATTTAAAATTTAAATTCTCAAAAATA Found at i:11626886 original size:25 final size:25 Alignment explanation

Indices: 11626759--11626901 Score: 169 Period size: 25 Copynumber: 5.7 Consensus size: 25 11626749 TGTAAATGTT * * * ** 11626759 AAGCTCCTCCGAGCTAAATAACGGG 1 AAGCTCATGCGAGCTGAATAATAGG 11626784 AAGCTCATGCGAGCTGAATAATAGG 1 AAGCTCATGCGAGCTGAATAATAGG 11626809 AAGCTCATGCGAGCTGAATAATAGG 1 AAGCTCATGCGAGCTGAATAATAGG * * 11626834 AAGCTCATGCGAGCTGAATAACATG 1 AAGCTCATGCGAGCTGAATAATAGG * * * * 11626859 AAGCTTATGCGAGCTGAGTATTGGG 1 AAGCTCATGCGAGCTGAATAATAGG ** 11626884 AAGCTCATAAGAGCTGAA 1 AAGCTCATGCGAGCTGAA 11626902 ATCGGTGACC Statistics Matches: 101, Mismatches: 17, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 25 101 1.00 ACGTcount: A:0.34, C:0.18, G:0.27, T:0.20 Consensus pattern (25 bp): AAGCTCATGCGAGCTGAATAATAGG Found at i:11626886 original size:75 final size:75 Alignment explanation

Indices: 11626759--11626901 Score: 187 Period size: 75 Copynumber: 1.9 Consensus size: 75 11626749 TGTAAATGTT * * ** 11626759 AAGCTCCTCCGAGCTAAATAACGGGAAGCTCATGCGAGCTGAATAATAGGAAGCTCATGCGAGCT 1 AAGCTCATCCGAGCTAAATAACAGGAAGCTCATGCGAGCTGAATAATAGGAAGCTCATAAGAGCT 11626824 GAATAATAGG 66 GAATAATAGG * * * * * * * 11626834 AAGCTCATGCGAGCTGAATAACATGAAGCTTATGCGAGCTGAGTATTGGGAAGCTCATAAGAGCT 1 AAGCTCATCCGAGCTAAATAACAGGAAGCTCATGCGAGCTGAATAATAGGAAGCTCATAAGAGCT 11626899 GAA 66 GAA 11626902 ATCGGTGACC Statistics Matches: 57, Mismatches: 11, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 75 57 1.00 ACGTcount: A:0.34, C:0.18, G:0.27, T:0.20 Consensus pattern (75 bp): AAGCTCATCCGAGCTAAATAACAGGAAGCTCATGCGAGCTGAATAATAGGAAGCTCATAAGAGCT GAATAATAGG Found at i:11629946 original size:52 final size:53 Alignment explanation

Indices: 11629817--11629982 Score: 178 Period size: 52 Copynumber: 3.1 Consensus size: 53 11629807 TCTTACACGG * * * * 11629817 ATCACATAACGTACCGATGCCATATCCCAGATATGGTCTTCTA-TGGAATCACATT 1 ATCACAT--CGTACCGATGCCATAGCCCAGCTATGGTCTTATACGGGAATCACA-T ** * 11629872 ATCACATCACACTGATGCCATAGCCCAGCTATGGTCTTATACGGGAA-CACGA- 1 ATCACATCGTACCGATGCCATAGCCCAGCTATGGTCTTATACGGGAATCAC-AT * * * 11629924 ATCACATTGTACCGATGCCATAGCCCAGCTATGGTCTTAAAC-GGAAGCACAT 1 ATCACATCGTACCGATGCCATAGCCCAGCTATGGTCTTATACGGGAATCACAT 11629976 ATCACAT 1 ATCACAT 11629983 ATTTTCTATC Statistics Matches: 95, Mismatches: 12, Indels: 11 0.81 0.10 0.09 Matches are distributed among these distances: 51 5 0.05 52 47 0.49 53 31 0.33 54 5 0.05 55 7 0.07 ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25 Consensus pattern (53 bp): ATCACATCGTACCGATGCCATAGCCCAGCTATGGTCTTATACGGGAATCACAT Found at i:11632257 original size:18 final size:18 Alignment explanation

Indices: 11632207--11632271 Score: 58 Period size: 18 Copynumber: 3.6 Consensus size: 18 11632197 CCGGCGCTCT * * 11632207 ATAACAGTCAGTTATGCA 1 ATAACAGTCAATTATTCA * * * * 11632225 GTAATAGTTATTTATTCA 1 ATAACAGTCAATTATTCA * 11632243 ATAACAGTCAATTATTCC 1 ATAACAGTCAATTATTCA * 11632261 ATAGCAGTCAA 1 ATAACAGTCAA 11632272 CCTTTAATAC Statistics Matches: 36, Mismatches: 11, Indels: 0 0.77 0.23 0.00 Matches are distributed among these distances: 18 36 1.00 ACGTcount: A:0.38, C:0.15, G:0.12, T:0.34 Consensus pattern (18 bp): ATAACAGTCAATTATTCA Found at i:11632398 original size:6 final size:6 Alignment explanation

Indices: 11632389--11632422 Score: 50 Period size: 6 Copynumber: 5.7 Consensus size: 6 11632379 GAAATACACC * * 11632389 GTAACG GTAACA GTAATA GTAACA GTAACA GTAA 1 GTAACA GTAACA GTAACA GTAACA GTAACA GTAA 11632423 TGGTACACAA Statistics Matches: 25, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 6 25 1.00 ACGTcount: A:0.47, C:0.12, G:0.21, T:0.21 Consensus pattern (6 bp): GTAACA Found at i:11632416 original size:18 final size:18 Alignment explanation

Indices: 11632389--11632423 Score: 61 Period size: 18 Copynumber: 1.9 Consensus size: 18 11632379 GAAATACACC * 11632389 GTAACGGTAACAGTAATA 1 GTAACAGTAACAGTAATA 11632407 GTAACAGTAACAGTAAT 1 GTAACAGTAACAGTAAT 11632424 GGTACACAAA Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 16 1.00 ACGTcount: A:0.46, C:0.11, G:0.20, T:0.23 Consensus pattern (18 bp): GTAACAGTAACAGTAATA Found at i:11632512 original size:51 final size:53 Alignment explanation

Indices: 11632406--11632520 Score: 137 Period size: 51 Copynumber: 2.2 Consensus size: 53 11632396 TAACAGTAAT 11632406 AGTAACAGTAACAGTAATGGTACACAAAGTACCTCATCGAAACAAATCTGAAAC 1 AGTAACAGTAACAGTAATGGTA-ACAAAGTACCTCATCGAAACAAATCTGAAAC * * * * * 11632460 AGTAACAGTAACAGTCA-GGT-ACAGAGTACCTCTTCGGAACGAAT-TCGAAAC 1 AGTAACAGTAACAGTAATGGTAACAAAGTACCTCATCGAAACAAATCT-GAAAC * 11632511 AGTCACAGTA 1 AGTAACAGTA 11632521 GTCGACACAT Statistics Matches: 54, Mismatches: 6, Indels: 5 0.83 0.09 0.08 Matches are distributed among these distances: 50 1 0.02 51 34 0.63 53 3 0.06 54 16 0.30 ACGTcount: A:0.42, C:0.21, G:0.18, T:0.19 Consensus pattern (53 bp): AGTAACAGTAACAGTAATGGTAACAAAGTACCTCATCGAAACAAATCTGAAAC Found at i:11633587 original size:16 final size:18 Alignment explanation

Indices: 11633558--11633598 Score: 59 Period size: 17 Copynumber: 2.4 Consensus size: 18 11633548 TCATCCTTTC 11633558 TTTCTTTTTCTATT-CTT 1 TTTCTTTTTCTATTCCTT 11633575 TTTCTTTTT-TATTCCTT 1 TTTCTTTTTCTATTCCTT * 11633592 TTACTTT 1 TTTCTTT 11633599 ATATATATAT Statistics Matches: 22, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 16 4 0.18 17 18 0.82 ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76 Consensus pattern (18 bp): TTTCTTTTTCTATTCCTT Found at i:11633891 original size:29 final size:30 Alignment explanation

Indices: 11633858--11633917 Score: 79 Period size: 29 Copynumber: 2.0 Consensus size: 30 11633848 TTGTCTTTTC 11633858 TTAATTT-ATTTCATAATATAATAAC-ATAA 1 TTAATTTAATTT-ATAATATAATAACAATAA * * 11633887 TTAATTTAATTTGTAATATAATGACAATAA 1 TTAATTTAATTTATAATATAATAACAATAA 11633917 T 1 T 11633918 AACAATAATA Statistics Matches: 27, Mismatches: 2, Indels: 3 0.84 0.06 0.09 Matches are distributed among these distances: 29 18 0.67 30 9 0.33 ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45 Consensus pattern (30 bp): TTAATTTAATTTATAATATAATAACAATAA Found at i:11640368 original size:17 final size:19 Alignment explanation

Indices: 11640326--11640369 Score: 56 Period size: 19 Copynumber: 2.4 Consensus size: 19 11640316 ATGAAATTTT * 11640326 AATTAGTATTATGAGATAA 1 AATTATTATTATGAGATAA * 11640345 AATTATTATTATTAGA-AA 1 AATTATTATTATGAGATAA 11640363 AA-TATTA 1 AATTATTA 11640370 CTGTATGTAT Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 17 5 0.22 18 4 0.17 19 14 0.61 ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41 Consensus pattern (19 bp): AATTATTATTATGAGATAA Found at i:11640443 original size:2 final size:2 Alignment explanation

Indices: 11640436--11640468 Score: 57 Period size: 2 Copynumber: 16.5 Consensus size: 2 11640426 TTAGATAGGA * 11640436 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 11640469 AAAGTATTTT Statistics Matches: 29, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 2 29 1.00 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (2 bp): AT Found at i:11642181 original size:60 final size:59 Alignment explanation

Indices: 11642105--11642241 Score: 152 Period size: 60 Copynumber: 2.3 Consensus size: 59 11642095 AATTGTGTTA * * * 11642105 ATATGGGCAAGGCCCAATATA-TCTCGACT-TGTAATAGGGCTACGGCCCAGATTCATACTG 1 ATATGGGCTAGGCCCAATATACTCT-GA-TATGTAA-AGGGCTACGACCCAGATTAATACTG * * * 11642165 ATATGGGCTAGGCCCAATATACTCTGATACTGTAAGGGGCTATGACCCAGATTAATATTG 1 ATATGGGCTAGGCCCAATATACTCTGATA-TGTAAAGGGCTACGACCCAGATTAATACTG * 11642225 ATATGGACTAAGGCCCA 1 ATATGGGCT-AGGCCCA 11642242 GTTAACACTG Statistics Matches: 66, Mismatches: 7, Indels: 7 0.82 0.09 0.09 Matches are distributed among these distances: 59 1 0.02 60 50 0.76 61 15 0.23 ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26 Consensus pattern (59 bp): ATATGGGCTAGGCCCAATATACTCTGATATGTAAAGGGCTACGACCCAGATTAATACTG Found at i:11644060 original size:46 final size:46 Alignment explanation

Indices: 11643992--11644128 Score: 220 Period size: 46 Copynumber: 3.0 Consensus size: 46 11643982 TATATATACA * * * * 11643992 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC 1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC * * 11644038 CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTACCTCATATC 1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC 11644084 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATAT 1 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATAT 11644129 ATACACTTCC Statistics Matches: 83, Mismatches: 8, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 46 83 1.00 ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34 Consensus pattern (46 bp): CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATATC Found at i:11644173 original size:47 final size:47 Alignment explanation

Indices: 11644102--11644433 Score: 459 Period size: 47 Copynumber: 7.1 Consensus size: 47 11644092 ACACATTTCG * * * * * * * 11644102 CATTAGCCATTCGGCTTTACCACATATATACACT-TCCGCGTTCATCA 1 CATTGGCCATTCGGCCTTATCACATATATGCA-TGTTCACATTCATCA ** 11644149 CATTGGCCATTTTGCCTTATCACATATATGCATGTTCACATTCATCA 1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA * 11644196 CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCA 1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA * * 11644243 CATTGGCCATTCGGCCTTATCACACATATACATGTTCACATTCATCA 1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA 11644290 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA 1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA * * 11644337 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCATATTCATCA 1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA * * * * * ** 11644384 CATTTGCCATCCGGCCTTATCTCACATATACACATTCACATTCATCA 1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA 11644431 CAT 1 CAT 11644434 AAAATCCTAA Statistics Matches: 260, Mismatches: 24, Indels: 2 0.91 0.08 0.01 Matches are distributed among these distances: 46 1 0.00 47 259 1.00 ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34 Consensus pattern (47 bp): CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA Found at i:11644266 original size:22 final size:22 Alignment explanation

Indices: 11644192--11644266 Score: 57 Period size: 22 Copynumber: 3.3 Consensus size: 22 11644182 GTTCACATTC 11644192 ATCACATTGGCCATTCGGCCTT 1 ATCACATTGGCCATTCGGCCTT * * 11644214 ATCACACATAT-G-CATGTTC-ACATT 1 AT--CACAT-TGGCCA--TTCGGCCTT 11644238 CATCACATTGGCCATTCGGCCTT 1 -ATCACATTGGCCATTCGGCCTT 11644261 ATCACA 1 ATCACA 11644267 CATATACATG Statistics Matches: 40, Mismatches: 4, Indels: 18 0.65 0.06 0.29 Matches are distributed among these distances: 22 12 0.30 23 11 0.28 24 11 0.28 25 6 0.15 ACGTcount: A:0.25, C:0.31, G:0.13, T:0.31 Consensus pattern (22 bp): ATCACATTGGCCATTCGGCCTT Found at i:11644313 original size:22 final size:22 Alignment explanation

Indices: 11644286--11644357 Score: 58 Period size: 22 Copynumber: 3.1 Consensus size: 22 11644276 GTTCACATTC 11644286 ATCACATTGGCCATTCGGCCTT 1 ATCACATTGGCCATTCGGCCTT * * * 11644308 ATCACATATATG-CATGTTC-ACATT 1 ATCACAT-T-GGCCA--TTCGGCCTT 11644332 CATCACATTGGCCATTCGGCCTT 1 -ATCACATTGGCCATTCGGCCTT 11644355 ATC 1 ATC 11644358 TCATATATGC Statistics Matches: 37, Mismatches: 6, Indels: 14 0.65 0.11 0.25 Matches are distributed among these distances: 22 13 0.35 23 7 0.19 24 7 0.19 25 10 0.27 ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33 Consensus pattern (22 bp): ATCACATTGGCCATTCGGCCTT Found at i:11649782 original size:22 final size:23 Alignment explanation

Indices: 11649757--11649802 Score: 60 Period size: 23 Copynumber: 2.0 Consensus size: 23 11649747 CAACCAAACC 11649757 AATTCA-ACATATTT-TCAAGATA 1 AATTCATACATATTTAT-AAGATA * 11649779 AATTCATGCATATTTATAAGATA 1 AATTCATACATATTTATAAGATA 11649802 A 1 A 11649803 CGTCATCACA Statistics Matches: 21, Mismatches: 1, Indels: 3 0.84 0.04 0.12 Matches are distributed among these distances: 22 6 0.29 23 14 0.67 24 1 0.05 ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37 Consensus pattern (23 bp): AATTCATACATATTTATAAGATA Found at i:11649808 original size:23 final size:23 Alignment explanation

Indices: 11649764--11649808 Score: 56 Period size: 23 Copynumber: 2.0 Consensus size: 23 11649754 ACCAATTCAA * 11649764 CATATTTTCAAGATAAATTCATG 1 CATATTTTCAAGATAAAGTCATG * 11649787 CATATTTAT-AAGATAACGTCAT 1 CATATTT-TCAAGATAAAGTCAT 11649809 CACATACTTA Statistics Matches: 19, Mismatches: 2, Indels: 2 0.83 0.09 0.09 Matches are distributed among these distances: 23 18 0.95 24 1 0.05 ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38 Consensus pattern (23 bp): CATATTTTCAAGATAAAGTCATG Found at i:11656458 original size:22 final size:23 Alignment explanation

Indices: 11656433--11656478 Score: 60 Period size: 23 Copynumber: 2.0 Consensus size: 23 11656423 CAACCAAACC 11656433 AATTCA-CCATATTT-TCAAGATA 1 AATTCATCCATATTTAT-AAGATA * 11656455 AATTCATGCATATTTATAAGATA 1 AATTCATCCATATTTATAAGATA 11656478 A 1 A 11656479 CATCATCACA Statistics Matches: 21, Mismatches: 1, Indels: 3 0.84 0.04 0.12 Matches are distributed among these distances: 22 6 0.29 23 14 0.67 24 1 0.05 ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37 Consensus pattern (23 bp): AATTCATCCATATTTATAAGATA Found at i:11665204 original size:15 final size:15 Alignment explanation

Indices: 11665184--11665213 Score: 60 Period size: 15 Copynumber: 2.0 Consensus size: 15 11665174 ACACTTGTAC 11665184 TAAATCATCACCCTA 1 TAAATCATCACCCTA 11665199 TAAATCATCACCCTA 1 TAAATCATCACCCTA 11665214 CATTTGTCAA Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.40, C:0.33, G:0.00, T:0.27 Consensus pattern (15 bp): TAAATCATCACCCTA Found at i:11665811 original size:25 final size:25 Alignment explanation

Indices: 11665779--11665828 Score: 100 Period size: 25 Copynumber: 2.0 Consensus size: 25 11665769 TTAATTAAGA 11665779 AAAATTTGCCTAATTAAAACTTAAT 1 AAAATTTGCCTAATTAAAACTTAAT 11665804 AAAATTTGCCTAATTAAAACTTAAT 1 AAAATTTGCCTAATTAAAACTTAAT 11665829 TAAGCTCACT Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 25 25 1.00 ACGTcount: A:0.48, C:0.12, G:0.04, T:0.36 Consensus pattern (25 bp): AAAATTTGCCTAATTAAAACTTAAT Found at i:11673308 original size:11 final size:11 Alignment explanation

Indices: 11673292--11673334 Score: 61 Period size: 11 Copynumber: 4.0 Consensus size: 11 11673282 GTGGTTATAA 11673292 TATTTTAATAT 1 TATTTTAATAT 11673303 TATTTTAATAT 1 TATTTTAATAT 11673314 TATTTTAA-AT 1 TATTTTAATAT * * 11673324 TCTTATAATAT 1 TATTTTAATAT 11673335 GTGAAATGAC Statistics Matches: 29, Mismatches: 2, Indels: 2 0.88 0.06 0.06 Matches are distributed among these distances: 10 8 0.28 11 21 0.72 ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60 Consensus pattern (11 bp): TATTTTAATAT Found at i:11673334 original size:21 final size:22 Alignment explanation

Indices: 11673292--11673334 Score: 61 Period size: 21 Copynumber: 2.0 Consensus size: 22 11673282 GTGGTTATAA * 11673292 TATTTTAATATTATTTTAATAT 1 TATTTTAATATTATTATAATAT * 11673314 TATTTTAA-ATTCTTATAATAT 1 TATTTTAATATTATTATAATAT 11673335 GTGAAATGAC Statistics Matches: 19, Mismatches: 2, Indels: 1 0.86 0.09 0.05 Matches are distributed among these distances: 21 11 0.58 22 8 0.42 ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60 Consensus pattern (22 bp): TATTTTAATATTATTATAATAT Found at i:11673594 original size:87 final size:87 Alignment explanation

Indices: 11673448--11673621 Score: 348 Period size: 87 Copynumber: 2.0 Consensus size: 87 11673438 TGTTAAAAGT 11673448 GCCTATTTGATTTGTCTTCATAAAAGGGAGGTCCTTATGATGCAATTAGACCATTGAACATATGA 1 GCCTATTTGATTTGTCTTCATAAAAGGGAGGTCCTTATGATGCAATTAGACCATTGAACATATGA 11673513 GTGGACATTAATGGCCTTGATA 66 GTGGACATTAATGGCCTTGATA 11673535 GCCTATTTGATTTGTCTTCATAAAAGGGAGGTCCTTATGATGCAATTAGACCATTGAACATATGA 1 GCCTATTTGATTTGTCTTCATAAAAGGGAGGTCCTTATGATGCAATTAGACCATTGAACATATGA 11673600 GTGGACATTAATGGCCTTGATA 66 GTGGACATTAATGGCCTTGATA 11673622 TTAATGTTTT Statistics Matches: 87, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 87 87 1.00 ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33 Consensus pattern (87 bp): GCCTATTTGATTTGTCTTCATAAAAGGGAGGTCCTTATGATGCAATTAGACCATTGAACATATGA GTGGACATTAATGGCCTTGATA Found at i:11678035 original size:58 final size:58 Alignment explanation

Indices: 11677963--11678098 Score: 254 Period size: 58 Copynumber: 2.3 Consensus size: 58 11677953 TTAGGGTCTA * 11677963 ATTTAGCCTAGACTGGTAATTCAGATCCAAGCTCATTAGAGTAATTGTCGTTGCAGGG 1 ATTTAGCCTGGACTGGTAATTCAGATCCAAGCTCATTAGAGTAATTGTCGTTGCAGGG * 11678021 ATTTAGCCTGGACTGGTAATTCAGATCCAAGCTCATTAGAGTAATTTTCGTTGCAGGG 1 ATTTAGCCTGGACTGGTAATTCAGATCCAAGCTCATTAGAGTAATTGTCGTTGCAGGG 11678079 ATTTAGCCTGGACTGGTAAT 1 ATTTAGCCTGGACTGGTAAT 11678099 CTCGCTGCAA Statistics Matches: 76, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 58 76 1.00 ACGTcount: A:0.26, C:0.17, G:0.24, T:0.32 Consensus pattern (58 bp): ATTTAGCCTGGACTGGTAATTCAGATCCAAGCTCATTAGAGTAATTGTCGTTGCAGGG Found at i:11678752 original size:14 final size:14 Alignment explanation

Indices: 11678729--11678758 Score: 51 Period size: 14 Copynumber: 2.1 Consensus size: 14 11678719 TTGAAAATAT 11678729 GTTGAATTGGATTG 1 GTTGAATTGGATTG * 11678743 GTTGATTTGGATTG 1 GTTGAATTGGATTG 11678757 GT 1 GT 11678759 CTCGATATAA Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 14 15 1.00 ACGTcount: A:0.17, C:0.00, G:0.37, T:0.47 Consensus pattern (14 bp): GTTGAATTGGATTG Found at i:11683909 original size:204 final size:204 Alignment explanation

Indices: 11683553--11683972 Score: 822 Period size: 204 Copynumber: 2.1 Consensus size: 204 11683543 TTAGAAATAA * 11683553 AAAGATAAATTTGGTGAAAGTATTGTGGCAAAAGTACGGGATTGAGGAAGCGACATGGGAACTAG 1 AAAGAGAAATTTGGTGAAAGTATTGTGGCAAAAGTACGGGATTGAGGAAGCGACATGGGAACTAG 11683618 AGGAGGCAATGAGGAAACAATACCTAAATCTCTTTAATGGTAAGATTTTCGAGGACGAAAATCCT 66 AGGAGGCAATGAGGAAACAATACCTAAATCTCTTTAATGGTAAGATTTTCGAGGACGAAAATCCT * 11683683 TAAAAGGGGGAGAGTTGTAATGACCTAAATTTAAAGTTATCGGAACAGTGGTTTCGTAACCACAA 131 TAAAAGGGGGAGAGTTGTAATGACCTAAATTTAAAGTTATCGGAACAGTGGTTTCGGAACCACAA 11683748 ATCCAATTT 196 ATCCAATTT 11683757 AAAGAGAAATTTGGTGAAAGTATTGTGGCAAAAGTACGGGATTGAGGAAGCGACATGGGAACTAG 1 AAAGAGAAATTTGGTGAAAGTATTGTGGCAAAAGTACGGGATTGAGGAAGCGACATGGGAACTAG 11683822 AGGAGGCAATGAGGAAACAATACCTAAATCTCTTTAATGGTAAGATTTTCGAGGACGAAAATCCT 66 AGGAGGCAATGAGGAAACAATACCTAAATCTCTTTAATGGTAAGATTTTCGAGGACGAAAATCCT 11683887 TAAAAGGGGGAGAGTTGTAATGACCTAAATTTAAAGTTATCGGAACAGTGGTTTCGGAACCACAA 131 TAAAAGGGGGAGAGTTGTAATGACCTAAATTTAAAGTTATCGGAACAGTGGTTTCGGAACCACAA 11683952 ATCCAATTT 196 ATCCAATTT 11683961 AAAGAGAAATTT 1 AAAGAGAAATTT 11683973 ATTTCAATAT Statistics Matches: 214, Mismatches: 2, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 204 214 1.00 ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25 Consensus pattern (204 bp): AAAGAGAAATTTGGTGAAAGTATTGTGGCAAAAGTACGGGATTGAGGAAGCGACATGGGAACTAG AGGAGGCAATGAGGAAACAATACCTAAATCTCTTTAATGGTAAGATTTTCGAGGACGAAAATCCT TAAAAGGGGGAGAGTTGTAATGACCTAAATTTAAAGTTATCGGAACAGTGGTTTCGGAACCACAA ATCCAATTT Found at i:11685474 original size:27 final size:27 Alignment explanation

Indices: 11685420--11685525 Score: 135 Period size: 27 Copynumber: 4.0 Consensus size: 27 11685410 TGGCTGCCAA * * 11685420 AACAGATAA-TGTGACAGAGTCACCAG 1 AACAGATAATTGTGGCAGAGCCACCAG * 11685446 AACAGATAATTGTGGCAGAGCCACTAG 1 AACAGATAATTGTGGCAGAGCCACCAG 11685473 AACAGAT-ATATGTGGCAGAGCCACCAG 1 AACAGATAAT-TGTGGCAGAGCCACCAG * * * 11685500 ATCAGATAAATGTGGCATAGCCACCA 1 AACAGATAATTGTGGCAGAGCCACCA 11685526 TAATATAGCC Statistics Matches: 70, Mismatches: 7, Indels: 5 0.85 0.09 0.06 Matches are distributed among these distances: 26 11 0.16 27 58 0.83 28 1 0.01 ACGTcount: A:0.39, C:0.21, G:0.24, T:0.17 Consensus pattern (27 bp): AACAGATAATTGTGGCAGAGCCACCAG Found at i:11685498 original size:54 final size:53 Alignment explanation

Indices: 11685420--11685523 Score: 154 Period size: 54 Copynumber: 1.9 Consensus size: 53 11685410 TGGCTGCCAA * * 11685420 AACAGATAATGTGACAGAGTCACCAGAACAGATAATTGTGGCAGAGCCACTAG 1 AACAGATAATGTGACAGAGCCACCAGAACAGATAAATGTGGCAGAGCCACTAG * * * 11685473 AACAGATATATGTGGCAGAGCCACCAGATCAGATAAATGTGGCATAGCCAC 1 AACAGATA-ATGTGACAGAGCCACCAGAACAGATAAATGTGGCAGAGCCAC 11685524 CATAATATAG Statistics Matches: 45, Mismatches: 5, Indels: 1 0.88 0.10 0.02 Matches are distributed among these distances: 53 8 0.18 54 37 0.82 ACGTcount: A:0.38, C:0.20, G:0.24, T:0.17 Consensus pattern (53 bp): AACAGATAATGTGACAGAGCCACCAGAACAGATAAATGTGGCAGAGCCACTAG Found at i:11686950 original size:24 final size:24 Alignment explanation

Indices: 11686923--11686993 Score: 133 Period size: 24 Copynumber: 3.0 Consensus size: 24 11686913 CTAGATTTCC * 11686923 TCCCTTATCTACTCCTAAATCCTA 1 TCCCTTATCAACTCCTAAATCCTA 11686947 TCCCTTATCAACTCCTAAATCCTA 1 TCCCTTATCAACTCCTAAATCCTA 11686971 TCCCTTATCAACTCCTAAATCCT 1 TCCCTTATCAACTCCTAAATCCT 11686994 CTCCTGACAG Statistics Matches: 46, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 24 46 1.00 ACGTcount: A:0.27, C:0.38, G:0.00, T:0.35 Consensus pattern (24 bp): TCCCTTATCAACTCCTAAATCCTA Found at i:11686963 original size:48 final size:48 Alignment explanation

Indices: 11686900--11686993 Score: 120 Period size: 48 Copynumber: 1.9 Consensus size: 48 11686890 ACCTCTTGTT * * * 11686900 CCTTAATCAGCTCCTAGATTTCC-TCCCTTATCTACTCCTAAATCCTATC 1 CCTTAATCAACTCCTA-A-ATCCATCCCTTATCAACTCCTAAATCCTATC 11686949 CCTT-ATCAACTCCTAAATCCTATCCCTTATCAACTCCTAAATCCT 1 CCTTAATCAACTCCTAAATCC-ATCCCTTATCAACTCCTAAATCCT 11686994 CTCCTGACAG Statistics Matches: 40, Mismatches: 3, Indels: 5 0.83 0.06 0.10 Matches are distributed among these distances: 46 3 0.08 47 1 0.03 48 32 0.80 49 4 0.10 ACGTcount: A:0.26, C:0.37, G:0.02, T:0.35 Consensus pattern (48 bp): CCTTAATCAACTCCTAAATCCATCCCTTATCAACTCCTAAATCCTATC Found at i:11688934 original size:59 final size:59 Alignment explanation

Indices: 11688842--11689040 Score: 344 Period size: 59 Copynumber: 3.4 Consensus size: 59 11688832 ATTAGTGTCT * 11688842 GAATTTAGCCTGGACTGGTAATTCAGATCCAAGCTCATTAGAGTAATTGTCATTGCAGG 1 GAATTTAGCCTGGACTGGTAATTCAGATCCAAGCTCATTAGAGTAATTGTCGTTGCAGG * 11688901 GAATTTAGCCTGGACTGGTAATTCGGATCCAAGCTCATTAGAGTAATTGTCGTTGCAGG 1 GAATTTAGCCTGGACTGGTAATTCAGATCCAAGCTCATTAGAGTAATTGTCGTTGCAGG * * * 11688960 GGATTTAGCCTGTACTGGTAATTCAGATCCAAGCTCATTAGAGTAATTTTCGTTGCAGG 1 GAATTTAGCCTGGACTGGTAATTCAGATCCAAGCTCATTAGAGTAATTGTCGTTGCAGG * 11689019 GGATTTAGCCTGGACTGGTAAT 1 GAATTTAGCCTGGACTGGTAAT 11689041 CTCGCTGCAA Statistics Matches: 133, Mismatches: 7, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 59 133 1.00 ACGTcount: A:0.26, C:0.17, G:0.26, T:0.32 Consensus pattern (59 bp): GAATTTAGCCTGGACTGGTAATTCAGATCCAAGCTCATTAGAGTAATTGTCGTTGCAGG Found at i:11694575 original size:38 final size:38 Alignment explanation

Indices: 11694345--11694572 Score: 307 Period size: 38 Copynumber: 6.0 Consensus size: 38 11694335 CAATGTATAA * * * * 11694345 AACCCGAACATAACACCAGCACGAAGCCTACGGGACTTT 1 AACCCGGATATAATACCAGCACGAAGCCTGCGGGA-TTT * * * 11694384 AAACTCAGATATAATACCAGCAC-TAGCCTGCGGGATTT 1 -AACCCGGATATAATACCAGCACGAAGCCTGCGGGATTT 11694422 AACCCGGATATAATACCAGCACGAAGCCTGCGGGATTT 1 AACCCGGATATAATACCAGCACGAAGCCTGCGGGATTT * * 11694460 AACCCGGATATAATACCAGCACGAAGCTTGCGGAATTT 1 AACCCGGATATAATACCAGCACGAAGCCTGCGGGATTT * * 11694498 AACCCGGATATATTACCAGCACGAAGCCTGTGGGATTT 1 AACCCGGATATAATACCAGCACGAAGCCTGCGGGATTT * * 11694536 AACCCGGATATAATACCAGCACAAAGCCTAC-GGATTT 1 AACCCGGATATAATACCAGCACGAAGCCTGCGGGATTT 11694573 TAAGCTCGGA Statistics Matches: 167, Mismatches: 20, Indels: 5 0.87 0.10 0.03 Matches are distributed among these distances: 37 26 0.16 38 114 0.68 39 10 0.06 40 17 0.10 ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20 Consensus pattern (38 bp): AACCCGGATATAATACCAGCACGAAGCCTGCGGGATTT Found at i:11711942 original size:85 final size:85 Alignment explanation

Indices: 11711789--11711949 Score: 213 Period size: 85 Copynumber: 1.9 Consensus size: 85 11711779 TGTGTTATTG * * * 11711789 TGTAAGACCACGTCTGGGACGTTGGCACCGATTTTCTATTTACGTGTAAGACCACGTCTGGGACT 1 TGTAAGACCACGTCTGGGACGTTGGCACCGATTTTCGATTTACATGTAAGACCACGTCTAGGACT 11711854 TGGCATCGTATTTGATTTCA 66 TGGCATCGTATTTGATTTCA * 11711874 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATTT-GA-TTACATGTAAGACCACGTCTAGG 1 TGTAAGACCAC-GTCTGGGAC-GTTGGCACCGAT-TTTCGATTTACATGTAAGACCACGTCTAGG * 11711935 ACTTTGGCATTGTAT 63 AC-TTGGCATCGTAT 11711950 GAGCTTTCTG Statistics Matches: 67, Mismatches: 5, Indels: 8 0.84 0.06 0.10 Matches are distributed among these distances: 84 24 0.36 85 39 0.58 86 4 0.06 ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32 Consensus pattern (85 bp): TGTAAGACCACGTCTGGGACGTTGGCACCGATTTTCGATTTACATGTAAGACCACGTCTAGGACT TGGCATCGTATTTGATTTCA Found at i:11711943 original size:43 final size:42 Alignment explanation

Indices: 11711789--11711944 Score: 183 Period size: 43 Copynumber: 3.6 Consensus size: 42 11711779 TGTGTTATTG * * * 11711789 TGTAAGACCACGTCTGGGACGTTGGCACCGAT-TTTCTATTTACG 1 TGTAAGACCACGTCTGGGAC-TTGGCATCGATATTT-GA-TTACA * 11711833 TGTAAGACCACGTCTGGGACTTGGCATCG-TATTTGATTTCA 1 TGTAAGACCACGTCTGGGACTTGGCATCGATATTTGATTACA * 11711874 TGTAAGACC-CTGTCTGGGACAGTGGCATCGATATTTGATTACA 1 TGTAAGACCAC-GTCTGGGAC-TTGGCATCGATATTTGATTACA * 11711917 TGTAAGACCACGTCTAGGACTTTGGCAT 1 TGTAAGACCACGTCTGGGAC-TTGGCAT 11711945 TGTATGAGCT Statistics Matches: 98, Mismatches: 9, Indels: 11 0.83 0.08 0.09 Matches are distributed among these distances: 40 1 0.01 41 21 0.21 42 10 0.10 43 45 0.46 44 21 0.21 ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31 Consensus pattern (42 bp): TGTAAGACCACGTCTGGGACTTGGCATCGATATTTGATTACA Found at i:11715082 original size:25 final size:25 Alignment explanation

Indices: 11715054--11715157 Score: 138 Period size: 25 Copynumber: 4.2 Consensus size: 25 11715044 TAAGCTCCTT * 11715054 CGAGCCGAATAACGGGAAGATCATG 1 CGAGCTGAATAACGGGAAGATCATG * * 11715079 CGAGCTGAATAATGGGAAGCTCATG 1 CGAGCTGAATAACGGGAAGATCATG * * * 11715104 CAAGCTGAATAACGGGAAGCTCATA 1 CGAGCTGAATAACGGGAAGATCATG 11715129 CGAGCTGAATAACGGGAA-ACTCATG 1 CGAGCTGAATAACGGGAAGA-TCATG 11715154 CGAG 1 CGAG 11715158 TTGAGTATCA Statistics Matches: 69, Mismatches: 9, Indels: 2 0.86 0.11 0.03 Matches are distributed among these distances: 25 69 1.00 ACGTcount: A:0.36, C:0.19, G:0.30, T:0.15 Consensus pattern (25 bp): CGAGCTGAATAACGGGAAGATCATG Found at i:11715120 original size:50 final size:50 Alignment explanation

Indices: 11715060--11715154 Score: 154 Period size: 50 Copynumber: 1.9 Consensus size: 50 11715050 CCTTCGAGCC * * * 11715060 GAATAACGGGAAGATCATGCGAGCTGAATAATGGGAAGCTCATGCAAGCT 1 GAATAACGGGAAGATCATACGAGCTGAATAACGGGAAACTCATGCAAGCT * 11715110 GAATAACGGGAAGCTCATACGAGCTGAATAACGGGAAACTCATGC 1 GAATAACGGGAAGATCATACGAGCTGAATAACGGGAAACTCATGC 11715155 GAGTTGAGTA Statistics Matches: 41, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 50 41 1.00 ACGTcount: A:0.37, C:0.18, G:0.28, T:0.17 Consensus pattern (50 bp): GAATAACGGGAAGATCATACGAGCTGAATAACGGGAAACTCATGCAAGCT Found at i:11715172 original size:50 final size:50 Alignment explanation

Indices: 11715060--11715187 Score: 148 Period size: 50 Copynumber: 2.6 Consensus size: 50 11715050 CCTTCGAGCC * * * * * 11715060 GAATAACGGGAAGATCATGCGAGCTGAATAATGGGAAGCTCATGCAAGCT 1 GAATAACAGGAAGCTCATACGAGCTGAATAACGGGAAACTCATGCAAGCT * * * 11715110 GAATAACGGGAAGCTCATACGAGCTGAATAACGGGAAACTCATGCGAGTT 1 GAATAACAGGAAGCTCATACGAGCTGAATAACGGGAAACTCATGCAAGCT * * * * 11715160 GAGTATCAGGAAGCTCATAAGAGTTGAA 1 GAATAACAGGAAGCTCATACGAGCTGAA 11715188 ATCGGTGACC Statistics Matches: 67, Mismatches: 11, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 50 67 1.00 ACGTcount: A:0.37, C:0.16, G:0.29, T:0.19 Consensus pattern (50 bp): GAATAACAGGAAGCTCATACGAGCTGAATAACGGGAAACTCATGCAAGCT Found at i:11715172 original size:75 final size:75 Alignment explanation

Indices: 11715039--11715177 Score: 183 Period size: 75 Copynumber: 1.9 Consensus size: 75 11715029 ACGAGTTGTA * * * * 11715039 AACGGTAAGCTCCTTCGAGCCGAATAACGGGAAGATCATGCGAGCTGAATAATGGGAAGCTCATG 1 AACGGGAAGCTCATACGAGCCGAATAACGGGAAGATCATGCGAGCTGAATAATAGGAAGCTCATG 11715104 CAAGCTGAAT 66 CAAGCTGAAT * * * 11715114 AACGGGAAGCTCATACGAGCTGAATAACGGGAA-ACTCATGCGAGTTGAGT-ATCAGGAAGCTCA 1 AACGGGAAGCTCATACGAGCCGAATAACGGGAAGA-TCATGCGAGCTGAATAAT-AGGAAGCTCA 11715177 T 64 T 11715178 AAGAGTTGAA Statistics Matches: 55, Mismatches: 7, Indels: 4 0.83 0.11 0.06 Matches are distributed among these distances: 74 3 0.05 75 52 0.95 ACGTcount: A:0.34, C:0.19, G:0.28, T:0.19 Consensus pattern (75 bp): AACGGGAAGCTCATACGAGCCGAATAACGGGAAGATCATGCGAGCTGAATAATAGGAAGCTCATG CAAGCTGAAT Found at i:11718276 original size:75 final size:73 Alignment explanation

Indices: 11718188--11718359 Score: 217 Period size: 75 Copynumber: 2.4 Consensus size: 73 11718178 GGTTTTCCTC *** * * ** 11718188 ATTGAAATACCATACCTACATTTTTTAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC 1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC 11718252 TCAGTATGG 65 TCAGTATGG * 11718261 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA 1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA 11718326 CTCAGTATGG 64 CTCAGTATGG 11718336 A-TG--ATACCATACCTACATTTCACA 1 ATTGAAATACCATACCTACATTTCACA 11718360 CTTTGCCATG Statistics Matches: 88, Mismatches: 8, Indels: 9 0.84 0.08 0.09 Matches are distributed among these distances: 70 21 0.24 73 3 0.03 74 7 0.08 75 57 0.65 ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32 Consensus pattern (73 bp): ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT CAGTATGG Found at i:11718357 original size:35 final size:35 Alignment explanation

Indices: 11718193--11718359 Score: 192 Period size: 35 Copynumber: 4.6 Consensus size: 35 11718183 TCCTCATTGA *** * 11718193 AATACCATACCTACATTTTTTAACTCGGTATGGGA- 1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT * ** 11718228 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT 1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT * 11718268 AATACCATACCTACATTTCACAGCTCAGTATGGAT 1 AATACCATACCTACATTTCACAACTCAGTATGGAT 11718303 AATACCATACCTACATTTCACAACTCAGTATGGAT 1 AATACCATACCTACATTTCACAACTCAGTATGGAT * 11718338 GATACCATACCTACATTTCACA 1 AATACCATACCTACATTTCACA 11718360 CTTTGCCATG Statistics Matches: 118, Mismatches: 9, Indels: 10 0.86 0.07 0.07 Matches are distributed among these distances: 35 88 0.75 39 3 0.03 40 27 0.23 ACGTcount: A:0.34, C:0.24, G:0.11, T:0.32 Consensus pattern (35 bp): AATACCATACCTACATTTCACAACTCAGTATGGAT Found at i:11725774 original size:75 final size:73 Alignment explanation

Indices: 11725686--11725857 Score: 217 Period size: 75 Copynumber: 2.4 Consensus size: 73 11725676 GGTTTTCCTC *** * * ** 11725686 ATTGAAATACCATACCTACATTTTTTAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC 1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC 11725750 TCAGTATGG 65 TCAGTATGG * 11725759 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA 1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA 11725824 CTCAGTATGG 64 CTCAGTATGG 11725834 A-TG--ATACCATACCTACATTTCACA 1 ATTGAAATACCATACCTACATTTCACA 11725858 CTTTGCCATG Statistics Matches: 88, Mismatches: 8, Indels: 9 0.84 0.08 0.09 Matches are distributed among these distances: 70 21 0.24 73 3 0.03 74 7 0.08 75 57 0.65 ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32 Consensus pattern (73 bp): ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT CAGTATGG Found at i:11725855 original size:35 final size:35 Alignment explanation

Indices: 11725691--11725857 Score: 192 Period size: 35 Copynumber: 4.6 Consensus size: 35 11725681 TCCTCATTGA *** * 11725691 AATACCATACCTACATTTTTTAACTCGGTATGGGA- 1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT * ** 11725726 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT 1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT * 11725766 AATACCATACCTACATTTCACAGCTCAGTATGGAT 1 AATACCATACCTACATTTCACAACTCAGTATGGAT 11725801 AATACCATACCTACATTTCACAACTCAGTATGGAT 1 AATACCATACCTACATTTCACAACTCAGTATGGAT * 11725836 GATACCATACCTACATTTCACA 1 AATACCATACCTACATTTCACA 11725858 CTTTGCCATG Statistics Matches: 118, Mismatches: 9, Indels: 10 0.86 0.07 0.07 Matches are distributed among these distances: 35 88 0.75 39 3 0.03 40 27 0.23 ACGTcount: A:0.34, C:0.24, G:0.11, T:0.32 Consensus pattern (35 bp): AATACCATACCTACATTTCACAACTCAGTATGGAT Found at i:11728365 original size:23 final size:23 Alignment explanation

Indices: 11728338--11728381 Score: 88 Period size: 23 Copynumber: 1.9 Consensus size: 23 11728328 AGTGTGACTA 11728338 TGTGAGTGTTCTTTAGCCAATAT 1 TGTGAGTGTTCTTTAGCCAATAT 11728361 TGTGAGTGTTCTTTAGCCAAT 1 TGTGAGTGTTCTTTAGCCAAT 11728382 GTTGGATTAA Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 23 21 1.00 ACGTcount: A:0.20, C:0.14, G:0.23, T:0.43 Consensus pattern (23 bp): TGTGAGTGTTCTTTAGCCAATAT Found at i:11738697 original size:47 final size:47 Alignment explanation

Indices: 11738643--11738828 Score: 282 Period size: 47 Copynumber: 4.0 Consensus size: 47 11738633 TTAGGATTTT ** * * 11738643 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCCA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA 11738690 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA * * 11738737 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA * * * * 11738784 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGC 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGC 11738829 TAATATGAAA Statistics Matches: 127, Mismatches: 12, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 47 127 1.00 ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26 Consensus pattern (47 bp): ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA Found at i:11738743 original size:22 final size:22 Alignment explanation

Indices: 11738672--11738743 Score: 58 Period size: 22 Copynumber: 3.1 Consensus size: 22 11738662 GTATATATGA 11738672 GATAAGGCCGAATGGCCAATGT 1 GATAAGGCCGAATGGCCAATGT * * * 11738694 GATGAATG-TGAACAT-GCATATATGT 1 GAT-AAGGCCG-A-ATGGC-CA-ATGT 11738719 GATAAGGCCGAATGGCCAATGT 1 GATAAGGCCGAATGGCCAATGT 11738741 GAT 1 GAT 11738744 GAATGTGAGC Statistics Matches: 37, Mismatches: 6, Indels: 14 0.65 0.11 0.25 Matches are distributed among these distances: 22 11 0.30 23 9 0.24 24 9 0.24 25 8 0.22 ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24 Consensus pattern (22 bp): GATAAGGCCGAATGGCCAATGT Found at i:11738792 original size:25 final size:25 Alignment explanation

Indices: 11738717--11738792 Score: 63 Period size: 23 Copynumber: 3.2 Consensus size: 25 11738707 ATGCATATAT 11738717 GTGATAAGGCCGAATGGCCAATGTG 1 GTGATAAGGCCGAATGGCCAATGTG * * * * 11738742 ATGA-ATGTG-AGCAT-G-CATATGT- 1 GTGATAAG-GCCGAATGGCCA-ATGTG 11738764 GTGATAAGGCCGAATGGCCAATGTG 1 GTGATAAGGCCGAATGGCCAATGTG 11738789 GTGA 1 GTGA 11738793 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:0.13, G:0.34, T:0.24 Consensus pattern (25 bp): GTGATAAGGCCGAATGGCCAATGTG Found at i:11738863 original size:48 final size:48 Alignment explanation

Indices: 11738806--11739038 Score: 369 Period size: 48 Copynumber: 4.8 Consensus size: 48 11738796 TGAACATGCA * 11738806 TATATGTGGTAAAGCCGAATGGCTAATATGAAATATGTATGAGAAATG 1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAAATG 11738854 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAAATG 1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAAATG * 11738902 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG 1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAAATG * * * * 11738950 CATATGTGGTAAAGCTGAATGG-TCAATGTGAAATATATATATGAGATATG 1 TATATGTGGTAAAGCCGAATGGCT-AATGTG-AA-ATATGTATGAGAAATG * 11739000 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA 1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTA 11739039 GGCGATGTGC Statistics Matches: 172, Mismatches: 9, Indels: 8 0.91 0.05 0.04 Matches are distributed among these distances: 47 1 0.01 48 126 0.73 49 4 0.02 50 40 0.23 51 1 0.01 ACGTcount: A:0.37, C:0.06, G:0.26, T:0.30 Consensus pattern (48 bp): TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGAAATG Found at i:11739329 original size:37 final size:37 Alignment explanation

Indices: 11739184--11739328 Score: 254 Period size: 37 Copynumber: 3.9 Consensus size: 37 11739174 GGAAATATAT 11739184 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG 1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG 11739221 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG 1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG * * 11739258 TCCGGGTGAGACCCGATGACTACGTGTGGAGATTTTG 1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG * * 11739295 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATT 1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT 11739329 TCGTCTGAGC Statistics Matches: 103, Mismatches: 5, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 37 103 1.00 ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26 Consensus pattern (37 bp): TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG Found at i:11740432 original size:46 final size:46 Alignment explanation

Indices: 11740380--11740653 Score: 397 Period size: 46 Copynumber: 6.0 Consensus size: 46 11740370 AGTGTGCTCT * 11740380 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC 1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC * * 11740426 CTGATATGAAATGTGTAAGACCATGGTTAAAAGATACCATGGCAAC 1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC * 11740472 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC 1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC * * * * 11740518 ATGACAGGAAATGATTAAGACCATGGTTGAAAGATACCATGGCAAC 1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC * * 11740564 CTGATATGAAATGAATAAGACCATGGCTGAAAGATACCATGGCAAC 1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC * * * * * 11740610 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA 1 CTGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA 11740654 TCATGTCAAA Statistics Matches: 207, Mismatches: 20, Indels: 2 0.90 0.09 0.01 Matches are distributed among these distances: 45 1 0.00 46 206 1.00 ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21 Consensus pattern (46 bp): CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC Found at i:11742102 original size:11 final size:11 Alignment explanation

Indices: 11742086--11742110 Score: 50 Period size: 11 Copynumber: 2.3 Consensus size: 11 11742076 TCTAGATATT 11742086 TTATTATTTTA 1 TTATTATTTTA 11742097 TTATTATTTTA 1 TTATTATTTTA 11742108 TTA 1 TTA 11742111 ATAATTATTT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 14 1.00 ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72 Consensus pattern (11 bp): TTATTATTTTA Found at i:11744302 original size:46 final size:46 Alignment explanation

Indices: 11744250--11744513 Score: 395 Period size: 46 Copynumber: 5.7 Consensus size: 46 11744240 AGTGTGCTCT 11744250 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC 1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC * * 11744296 CTGATATGAAATGTGTAAGACCATAGTTGAAAGATACCATGACAGC 1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC * * 11744342 CTGATATGAAATGTGTAAAACCATGGTTGAAAGATACCATGGCAAC 1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC * 11744388 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC 1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC * *** 11744434 GTGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAGC 1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC * * * * 11744480 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGA 1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGA 11744514 CACTATGACA Statistics Matches: 200, Mismatches: 17, Indels: 2 0.91 0.08 0.01 Matches are distributed among these distances: 45 1 0.00 46 199 1.00 ACGTcount: A:0.39, C:0.14, G:0.24, T:0.22 Consensus pattern (46 bp): CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC Found at i:11745613 original size:12 final size:12 Alignment explanation

Indices: 11745582--11745607 Score: 52 Period size: 12 Copynumber: 2.2 Consensus size: 12 11745572 TTCAACTAAT 11745582 AAAGCAAACAAA 1 AAAGCAAACAAA 11745594 AAAGCAAACAAA 1 AAAGCAAACAAA 11745606 AA 1 AA 11745608 CTCAAATAGA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 14 1.00 ACGTcount: A:0.77, C:0.15, G:0.08, T:0.00 Consensus pattern (12 bp): AAAGCAAACAAA Found at i:11745924 original size:101 final size:101 Alignment explanation

Indices: 11745781--11745976 Score: 286 Period size: 101 Copynumber: 1.9 Consensus size: 101 11745771 TTTTATTAAA * * * * 11745781 TGTACTTGGTGTCGACCATTACATGGTCCGCACCTAATTTTTTTTTAAATACACTGGTATCGGCC 1 TGTACTTGGTGTCGACCATTACATGGTCCGCACCCAAATTTTTTTTAAATACACTGGTACCGGCA 11745846 ATCAGTGTTCCAAAAAAAATGCATTGGGAGTCGAAT 66 ATCAGTGTTCCAAAAAAAATGCATTGGGAGTCGAAT * * * * 11745882 TGTACTTGGTGTCGGCCATTACATGG-CCAGCACCCAAATTTTTTTTAAATACATTGGTGCCGGT 1 TGTACTTGGTGTCGACCATTACATGGTCC-GCACCCAAATTTTTTTTAAATACACTGGTACCGGC * * 11745946 AATCAGTGTTCCAAAAAAATTGTATTGGGAG 65 AATCAGTGTTCCAAAAAAAATGCATTGGGAG 11745977 CCAAAGTTGT Statistics Matches: 84, Mismatches: 10, Indels: 2 0.88 0.10 0.02 Matches are distributed among these distances: 100 2 0.02 101 82 0.98 ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33 Consensus pattern (101 bp): TGTACTTGGTGTCGACCATTACATGGTCCGCACCCAAATTTTTTTTAAATACACTGGTACCGGCA ATCAGTGTTCCAAAAAAAATGCATTGGGAGTCGAAT Found at i:11748251 original size:18 final size:18 Alignment explanation

Indices: 11748228--11748288 Score: 77 Period size: 18 Copynumber: 3.4 Consensus size: 18 11748218 GAATAATTAT 11748228 TTATTCAATAACAGTCAG 1 TTATTCAATAACAGTCAG * * 11748246 TTATTCAGTAACAGTCAA 1 TTATTCAATAACAGTCAG * ** 11748264 TTATTCAATAATAACCAG 1 TTATTCAATAACAGTCAG 11748282 TTATTCA 1 TTATTCA 11748289 GTATCGATCA Statistics Matches: 36, Mismatches: 7, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 18 36 1.00 ACGTcount: A:0.39, C:0.16, G:0.08, T:0.36 Consensus pattern (18 bp): TTATTCAATAACAGTCAG Found at i:11748273 original size:36 final size:36 Alignment explanation

Indices: 11748228--11748497 Score: 120 Period size: 36 Copynumber: 7.8 Consensus size: 36 11748218 GAATAATTAT * * 11748228 TTATTCAATAACAGTCAGTTATTCAGTAACAGTCAA 1 TTATTCAGTAACAATCAGTTATTCAGTAACAGTCAA * * * * 11748264 TTATTCAATAATAACCAGTTATTCAGTATC-GATC-A 1 TTATTCAGTAACAATCAGTTATTCAGTAACAG-TCAA * * 11748299 --ATT--G-----ATCGGTTATCCAGTAACAGTCAA 1 TTATTCAGTAACAATCAGTTATTCAGTAACAGTCAA * * * 11748326 TTATTCAGTAA-AATCAGATATTCAGTAACAATTAA 1 TTATTCAGTAACAATCAGTTATTCAGTAACAGTCAA ** * * * * 11748361 GTTATTCAGTAGTAGTCA-TTCATTCAGTGACAATCAG 1 -TTATTCAGTAACAATCAGTT-ATTCAGTAACAGTCAA * ** * * * * 11748398 TTATTTAGTAATGATCAATTATTCAGTAATATTCAG 1 TTATTCAGTAACAATCAGTTATTCAGTAACAGTCAA * * * 11748434 TTATTCAGTAACAGTC--TAAATCCAGTAACAGTCAA 1 TTATTCAGTAACAATCAGT-TATTCAGTAACAGTCAA * * * * 11748469 TTATCCGGTAACAGTCAATTATTCAGTAA 1 TTATTCAGTAACAATCAGTTATTCAGTAA 11748498 TAATCAGTTA Statistics Matches: 176, Mismatches: 40, Indels: 36 0.70 0.16 0.14 Matches are distributed among these distances: 26 15 0.09 27 2 0.01 29 3 0.02 31 1 0.01 33 3 0.02 34 1 0.01 35 46 0.26 36 85 0.48 37 20 0.11 ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35 Consensus pattern (36 bp): TTATTCAGTAACAATCAGTTATTCAGTAACAGTCAA Found at i:11748334 original size:18 final size:18 Alignment explanation

Indices: 11748308--11748497 Score: 140 Period size: 18 Copynumber: 10.6 Consensus size: 18 11748298 AATTGATCGG * 11748308 TTATCCAGTAACAGTCAA 1 TTATTCAGTAACAGTCAA * 11748326 TTATTCAGTAA-AATCAGA 1 TTATTCAGTAACAGTCA-A * * 11748344 -TATTCAGTAACAATTAA 1 TTATTCAGTAACAGTCAA ** 11748361 GTTATTCAGTAGTAGTC-A 1 -TTATTCAGTAACAGTCAA * * * 11748379 TTCATTCAGTGACAATCAG 1 TT-ATTCAGTAACAGTCAA * * 11748398 TTATTTAGTAA-TGATCAA 1 TTATTCAGTAACAG-TCAA * * * 11748416 TTATTCAGTAATATTCAG 1 TTATTCAGTAACAGTCAA 11748434 TTATTCAGTAACAGTCTAA 1 TTATTCAGTAACAGTC-AA * 11748453 --ATCCAGTAACAGTCAA 1 TTATTCAGTAACAGTCAA * * 11748469 TTATCCGGTAACAGTCAA 1 TTATTCAGTAACAGTCAA 11748487 TTATTCAGTAA 1 TTATTCAGTAA 11748498 TAATCAGTTA Statistics Matches: 133, Mismatches: 28, Indels: 22 0.73 0.15 0.12 Matches are distributed among these distances: 16 2 0.02 17 30 0.23 18 87 0.65 19 14 0.11 ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35 Consensus pattern (18 bp): TTATTCAGTAACAGTCAA Found at i:11748736 original size:45 final size:45 Alignment explanation

Indices: 11748685--11748873 Score: 279 Period size: 45 Copynumber: 4.2 Consensus size: 45 11748675 ATTCAGAACA * * * * 11748685 GTAACAGTAACAGTATTCAACACACAAAGTGTTGAATCGGTAATG 1 GTAACAGTAACAATATTCGACACACAAAGTGTCGAATCGGTAACG 11748730 GTAACAGTAACAATATTCGACACACAAAGTGTCGAATCGGTAACG 1 GTAACAGTAACAATATTCGACACACAAAGTGTCGAATCGGTAACG * * 11748775 GTAACAGTAACAATATTCGACACACAAAGTGCCGAATCGGTAACA 1 GTAACAGTAACAATATTCGACACACAAAGTGTCGAATCGGTAACG * * * * 11748820 GTAGCAGTAACAATATTCGACACACAAAGTGCCGAATCAGTAACA 1 GTAACAGTAACAATATTCGACACACAAAGTGTCGAATCGGTAACG * 11748865 GTAGCAGTA 1 GTAACAGTA 11748874 GCAGTAACAG Statistics Matches: 136, Mismatches: 8, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 45 136 1.00 ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20 Consensus pattern (45 bp): GTAACAGTAACAATATTCGACACACAAAGTGTCGAATCGGTAACG Found at i:11749293 original size:5 final size:5 Alignment explanation

Indices: 11749282--11749333 Score: 77 Period size: 5 Copynumber: 10.2 Consensus size: 5 11749272 AATTAATCAT * * 11749282 AATTC CATTC CATTC AATTC AATTC AATTC AATTC AATTC AATTC AAATTC 1 AATTC AATTC AATTC AATTC AATTC AATTC AATTC AATTC AATTC -AATTC 11749333 A 1 A 11749334 CTTTTCCACT Statistics Matches: 44, Mismatches: 2, Indels: 2 0.92 0.04 0.04 Matches are distributed among these distances: 5 39 0.89 6 5 0.11 ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38 Consensus pattern (5 bp): AATTC Found at i:11751007 original size:3 final size:3 Alignment explanation

Indices: 11750999--11751048 Score: 100 Period size: 3 Copynumber: 16.7 Consensus size: 3 11750989 TTATATATAT 11750999 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA 1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA 11751047 AT 1 AT 11751049 GACTTTATTA Statistics Matches: 47, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 47 1.00 ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34 Consensus pattern (3 bp): ATA Found at i:11751847 original size:2 final size:2 Alignment explanation

Indices: 11751840--11751875 Score: 72 Period size: 2 Copynumber: 18.0 Consensus size: 2 11751830 GTCAAACTTA 11751840 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 11751876 CTCCCTACGG Statistics Matches: 34, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 34 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:11752975 original size:128 final size:127 Alignment explanation

Indices: 11752673--11753021 Score: 434 Period size: 128 Copynumber: 2.7 Consensus size: 127 11752663 ATGCAAACGG ** * * * * 11752673 AATTTTAAAGGGATGTTTGATTATTTATATAAACAGAAA-ATCGAAACCCAGCACATTAGGACAC 1 AATTTTAAAGGGAAATTTGATTATTTAGACAAAC-GAAAGATCGAAACCCAACACATTAGGGCAC ** * * * * 11752737 GAT-TTTCCGAA-TTCTCAAACATCAATCATCGCTTTTGTTTTAAAGCTTAGAAAACGCGGATGA 65 GATCCCT-CGAATTTCT-AAACATCAAACATCGCCTTTGTTTTAAAGCTTAGAAAACGCAGATCA * * ** 11752800 AATTTAAAAGGGAAATCTGATTATTTAGACAAATAAAAGATCGAAACCCAACACATTAGGGCACG 1 AATTTTAAAGGGAAATTTGATTATTTAGACAAACGAAAGATCGAAACCCAACACATTAGGGCACG * * * 11752865 ATCCCTCGAATTTCTAAACATCAAACATTGCCTTTGTTTTAATGGTTTAGAAAACGCAGATCA 66 ATCCCTCGAATTTCTAAACATCAAACATCGCCTTTGTTTTAA-AGCTTAGAAAACGCAGATCA * * * * 11752928 AATTTTAAAGGGAAATTTGACTATTTAGACAAACGAAAGACCGAAACCCAACACATTAGGGTACA 1 AATTTTAAAGGGAAATTTGATTATTTAGACAAACGAAAGATCGAAACCCAACACATTAGGGCACG 11752993 ATCCCTCGAATTTCTAAACATCAAACATC 66 ATCCCTCGAATTTCTAAACATCAAACATC 11753022 ACTTTCGTTT Statistics Matches: 190, Mismatches: 28, Indels: 7 0.84 0.12 0.03 Matches are distributed among these distances: 126 3 0.02 127 81 0.43 128 106 0.56 ACGTcount: A:0.40, C:0.18, G:0.15, T:0.28 Consensus pattern (127 bp): AATTTTAAAGGGAAATTTGATTATTTAGACAAACGAAAGATCGAAACCCAACACATTAGGGCACG ATCCCTCGAATTTCTAAACATCAAACATCGCCTTTGTTTTAAAGCTTAGAAAACGCAGATCA Found at i:11756347 original size:33 final size:33 Alignment explanation

Indices: 11756308--11756379 Score: 108 Period size: 33 Copynumber: 2.2 Consensus size: 33 11756298 AAACATATTT * 11756308 TTATTATTGTATTATTATTAAATATTATAAGTA 1 TTATTATTGTATGATTATTAAATATTATAAGTA * * * 11756341 TTATTATTGTATGATTGTTAAATATTATTATTA 1 TTATTATTGTATGATTATTAAATATTATAAGTA 11756374 TTATTA 1 TTATTA 11756380 AAGTTATAAG Statistics Matches: 35, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 33 35 1.00 ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57 Consensus pattern (33 bp): TTATTATTGTATGATTATTAAATATTATAAGTA Found at i:11756707 original size:18 final size:19 Alignment explanation

Indices: 11756684--11756728 Score: 74 Period size: 19 Copynumber: 2.4 Consensus size: 19 11756674 AAATGTACTA * 11756684 ATTAATTT-TTTGGATCAC 1 ATTAATTTCTTTGGACCAC 11756702 ATTAATTTCTTTGGACCAC 1 ATTAATTTCTTTGGACCAC 11756721 ATTAATTT 1 ATTAATTT 11756729 AAGATCTTGA Statistics Matches: 25, Mismatches: 1, Indels: 1 0.93 0.04 0.04 Matches are distributed among these distances: 18 8 0.32 19 17 0.68 ACGTcount: A:0.29, C:0.13, G:0.09, T:0.49 Consensus pattern (19 bp): ATTAATTTCTTTGGACCAC Found at i:11760791 original size:3 final size:3 Alignment explanation

Indices: 11760783--11760821 Score: 60 Period size: 3 Copynumber: 13.0 Consensus size: 3 11760773 TACAACAGTT * * 11760783 TAA TAA TAA TAA TAA TAA TAA TGA CAA TAA TAA TAA TAA 1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA 11760822 AATGATTAAT Statistics Matches: 32, Mismatches: 4, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 3 32 1.00 ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31 Consensus pattern (3 bp): TAA Found at i:11760831 original size:18 final size:20 Alignment explanation

Indices: 11760787--11760826 Score: 64 Period size: 21 Copynumber: 2.0 Consensus size: 20 11760777 ACAGTTTAAT 11760787 AATAATAATAATAATAATGA 1 AATAATAATAATAATAATGA 11760807 CAATAATAATAATAA-AATGA 1 -AATAATAATAATAATAATGA 11760827 TTAATTTGAA Statistics Matches: 19, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 20 5 0.26 21 14 0.74 ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28 Consensus pattern (20 bp): AATAATAATAATAATAATGA Found at i:11765359 original size:9 final size:9 Alignment explanation

Indices: 11765341--11765426 Score: 100 Period size: 9 Copynumber: 9.6 Consensus size: 9 11765331 TTTATACAAA * 11765341 TAATTTGGT 1 TAATTCGGT 11765350 TAATTCGGT 1 TAATTCGGT * * 11765359 TAATTTGGG 1 TAATTCGGT * 11765368 TAATTCGGG 1 TAATTCGGT * * 11765377 TATTTCGGG 1 TAATTCGGT * 11765386 TAATTTGGT 1 TAATTCGGT * 11765395 TAATTCGAT 1 TAATTCGGT 11765404 TAATTCGGT 1 TAATTCGGT 11765413 TAATTCGGT 1 TAATTCGGT 11765422 TAATT 1 TAATT 11765427 TTATACTTAT Statistics Matches: 66, Mismatches: 11, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 9 66 1.00 ACGTcount: A:0.23, C:0.07, G:0.23, T:0.47 Consensus pattern (9 bp): TAATTCGGT Found at i:11766215 original size:18 final size:18 Alignment explanation

Indices: 11766192--11766245 Score: 57 Period size: 18 Copynumber: 3.3 Consensus size: 18 11766182 CCACCACCAA 11766192 CTCCACTAGCCACACTTG 1 CTCCACTAGCCACACTTG * 11766210 CTCCACT----AC-C-TA 1 CTCCACTAGCCACACTTG 11766222 CTCCACTAGCCACACTTG 1 CTCCACTAGCCACACTTG 11766240 CTCCAC 1 CTCCAC 11766246 CACCACTTGT Statistics Matches: 28, Mismatches: 2, Indels: 12 0.67 0.05 0.29 Matches are distributed among these distances: 12 8 0.29 13 1 0.04 14 2 0.07 16 2 0.07 17 1 0.04 18 14 0.50 ACGTcount: A:0.22, C:0.48, G:0.07, T:0.22 Consensus pattern (18 bp): CTCCACTAGCCACACTTG Found at i:11766225 original size:30 final size:30 Alignment explanation

Indices: 11766182--11766250 Score: 120 Period size: 30 Copynumber: 2.3 Consensus size: 30 11766172 TTAGCCTTTG 11766182 CCACCACCAACTCCACTAGCCACACTTGCT 1 CCACCACCAACTCCACTAGCCACACTTGCT * * 11766212 CCACTACCTACTCCACTAGCCACACTTGCT 1 CCACCACCAACTCCACTAGCCACACTTGCT 11766242 CCACCACCA 1 CCACCACCA 11766251 CTTGTACCTA Statistics Matches: 35, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 30 35 1.00 ACGTcount: A:0.26, C:0.51, G:0.06, T:0.17 Consensus pattern (30 bp): CCACCACCAACTCCACTAGCCACACTTGCT Found at i:11766443 original size:18 final size:18 Alignment explanation

Indices: 11766420--11766463 Score: 88 Period size: 18 Copynumber: 2.4 Consensus size: 18 11766410 GAACAGTTTG 11766420 TGGAGAGGAGAGAATTTT 1 TGGAGAGGAGAGAATTTT 11766438 TGGAGAGGAGAGAATTTT 1 TGGAGAGGAGAGAATTTT 11766456 TGGAGAGG 1 TGGAGAGG 11766464 CTAAGTTTTG Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 26 1.00 ACGTcount: A:0.32, C:0.00, G:0.43, T:0.25 Consensus pattern (18 bp): TGGAGAGGAGAGAATTTT Found at i:11766763 original size:3 final size:3 Alignment explanation

Indices: 11766745--11766787 Score: 59 Period size: 3 Copynumber: 14.0 Consensus size: 3 11766735 GAGGAGAGTG * * 11766745 TTA TTT TTA ATA TTA TTA TTA TTA TTA TATA TTA TTA TTA TTA 1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA 11766788 CTTACACACT Statistics Matches: 35, Mismatches: 4, Indels: 2 0.85 0.10 0.05 Matches are distributed among these distances: 3 32 0.91 4 3 0.09 ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65 Consensus pattern (3 bp): TTA Found at i:11766778 original size:19 final size:18 Alignment explanation

Indices: 11766745--11766787 Score: 68 Period size: 19 Copynumber: 2.3 Consensus size: 18 11766735 GAGGAGAGTG * 11766745 TTATTTTTAATATTATTA 1 TTATTATTAATATTATTA 11766763 TTATTATTATATATTATTA 1 TTATTATTA-ATATTATTA 11766782 TTATTA 1 TTATTA 11766788 CTTACACACT Statistics Matches: 23, Mismatches: 1, Indels: 1 0.92 0.04 0.04 Matches are distributed among these distances: 18 8 0.35 19 15 0.65 ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65 Consensus pattern (18 bp): TTATTATTAATATTATTA Found at i:11777010 original size:25 final size:25 Alignment explanation

Indices: 11776960--11777010 Score: 59 Period size: 25 Copynumber: 2.0 Consensus size: 25 11776950 AGTTTCTCAT * * 11776960 TATTTAGCTCTTATGAGCATCTCGA 1 TATTTAGCTCTTACGAGCATCCCGA * 11776985 TATTTAGCT-TTCACGAGCTTCCCGA 1 TATTTAGCTCTT-ACGAGCATCCCGA 11777010 T 1 T 11777011 TAATGGCTCT Statistics Matches: 22, Mismatches: 3, Indels: 2 0.81 0.11 0.07 Matches are distributed among these distances: 24 2 0.09 25 20 0.91 ACGTcount: A:0.22, C:0.24, G:0.16, T:0.39 Consensus pattern (25 bp): TATTTAGCTCTTACGAGCATCCCGA Found at i:11777067 original size:25 final size:25 Alignment explanation

Indices: 11776999--11777069 Score: 65 Period size: 25 Copynumber: 2.8 Consensus size: 25 11776989 TAGCTTTCAC * 11776999 GAGCTTCCCGATTA-ATGGCTCTCTT 1 GAGCTTCCCG-TTATATGGCTCTCAT * * * * 11777024 AAGCTTCCCGATGTTTGGCTCGT-AT 1 GAGCTTCCCGTTATATGGCTC-TCAT 11777049 GAGCTTCCCGTTATATGGCTC 1 GAGCTTCCCGTTATATGGCTC 11777070 AGAAGAAGGT Statistics Matches: 35, Mismatches: 9, Indels: 4 0.73 0.19 0.08 Matches are distributed among these distances: 24 1 0.03 25 33 0.94 26 1 0.03 ACGTcount: A:0.15, C:0.27, G:0.23, T:0.35 Consensus pattern (25 bp): GAGCTTCCCGTTATATGGCTCTCAT Found at i:11779290 original size:2 final size:2 Alignment explanation

Indices: 11779283--11779309 Score: 54 Period size: 2 Copynumber: 13.5 Consensus size: 2 11779273 GAGACTAGTC 11779283 AT AT AT AT AT AT AT AT AT AT AT AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT AT A 11779310 CATGTCATGA Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 25 1.00 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (2 bp): AT Found at i:11780638 original size:68 final size:64 Alignment explanation

Indices: 11780497--11780845 Score: 191 Period size: 68 Copynumber: 5.3 Consensus size: 64 11780487 TGGAACCACG ** * * * 11780497 CATGCGACCTAGCTACATAT-ATCCCGTAGCTCTCTTGTCTACATGGTGTACACAT-AGTA-TCA 1 CATGCGACCTAGCTACATATAATCTTGTAGCTCTCTTGTC-ACATGATGTGCAC-TCAGCACT-A * 11780559 CC 63 CA 11780561 CATGCGACCTAGCTACATCATAATGTCTTGTAGCTCTCTTGTACACATGATGTGCACTCAGCACT 1 CATGCGACCTAGCTACAT-ATAA--TCTTGTAGCTCTCTTGT-CACATGATGTGCACTCAGCACT * 11780626 ATA 62 ACA * ** * * * * 11780629 CATGTGACCTAGCTACATACCATC-TGTATCATCCAATCTT-TC-C--GAAGGTTCAAC-CGGGG 1 CATGCGACCTAGCTACATATAATCTTGTAGC-T-C--TCTTGTCACATG-ATGTGC-ACTC--AG * * * 11780688 AACCACG 58 CACTACA ** * * * 11780695 CATGCGACCTAGCTACATAT-ATCCCGTAGCTCTCTTGTCTACATGGTGTACACAT-AGTA-TCA 1 CATGCGACCTAGCTACATATAATCTTGTAGCTCTCTTGTC-ACATGATGTGCAC-TCAGCACT-A * 11780757 CC 63 CA 11780759 CATGCGACCTAGCTACATCATAATGTCTTGTAGCTCTCTTGTACACATGATGTGCACTCAGCACT 1 CATGCGACCTAGCTACAT-ATAA--TCTTGTAGCTCTCTTGT-CACATGATGTGCACTCAGCACT * 11780824 ATA 62 ACA * 11780827 CATGTGACCTAGCTACATA 1 CATGCGACCTAGCTACATA 11780846 CCATCTGTAT Statistics Matches: 217, Mismatches: 37, Indels: 59 0.69 0.12 0.19 Matches are distributed among these distances: 62 4 0.02 63 3 0.01 64 51 0.24 65 17 0.08 66 33 0.15 67 7 0.03 68 98 0.45 69 4 0.02 ACGTcount: A:0.26, C:0.28, G:0.16, T:0.29 Consensus pattern (64 bp): CATGCGACCTAGCTACATATAATCTTGTAGCTCTCTTGTCACATGATGTGCACTCAGCACTACA Found at i:11780733 original size:198 final size:198 Alignment explanation

Indices: 11780488--11780884 Score: 794 Period size: 198 Copynumber: 2.0 Consensus size: 198 11780478 TCCTTCACTT 11780488 GGAACCACGCATGCGACCTAGCTACATATATCCCGTAGCTCTCTTGTCTACATGGTGTACACATA 1 GGAACCACGCATGCGACCTAGCTACATATATCCCGTAGCTCTCTTGTCTACATGGTGTACACATA 11780553 GTATCACCCATGCGACCTAGCTACATCATAATGTCTTGTAGCTCTCTTGTACACATGATGTGCAC 66 GTATCACCCATGCGACCTAGCTACATCATAATGTCTTGTAGCTCTCTTGTACACATGATGTGCAC 11780618 TCAGCACTATACATGTGACCTAGCTACATACCATCTGTATCATCCAATCTTTCCGAAGGTTCAAC 131 TCAGCACTATACATGTGACCTAGCTACATACCATCTGTATCATCCAATCTTTCCGAAGGTTCAAC 11780683 CGG 196 CGG 11780686 GGAACCACGCATGCGACCTAGCTACATATATCCCGTAGCTCTCTTGTCTACATGGTGTACACATA 1 GGAACCACGCATGCGACCTAGCTACATATATCCCGTAGCTCTCTTGTCTACATGGTGTACACATA 11780751 GTATCACCCATGCGACCTAGCTACATCATAATGTCTTGTAGCTCTCTTGTACACATGATGTGCAC 66 GTATCACCCATGCGACCTAGCTACATCATAATGTCTTGTAGCTCTCTTGTACACATGATGTGCAC 11780816 TCAGCACTATACATGTGACCTAGCTACATACCATCTGTATCATCCAATCTTTCCGAAGGTTCAAC 131 TCAGCACTATACATGTGACCTAGCTACATACCATCTGTATCATCCAATCTTTCCGAAGGTTCAAC 11780881 CGG 196 CGG 11780884 G 1 G 11780885 ATTTCTCTCT Statistics Matches: 199, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 198 199 1.00 ACGTcount: A:0.26, C:0.29, G:0.17, T:0.28 Consensus pattern (198 bp): GGAACCACGCATGCGACCTAGCTACATATATCCCGTAGCTCTCTTGTCTACATGGTGTACACATA GTATCACCCATGCGACCTAGCTACATCATAATGTCTTGTAGCTCTCTTGTACACATGATGTGCAC TCAGCACTATACATGTGACCTAGCTACATACCATCTGTATCATCCAATCTTTCCGAAGGTTCAAC CGG Found at i:11782882 original size:15 final size:16 Alignment explanation

Indices: 11782853--11782882 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 11782843 AGGATTCAGT 11782853 TTTTTTTCTTCTTCTA 1 TTTTTTTCTTCTTCTA 11782869 TTTTTTTCTT-TTCT 1 TTTTTTTCTTCTTCT 11782883 TTTCTCCTCT Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 15 4 0.29 16 10 0.71 ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80 Consensus pattern (16 bp): TTTTTTTCTTCTTCTA Found at i:11783692 original size:8 final size:8 Alignment explanation

Indices: 11783675--11783707 Score: 57 Period size: 8 Copynumber: 4.1 Consensus size: 8 11783665 CTAGATCGGC * 11783675 AAAAGCCG 1 AAAAGTCG 11783683 AAAAGTCG 1 AAAAGTCG 11783691 AAAAGTCG 1 AAAAGTCG 11783699 AAAAGTCG 1 AAAAGTCG 11783707 A 1 A 11783708 CATTTGTGAA Statistics Matches: 24, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 8 24 1.00 ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09 Consensus pattern (8 bp): AAAAGTCG Found at i:11789899 original size:16 final size:17 Alignment explanation

Indices: 11789867--11789899 Score: 50 Period size: 18 Copynumber: 1.9 Consensus size: 17 11789857 CATCAAGAAG 11789867 GGTTTTCAATGAAAACAT 1 GGTTTTCAA-GAAAACAT 11789885 GGTTTTCAA-AAAACA 1 GGTTTTCAAGAAAACA 11789900 CTTCAATGTG Statistics Matches: 15, Mismatches: 0, Indels: 2 0.88 0.00 0.12 Matches are distributed among these distances: 16 6 0.40 18 9 0.60 ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30 Consensus pattern (17 bp): GGTTTTCAAGAAAACAT Found at i:11790994 original size:19 final size:19 Alignment explanation

Indices: 11790982--11791028 Score: 78 Period size: 19 Copynumber: 2.5 Consensus size: 19 11790972 AATAAAAATG 11790982 AATGAAATGAATAGAAAAA 1 AATGAAATGAATAGAAAAA * 11791001 AATGGAATGAATAGAAAAA 1 AATGAAATGAATAGAAAAA 11791020 AA-GAAATGA 1 AATGAAATGA 11791029 GAAACATTTA Statistics Matches: 26, Mismatches: 2, Indels: 1 0.90 0.07 0.03 Matches are distributed among these distances: 18 6 0.23 19 20 0.77 ACGTcount: A:0.66, C:0.00, G:0.19, T:0.15 Consensus pattern (19 bp): AATGAAATGAATAGAAAAA Found at i:11791942 original size:21 final size:20 Alignment explanation

Indices: 11791900--11791948 Score: 55 Period size: 20 Copynumber: 2.5 Consensus size: 20 11791890 TTAAGTTATA ** 11791900 AATTATAAATATATTATTTT 1 AATTATAAATATATTAAATT * 11791920 AATTATAAATTGTATTAAATT 1 AATTATAAA-TATATTAAATT 11791941 AATT-TAAA 1 AATTATAAA 11791949 ATAATTATAT Statistics Matches: 25, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 20 13 0.52 21 12 0.48 ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49 Consensus pattern (20 bp): AATTATAAATATATTAAATT Found at i:11793272 original size:18 final size:18 Alignment explanation

Indices: 11793249--11793285 Score: 65 Period size: 18 Copynumber: 2.1 Consensus size: 18 11793239 TTTGCGATCA 11793249 AAATTGAAAGTGAAAGTG 1 AAATTGAAAGTGAAAGTG * 11793267 AAATTGAAATTGAAAGTG 1 AAATTGAAAGTGAAAGTG 11793285 A 1 A 11793286 TATGAATTGT Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 18 18 1.00 ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24 Consensus pattern (18 bp): AAATTGAAAGTGAAAGTG Found at i:11793274 original size:12 final size:12 Alignment explanation

Indices: 11793249--11793285 Score: 56 Period size: 12 Copynumber: 3.1 Consensus size: 12 11793239 TTTGCGATCA 11793249 AAATTGAAAGTG 1 AAATTGAAAGTG * * 11793261 AAAGTGAAATTG 1 AAATTGAAAGTG 11793273 AAATTGAAAGTG 1 AAATTGAAAGTG 11793285 A 1 A 11793286 TATGAATTGT Statistics Matches: 21, Mismatches: 4, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 12 21 1.00 ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24 Consensus pattern (12 bp): AAATTGAAAGTG Found at i:11793298 original size:18 final size:19 Alignment explanation

Indices: 11793249--11793298 Score: 61 Period size: 18 Copynumber: 2.8 Consensus size: 19 11793239 TTTGCGATCA 11793249 AAATTGAAA-GTGAAAGTG 1 AAATTGAAATGTGAAAGTG 11793267 AAATTGAAAT-TGAAAGTG 1 AAATTGAAATGTGAAAGTG * * 11793285 ATA-TGAATTGTGAA 1 AAATTGAAATGTGAA 11793299 TTGAAAATCC Statistics Matches: 28, Mismatches: 2, Indels: 4 0.82 0.06 0.12 Matches are distributed among these distances: 17 5 0.18 18 23 0.82 ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28 Consensus pattern (19 bp): AAATTGAAATGTGAAAGTG Found at i:11795810 original size:39 final size:39 Alignment explanation

Indices: 11795748--11796024 Score: 446 Period size: 39 Copynumber: 7.1 Consensus size: 39 11795738 AATTATATTA * * * * * 11795748 CCAGCACAAAGCCCGCGGGACTTTAGCTCGGACACGTTT 1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT * * * 11795787 CCAACACGAAGCCTACGGGACTTTAGCCTGGATACATTT 1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT 11795826 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT 1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT 11795865 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT 1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT 11795904 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT 1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT * * 11795943 CCAGCAGGAAGCCTGCGGGACTTTAGCCCAGATACATTT 1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT * * 11795982 CCAGCATGAAGCCTGCGGGACTTTAGCCCGTATACATTT 1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT 11796021 CCAG 1 CCAG 11796025 TGTCTTGCAT Statistics Matches: 222, Mismatches: 16, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 39 222 1.00 ACGTcount: A:0.24, C:0.30, G:0.25, T:0.21 Consensus pattern (39 bp): CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT Found at i:11798442 original size:26 final size:26 Alignment explanation

Indices: 11798405--11798488 Score: 150 Period size: 26 Copynumber: 3.2 Consensus size: 26 11798395 TGATACAAAT * * 11798405 TGATAATAGGTTAGGTAAATGTTCCA 1 TGATAATGGGTTAGGTAAATGTTTCA 11798431 TGATAATGGGTTAGGTAAATGTTTCA 1 TGATAATGGGTTAGGTAAATGTTTCA 11798457 TGATAATGGGTTAGGTAAATGTTTCA 1 TGATAATGGGTTAGGTAAATGTTTCA 11798483 TGATAA 1 TGATAA 11798489 GAATTTCATG Statistics Matches: 56, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 26 56 1.00 ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37 Consensus pattern (26 bp): TGATAATGGGTTAGGTAAATGTTTCA Found at i:11800149 original size:27 final size:27 Alignment explanation

Indices: 11800108--11800220 Score: 129 Period size: 27 Copynumber: 4.2 Consensus size: 27 11800098 GAGGAAGCGT * 11800108 TCTGGTGGCTATGCCACAAATATCTGA 1 TCTGGTGGCTCTGCCACAAATATCTGA * * 11800135 TCTGGTGGCTCTGCCACATATATCTGT 1 TCTGGTGGCTCTGCCACAAATATCTGA * * 11800162 TCTGGTGGCTCTGCCACGATTATCTGTA 1 TCTGGTGGCTCTGCCACAAATATCTG-A * * * * 11800190 TCTGGTGACTCTGTCAC-ATTATCTGT 1 TCTGGTGGCTCTGCCACAAATATCTGA 11800216 TCTGG 1 TCTGG 11800221 CAGCCATGCT Statistics Matches: 75, Mismatches: 10, Indels: 3 0.85 0.11 0.03 Matches are distributed among these distances: 26 5 0.07 27 55 0.73 28 15 0.20 ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36 Consensus pattern (27 bp): TCTGGTGGCTCTGCCACAAATATCTGA Found at i:11800213 original size:54 final size:54 Alignment explanation

Indices: 11800106--11800220 Score: 169 Period size: 54 Copynumber: 2.1 Consensus size: 54 11800096 TGGAGGAAGC * 11800106 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT 1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT * * * * 11800160 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT 1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCT 11800214 GTTCTGG 1 GTTCTGG 11800221 CAGCCATGCT Statistics Matches: 55, Mismatches: 5, Indels: 2 0.89 0.08 0.03 Matches are distributed among these distances: 54 37 0.67 55 18 0.33 ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37 Consensus pattern (54 bp): GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT Found at i:11806012 original size:46 final size:46 Alignment explanation

Indices: 11805936--11806430 Score: 631 Period size: 46 Copynumber: 10.8 Consensus size: 46 11805926 TGATGTCATA * * * * 11805936 GTATCTTTCAACTATGGTTTTACTCGTTTTC-TGTCATGTTGCCATG 1 GTATCTTTCAACCATGGTCTTACTC-ATTTCATATCATGTTGCCATG * * *** 11805982 GTATCTTTCAACCATCGTCTTATTCATTTTCCCGTCATGTTGCCATG 1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATATCATGTTGCCATG * * * 11806029 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG 1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATATCATGTTGCCATG * * 11806076 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATG 1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATG * * 11806122 GTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATG 1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATG * * 11806168 GTATC-TT---CCATGGTCTTATTCATTTCATATCACGTTGCCATG 1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATG * * 11806210 GTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATG 1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATG * * *** 11806256 GTATCCTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATG 1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATATCATGTTGCCATG * 11806303 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG 1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATG * * * * 11806349 GTATGTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCTTG 1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATG * * 11806395 GTATCTTTCAACCATGGTCTTACACATTCCATATCA 1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCA 11806431 GAGAGCACAC Statistics Matches: 408, Mismatches: 34, Indels: 14 0.89 0.07 0.03 Matches are distributed among these distances: 42 40 0.10 43 2 0.00 45 2 0.00 46 240 0.59 47 124 0.30 ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41 Consensus pattern (46 bp): GTATCTTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATG Found at i:11806125 original size:93 final size:92 Alignment explanation

Indices: 11805936--11806430 Score: 649 Period size: 93 Copynumber: 5.4 Consensus size: 92 11805926 TGATGTCATA * * * * * * 11805936 GTATCTTTCAACTATGGTTTTACTCGTTTTC-TGTCATGTTGCCATGGTATCTTTCAACCATCGT 1 GTATCTTTCAACCATGGTCTTACTC-ATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGT ** * 11806000 CTTATTCATTTTCCCGTCATGTTGCCATG 65 CTTATTCA-TTTCATGTCAGGTTGCCATG * * * * 11806029 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATGGTATCTTTCAACCATGGT 1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATATCACGTTGCCATGGTATCTTTCAACCATGGT * 11806094 CTTACTCATTTCATGTCAGGTTGCCATG 65 CTTATTCATTTCATGTCAGGTTGCCATG * 11806122 GTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATGGTATC-TT---CCATGGTC 1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTC * * 11806183 TTATTCATTTCATATCACGTTGCCATG 66 TTATTCATTTCATGTCAGGTTGCCATG * * 11806210 GTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATGGTATCCTTCAACCATGGTC 1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTC ** * 11806275 TTATTCATTTTCCCGTCATGTTGCCATG 66 TTATTCA-TTTCATGTCAGGTTGCCATG * * 11806303 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATGGTATGTTTCAACCATGGTC 1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTC ** * * 11806368 TTACACATTTCATATCAGGTTGCCTTG 66 TTATTCATTTCATGTCAGGTTGCCATG * * 11806395 GTATCTTTCAACCATGGTCTTACACATTCCATATCA 1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCA 11806431 GAGAGCACAC Statistics Matches: 361, Mismatches: 34, Indels: 15 0.88 0.08 0.04 Matches are distributed among these distances: 88 81 0.22 89 2 0.01 91 2 0.01 92 86 0.24 93 151 0.42 94 39 0.11 ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41 Consensus pattern (92 bp): GTATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTC TTATTCATTTCATGTCAGGTTGCCATG Found at i:11806369 original size:227 final size:228 Alignment explanation

Indices: 11805973--11806401 Score: 716 Period size: 227 Copynumber: 1.9 Consensus size: 228 11805963 TTTCTGTCAT ** * * * * 11805973 GTTGCCATGGTATCTTTCAACCATCGTCTTATTCATTTTCCCGTCATGTTGCCATGGTATCTTTC 1 GTTGCCATGGTATCTTTCAACCATCGTCTTACACATTTTCACATCACGTTGCCATGGTATCCTTC * 11806038 AACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCAT 66 AACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCAT * ** 11806103 TTCATGTCAGGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATG 131 TTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATG 11806168 GTATCTTCCATGGTCTTATTCATTTCATATCAC 196 GTATCTTCCATGGTCTTATTCATTTCATATCAC * * 11806201 GTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCACGTTGCCATGGTATCCTTC 1 GTTGCCATGGTATCTTTCAACCATCGTCTTACACATTTTCACATCACGTTGCCATGGTATCCTTC 11806265 AACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCAT 66 AACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCAT * * * 11806330 TTCATATCAGGTTGCCATGGTATGTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCTTG 131 TTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATG 11806395 GTATCTT 196 GTATCTT 11806402 TCAACCATGG Statistics Matches: 186, Mismatches: 15, Indels: 1 0.92 0.07 0.00 Matches are distributed among these distances: 227 154 0.83 228 32 0.17 ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41 Consensus pattern (228 bp): GTTGCCATGGTATCTTTCAACCATCGTCTTACACATTTTCACATCACGTTGCCATGGTATCCTTC AACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCAT TTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATG GTATCTTCCATGGTCTTATTCATTTCATATCAC Found at i:11808819 original size:50 final size:50 Alignment explanation

Indices: 11808744--11808892 Score: 246 Period size: 50 Copynumber: 3.0 Consensus size: 50 11808734 CCATGGAAAC 11808744 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA 1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA * * * * 11808794 AAGTGATAAGTAATAACTTCGGCTACACTTATCTGATTAAGGACAAGTGA 1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA 11808844 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGG-CAAATG 1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAA-GGACAAATG 11808893 GCAAATGACA Statistics Matches: 90, Mismatches: 8, Indels: 2 0.90 0.08 0.02 Matches are distributed among these distances: 50 88 0.98 51 2 0.02 ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28 Consensus pattern (50 bp): AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA Found at i:11808943 original size:31 final size:31 Alignment explanation

Indices: 11808905--11809113 Score: 328 Period size: 31 Copynumber: 6.7 Consensus size: 31 11808895 AAATGACAAC * * 11808905 TGAAAAGTGGTAACTTCAGCTACCTGATCAG 1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG * 11808936 TGAAAAGTGGTAGCTTCTGCTACCTGATCAG 1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG 11808967 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG 1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG * 11808998 TGAAAATTGGTAGCTTCGGCTACCTGATCAG 1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG * 11809029 TGAAAAGTGGTAGCTCCGGCTACCTGATCAG 1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG ** * 11809060 TGAAAAGTGGTAGCACCAGCTACCTGATCAG 1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG * * 11809091 TGAATAGTGGTAGCTTTGGCTAC 1 TGAAAAGTGGTAGCTTCGGCTAC 11809114 AAGTGACAAG Statistics Matches: 165, Mismatches: 13, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 31 165 1.00 ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26 Consensus pattern (31 bp): TGAAAAGTGGTAGCTTCGGCTACCTGATCAG Found at i:11809124 original size:7 final size:7 Alignment explanation

Indices: 11809112--11809140 Score: 58 Period size: 7 Copynumber: 4.1 Consensus size: 7 11809102 AGCTTTGGCT 11809112 ACAAGTG 1 ACAAGTG 11809119 ACAAGTG 1 ACAAGTG 11809126 ACAAGTG 1 ACAAGTG 11809133 ACAAGTG 1 ACAAGTG 11809140 A 1 A 11809141 TTTCTGTATA Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 22 1.00 ACGTcount: A:0.45, C:0.14, G:0.28, T:0.14 Consensus pattern (7 bp): ACAAGTG Found at i:11810975 original size:7 final size:8 Alignment explanation

Indices: 11810960--11810985 Score: 52 Period size: 8 Copynumber: 3.2 Consensus size: 8 11810950 AGTCCGGAAT 11810960 ATAAAAAA 1 ATAAAAAA 11810968 ATAAAAAA 1 ATAAAAAA 11810976 ATAAAAAA 1 ATAAAAAA 11810984 AT 1 AT 11810986 TCTTGATTCC Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 8 18 1.00 ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15 Consensus pattern (8 bp): ATAAAAAA Found at i:11813369 original size:50 final size:50 Alignment explanation

Indices: 11813294--11813441 Score: 237 Period size: 50 Copynumber: 3.0 Consensus size: 50 11813284 CCATGGAAAC 11813294 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA 1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA * * * * 11813344 AAGTGATAAGTAATAACTTCGGCTACACTTATCTGATTAAGGACAAGTGA 1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA 11813394 AAGTGATAAGTGATAGCTTCGG-TACACTTATCTGATCAATGG-CAAATG 1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAA-GGACAAATG 11813442 GCAAATGACA Statistics Matches: 89, Mismatches: 8, Indels: 3 0.89 0.08 0.03 Matches are distributed among these distances: 49 21 0.24 50 68 0.76 ACGTcount: A:0.36, C:0.15, G:0.22, T:0.28 Consensus pattern (50 bp): AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA Found at i:11813692 original size:31 final size:31 Alignment explanation

Indices: 11813454--11813692 Score: 354 Period size: 31 Copynumber: 7.7 Consensus size: 31 11813444 AAATGACAAC * 11813454 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG 1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG * * 11813485 TGAAAAGT-GTAGTTTCAGCTACCTGATCAG 1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG * * 11813515 TGAAAAGTGGTAGCTTCTGCTACCTAATCAG 1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG 11813546 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG 1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG * 11813577 TGAAAATTGGTAGCTTCGGCTACCTGATCAG 1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG * 11813608 TGAAAAGTGGTAGCTCCGGCTACCTGATCAG 1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG * ** * 11813639 TGAAAAATGGTAGCACCAGCTACCTGATCAG 1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG * * 11813670 TGAATAGTGGTAGCTTTGGCTAC 1 TGAAAAGTGGTAGCTTCGGCTAC 11813693 AAGTGACAAG Statistics Matches: 189, Mismatches: 18, Indels: 2 0.90 0.09 0.01 Matches are distributed among these distances: 30 29 0.15 31 160 0.85 ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27 Consensus pattern (31 bp): TGAAAAGTGGTAGCTTCGGCTACCTGATCAG Done.