Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1450

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: 71457
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30


Found at i:1072 original size:28 final size:28

Alignment explanation

Indices: 1028--1581 Score: 444 Period size: 28 Copynumber: 20.4 Consensus size: 28 1018 TATACAACCC * * 1028 CTTTTCAAAGCCCACAAGTCAATGGCAA 1 CTTTTCAAAGCCCACAAGTCAGTGGCAT * * * 1056 CTTTTCAAAGCCTACAATTCAGTGGAAT 1 CTTTTCAAAGCCCACAAGTCAGTGGCAT * * * 1084 CCTTTCAAAGCCTACAGGTCAGTGGCAT 1 CTTTTCAAAGCCCACAAGTCAGTGGCAT 1112 CTTTTCAAAGCCCACAAGTCAAG-GGCAT 1 CTTTTCAAAGCCCACAAGTC-AGTGGCAT * * * 1140 CCTTTCAAAGCCCATAAGTCAGTGGCAC 1 CTTTTCAAAGCCCACAAGTCAGTGGCAT * 1168 CTTTTCAAAGTCCACAAGTCAGTGGCAT 1 CTTTTCAAAGCCCACAAGTCAGTGGCAT * 1196 CCTTTCAAAGCCCACAAGTCAGTGGCA- 1 CTTTTCAAAGCCCACAAGTCAGTGGCAT * * * * 1223 CGTTTCCAACGCCCACATGTCAATGGCAT 1 C-TTTTCAAAGCCCACAAGTCAGTGGCAT * * 1252 CCTTT-------CA-AAGTCAGTGGCAC 1 CTTTTCAAAGCCCACAAGTCAGTGGCAT ** * * * 1272 CTTTAAAAATCCCACAAGTGAGTGGCAC 1 CTTTTCAAAGCCCACAAGTCAGTGGCAT * * 1300 CTTTTTAAAGCCCACAAGTCAATGGCAT 1 CTTTTCAAAGCCCACAAGTCAGTGGCAT * * * * * 1328 CCTTTCGAAGCCCACAAGTCAATGGAAC 1 CTTTTCAAAGCCCACAAGTCAGTGGCAT * *** 1356 CTTTTCAAAGCCCACATGT-AGTCTTAT 1 CTTTTCAAAGCCCACAAGTCAGTGGCAT * * * 1383 CCTTTC--A----A-AATTCAGTGGCAC 1 CTTTTCAAAGCCCACAAGTCAGTGGCAT * * 1404 CTTTTCAAATCCCACATGTCAGTGGCAT 1 CTTTTCAAAGCCCACAAGTCAGTGGCAT * * * * * 1432 CCTTTCAAAGTCCAAAAGTTAGTGGCAC 1 CTTTTCAAAGCCCACAAGTCAGTGGCAT * * 1460 CTTTTCAAAACCCACAAGTCAATGGCAT 1 CTTTTCAAAGCCCACAAGTCAGTGGCAT * * * * 1488 CCTTTCAAAGCCTACAAGTCAGTGGAAC 1 CTTTTCAAAGCCCACAAGTCAGTGGCAT * 1516 CTTTTCAAAGCCCACAAGTTAGTGGCAT 1 CTTTTCAAAGCCCACAAGTCAGTGGCAT * * * * 1544 CCTTTCAAAGCCTATAAGTCAATGGCA- 1 CTTTTCAAAGCCCACAAGTCAGTGGCAT 1571 CATTTTCAAAG 1 C-TTTTCAAAG 1582 TGGCATTCTT Statistics Matches: 410, Mismatches: 95, Indels: 42 0.75 0.17 0.08 Matches are distributed among these distances: 20 15 0.04 21 12 0.03 23 1 0.00 25 1 0.00 27 15 0.04 28 363 0.89 29 3 0.01 ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26 Consensus pattern (28 bp): CTTTTCAAAGCCCACAAGTCAGTGGCAT Found at i:1091 original size:56 final size:56 Alignment explanation

Indices: 1027--1771 Score: 526 Period size: 56 Copynumber: 13.8 Consensus size: 56 1017 CTATACAACC * * * * * * 1027 CCTTTTCAAAGCCCACAAGTCAATGGCAACTTTTCAAAGCCTACAATTCAGTGGAA 1 CCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA * * * 1083 TCC-TTTCAAAGCCTACAGGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAAG-GGCA 1 -CCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTC-AGTGGCA * * 1139 TCC-TTTCAAAGCCCATAAGTCAGTGGCA-CCTTTTCAAAGTCCACAAGTCAGTGGCA 1 -CCTTTTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTCAGTGGCA * * * * 1195 TCC-TTTCAAAGCCCACAAGTCAGTGGCA-CGTTTCCAACGCCCACATGTCAATGGCA 1 -CCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTT-CAAAGCCCACAAGTCAGTGGCA * * * 1251 TCC-TTT-------CA-AAGTCAGTGGCA-CCTTTAAAAATCCCACAAGTGAGTGGCA 1 -CCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTT-CAAAGCCCACAAGTCAGTGGCA * * * * * 1299 CCTTTTTAAAGCCCACAAGTCAATGGCATCCTTTCGAAGCCCACAAGTCAATGGAA 1 CCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA * *** * 1355 CCTTTTCAAAGCCCACATGT-AGTCTTATCCTTTC--A----A-AATTCAGTGGCA 1 CCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA * * * * * 1403 CCTTTTCAAATCCCACATGTCAGTGGCATCCTTTCAAAGTCCAAAAGTTAGTGGCA 1 CCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA * * * * 1459 CCTTTTCAAAACCCACAAGTCAATGGCATCCTTTCAAAGCCTACAAGTCAGTGGAA 1 CCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA * * * * 1515 CCTTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCTATAAGTCAATGGCA 1 CCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA * * * * 1571 CATTTT---------CAA---AGTGGCATTCTTTCAAAGCCCACAAGTTACTGGCA 1 CCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA * * * * * * * 1615 CCTTTTCAAAACCCATAAGTTAGTGG--TCCCTTCCAAGCCCACAAGTTAGTGGTA 1 CCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA * * * * 1669 TCTTTTCAAAG-CCATCAAGTCAATGGCA-CATTTTCAAAGCCCACATGTCAGTGGCAA 1 CCTTTTCAAAGCCCA-CAAGTCAGTGGCATC-CTTTCAAAGCCCACAAGTCAGTGGC-A * * * * * 1726 CCCTTTTTAAAACCCACACAAGTTAGTGGCACCCTAGTCAAAGCCC 1 -CC-TTTTCAAAGCC-CACAAGTCAGTGGCATCCT-TTCAAAGCCC 1772 GCACGAGTTA Statistics Matches: 550, Mismatches: 93, Indels: 86 0.75 0.13 0.12 Matches are distributed among these distances: 44 35 0.06 47 5 0.01 48 63 0.11 49 14 0.03 51 1 0.00 53 6 0.01 54 40 0.07 55 20 0.04 56 323 0.59 57 10 0.02 58 1 0.00 59 7 0.01 60 13 0.02 61 12 0.02 ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26 Consensus pattern (56 bp): CCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA Found at i:1313 original size:76 final size:76 Alignment explanation

Indices: 1183--1333 Score: 214 Period size: 76 Copynumber: 2.0 Consensus size: 76 1173 CAAAGTCCAC * * * * 1183 AAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACGTTTCCAACGCCCACATGTCAATG 1 AAGTCAGTGGCATCCTTTAAAAGCCCACAAGTCAGTGGCACCTTTCCAAAGCCCACAAGTCAATG 1248 GCATCCTTTCA 66 GCATCCTTTCA * * ** 1259 AAGTCAGTGGCA-CCTTTAAAAATCCCACAAGTGAGTGGCACCTTTTTAAAGCCCACAAGTCAAT 1 AAGTCAGTGGCATCCTTT-AAAAGCCCACAAGTCAGTGGCACCTTTCCAAAGCCCACAAGTCAAT 1323 GGCATCCTTTC 65 GGCATCCTTTC 1334 GAAGCCCACA Statistics Matches: 66, Mismatches: 8, Indels: 2 0.87 0.11 0.03 Matches are distributed among these distances: 75 5 0.08 76 61 0.92 ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25 Consensus pattern (76 bp): AAGTCAGTGGCATCCTTTAAAAGCCCACAAGTCAGTGGCACCTTTCCAAAGCCCACAAGTCAATG GCATCCTTTCA Found at i:1519 original size:132 final size:131 Alignment explanation

Indices: 1027--1524 Score: 468 Period size: 132 Copynumber: 3.7 Consensus size: 131 1017 CTATACAACC * * * * * * * * 1027 CCTTTTCAAAGCCCACAAGTCAATGGCAACTTTTCAAAGCCTACAATTCAGTGGAATCCTTTCAA 1 CCTTTTCAAAGTCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCA-CCTTTCAA * * * * * 1092 AGCCTACAGGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAAG-GGCATCC-TTTCAAAGCCCAT 65 AGCCCACATGTCAGTGG-ATCCTTTC--A----A-AAGTC-AGTGGCA-CCTTTTCAAATCCCAC 1155 AAGTCAGTGGCA 120 AAGTCAGTGGCA * * 1167 CCTTTTCAAAGTCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACGTTTCCAA 1 CCTTTTCAAAGTCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCACCTTT-CAA * * ** * 1232 CGCCCACATGTCAATGGCATCCTTTC-AAAGTCAGTGGCACCTTTAAAAATCCCACAAGTGAGTG 65 AGCCCACATGTCAGTGG-ATCCTTTCAAAAGTCAGTGGCACCTTTTCAAATCCCACAAGTCAGTG 1296 GCA 129 GCA * * * * * 1299 CCTTTTTAAAGCCCACAAGTCAATGGCATCCTTTCGAAGCCCACAAGTCAATGGAACCTTTTCAA 1 CCTTTTCAAAGTCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCACC-TTTCAA ** * * 1364 AGCCCACATGT-AGTCTTATCCTTTCAAAATTCAGTGGCACCTTTTCAAATCCCACATGTCAGTG 65 AGCCCACATGTCAGT-GGATCCTTTCAAAAGTCAGTGGCACCTTTTCAAATCCCACAAGTCAGTG 1428 GCA 129 GCA * * * 1431 TCC-TTTCAAAGTCCAAAAGTTAGTGGCA-CCTTTTCAAAACCCACAAGTCAATGGCATCCTTTC 1 -CCTTTTCAAAGTCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTCAATGGCA-CCTTTC * * * 1494 AAAGCCTACAAGTCAGTGGAACCTTTTCAAA 63 AAAGCCCACATGTCAGTGGATCC-TTTCAAA 1525 GCCCACAAGT Statistics Matches: 300, Mismatches: 47, Indels: 29 0.80 0.12 0.08 Matches are distributed among these distances: 131 16 0.05 132 189 0.63 133 18 0.06 139 4 0.01 140 73 0.24 ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26 Consensus pattern (131 bp): CCTTTTCAAAGTCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCACCTTTCAAA GCCCACATGTCAGTGGATCCTTTCAAAAGTCAGTGGCACCTTTTCAAATCCCACAAGTCAGTGGC A Found at i:1599 original size:44 final size:44 Alignment explanation

Indices: 1536--1624 Score: 124 Period size: 44 Copynumber: 2.0 Consensus size: 44 1526 CCCACAAGTT * * 1536 AGTGGCATCCTTTCAAAGCCTATAAGTCAATGGCACATTTTCAA 1 AGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCACATTTTCAA * * * * 1580 AGTGGCATTCTTTCAAAGCCCACAAGTTACTGGCACCTTTTCAA 1 AGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCACATTTTCAA 1624 A 1 A 1625 ACCCATAAGT Statistics Matches: 39, Mismatches: 6, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 44 39 1.00 ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29 Consensus pattern (44 bp): AGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCACATTTTCAA Found at i:1622 original size:28 final size:28 Alignment explanation

Indices: 1590--1785 Score: 139 Period size: 28 Copynumber: 6.8 Consensus size: 28 1580 AGTGGCATTC * 1590 TTTCAAAGCCCACAAGTTACTGGCACCT 1 TTTCAAAGCCCACAAGTTAGTGGCACCT * * 1618 TTTCAAAACCCATAAGTTAGTGGTC-CC- 1 TTTCAAAGCCCACAAGTTAGTGG-CACCT * * * 1645 -TTCCAAGCCCACAAGTTAGTGGTATCT 1 TTTCAAAGCCCACAAGTTAGTGGCACCT * * * 1672 TTTCAAAG-CCATCAAGTCAATGGCACAT 1 TTTCAAAGCCCA-CAAGTTAGTGGCACCT * * 1700 TTTCAAAGCCCACATGTCAGTGGCAACCCTT 1 TTTCAAAGCCCACAAGTTAGTGGC-A-CC-T * * 1731 TTTAAAACCCACACAAGTTAGTGGCACCCT 1 TTTCAAAGCC-CACAAGTTAGTGGCA-CCT ** * 1761 AGTCAAAGCCCGCACGAGTTAGTGG 1 TTTCAAAG-CC-CACAAGTTAGTGG 1786 TGCTCGAGTC Statistics Matches: 130, Mismatches: 27, Indels: 19 0.74 0.15 0.11 Matches are distributed among these distances: 26 20 0.15 27 3 0.02 28 57 0.44 29 5 0.04 30 6 0.05 31 27 0.21 32 12 0.09 ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25 Consensus pattern (28 bp): TTTCAAAGCCCACAAGTTAGTGGCACCT Found at i:1781 original size:31 final size:31 Alignment explanation

Indices: 1738--1820 Score: 103 Period size: 31 Copynumber: 2.7 Consensus size: 31 1728 CTTTTTAAAA * 1738 CCCACACAAGTTAGTGGCACCCTAGTCAAAG 1 CCCACACAAGTTAGTGGCACCCGAGTCAAAG * * ** * 1769 CCCGCACGAGTTAGTGGTGCTCGAGTCAAAG 1 CCCACACAAGTTAGTGGCACCCGAGTCAAAG * 1800 CCCACACAAGTTGGTGGCACC 1 CCCACACAAGTTAGTGGCACC 1821 TATGTTTGAG Statistics Matches: 40, Mismatches: 12, Indels: 0 0.77 0.23 0.00 Matches are distributed among these distances: 31 40 1.00 ACGTcount: A:0.27, C:0.31, G:0.25, T:0.17 Consensus pattern (31 bp): CCCACACAAGTTAGTGGCACCCGAGTCAAAG Found at i:4865 original size:21 final size:21 Alignment explanation

Indices: 4832--4872 Score: 57 Period size: 21 Copynumber: 2.0 Consensus size: 21 4822 ATAAGTAAAA 4832 ATACATATTGTATCAATACAT 1 ATACATATTGTATCAATACAT * 4853 ATAC-TATTGGTATTAATACA 1 ATACATATT-GTATCAATACA 4873 CAAGGTTGAC Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 20 4 0.22 21 14 0.78 ACGTcount: A:0.41, C:0.12, G:0.07, T:0.39 Consensus pattern (21 bp): ATACATATTGTATCAATACAT Found at i:5026 original size:10 final size:10 Alignment explanation

Indices: 5007--5037 Score: 53 Period size: 10 Copynumber: 3.1 Consensus size: 10 4997 AATCTCATTT 5007 TCACTGTTCA 1 TCACTGTTCA * 5017 TCACTATTCA 1 TCACTGTTCA 5027 TCACTGTTCA 1 TCACTGTTCA 5037 T 1 T 5038 GTATCGATGC Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 10 19 1.00 ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42 Consensus pattern (10 bp): TCACTGTTCA Found at i:5266 original size:34 final size:35 Alignment explanation

Indices: 5203--5269 Score: 102 Period size: 37 Copynumber: 1.9 Consensus size: 35 5193 CTAAGTGATT 5203 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA 1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA 5239 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG 1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG 5270 TGTTGTAAGG Statistics Matches: 30, Mismatches: 0, Indels: 4 0.88 0.00 0.12 Matches are distributed among these distances: 34 8 0.27 36 9 0.30 37 13 0.43 ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30 Consensus pattern (35 bp): GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA Found at i:5851 original size:51 final size:51 Alignment explanation

Indices: 5787--5894 Score: 182 Period size: 51 Copynumber: 2.1 Consensus size: 51 5777 TTTTGTTATT * 5787 TGTATCGATACATTATTCATTGTATC-GATACATTTTGGGTTTTTACCCAGA 1 TGTATCGATACATTATTCATTGTATCAG-TACATTTTGGGTTTGTACCCAGA * 5838 TGTATCGATACATTATTCATTGTATCAGTGCATTTTGGGTTTGTACCCAGA 1 TGTATCGATACATTATTCATTGTATCAGTACATTTTGGGTTTGTACCCAGA 5889 TGTATC 1 TGTATC 5895 ATGCAGGCAA Statistics Matches: 54, Mismatches: 2, Indels: 2 0.93 0.03 0.03 Matches are distributed among these distances: 51 53 0.98 52 1 0.02 ACGTcount: A:0.24, C:0.16, G:0.18, T:0.43 Consensus pattern (51 bp): TGTATCGATACATTATTCATTGTATCAGTACATTTTGGGTTTGTACCCAGA Found at i:19831 original size:7 final size:7 Alignment explanation

Indices: 19816--19927 Score: 65 Period size: 7 Copynumber: 16.0 Consensus size: 7 19806 GCATCTTTCG 19816 CAAAAAA 1 CAAAAAA * 19823 -AACAAA 1 CAAAAAA 19829 -AAAAAA 1 CAAAAAA 19835 CAACAAAA 1 CAA-AAAA * 19843 TAAAAAA 1 CAAAAAA 19850 CAAAATAA 1 CAAAA-AA 19858 GCAACAAAA 1 -CAA-AAAA 19867 -AAACAAA 1 CAAA-AAA 19874 -AAACAAA 1 CAAA-AAA 19881 CAAAAAA 1 CAAAAAA * 19888 CCAAAAA 1 CAAAAAA * * 19895 TAAACAA 1 CAAAAAA * 19902 CAACAAA 1 CAAAAAA * 19909 -AAACAA 1 CAAAAAA 19915 -AAAAAA 1 CAAAAAA 19921 CAAAAAA 1 CAAAAAA 19928 AAGAGGAAAA Statistics Matches: 83, Mismatches: 14, Indels: 16 0.73 0.12 0.14 Matches are distributed among these distances: 6 20 0.24 7 45 0.54 8 11 0.13 9 5 0.06 10 2 0.02 ACGTcount: A:0.81, C:0.15, G:0.01, T:0.03 Consensus pattern (7 bp): CAAAAAA Found at i:19883 original size:43 final size:42 Alignment explanation

Indices: 19818--19929 Score: 120 Period size: 45 Copynumber: 2.6 Consensus size: 42 19808 ATCTTTCGCA * * * 19818 AAAAAAACAAAAAA-AAACAACAAAATAAAAAACAAAATAAGCAAC 1 AAAAAAACAAAAAACAAACAA-AAAA-CAAAAA-TAAACAA-CAAC 19863 AAAAAAACAAAAAACAAACAAAAAACCAAAAATAAACAACAAC 1 AAAAAAACAAAAAACAAACAAAAAA-CAAAAATAAACAACAAC * 19906 AAAAAACAAAAAAAACAAA-AAAAA 1 AAAAAA-ACAAAAAACAAACAAAAA 19930 GAGGAAAAAG Statistics Matches: 60, Mismatches: 5, Indels: 6 0.85 0.07 0.08 Matches are distributed among these distances: 43 15 0.25 44 16 0.27 45 23 0.38 46 6 0.10 ACGTcount: A:0.82, C:0.14, G:0.01, T:0.03 Consensus pattern (42 bp): AAAAAAACAAAAAACAAACAAAAAACAAAAATAAACAACAAC Found at i:19922 original size:40 final size:37 Alignment explanation

Indices: 19827--19927 Score: 116 Period size: 40 Copynumber: 2.6 Consensus size: 37 19817 AAAAAAAACA * * * 19827 AAAAAAAAC-AACAAAATAAAAAACAAAATAAGCAAC 1 AAAAAAAACAAAAAAAACAAAAAACAAAATAAACAAC 19863 -AAAAAAACAAAAAACAAACAAAAAACCAAAAATAAACAAC 1 AAAAAAAAC-AAAAA-AAACAAAAAA-C-AAAATAAACAAC 19903 AACAAAAAACAAAAAAAACAAAAAA 1 AA-AAAAAACAAAAAAAACAAAAAA 19928 AAGAGGAAAA Statistics Matches: 55, Mismatches: 3, Indels: 10 0.81 0.04 0.15 Matches are distributed among these distances: 35 8 0.15 37 3 0.05 38 9 0.16 39 1 0.02 40 21 0.38 41 6 0.11 42 7 0.13 ACGTcount: A:0.81, C:0.15, G:0.01, T:0.03 Consensus pattern (37 bp): AAAAAAAACAAAAAAAACAAAAAACAAAATAAACAAC Found at i:19928 original size:52 final size:52 Alignment explanation

Indices: 19818--19928 Score: 140 Period size: 52 Copynumber: 2.1 Consensus size: 52 19808 ATCTTTCGCA 19818 AAAAAAACAAAAAAAAACAACAAAATAAAAAACAAAATAAGCAACAAAAAAAC 1 AAAAAAACAAAAAAAAACAACAAAATAAAAAACAAAATAA-CAACAAAAAAAC * * 19871 -AAAAAACAAACAAAAAACCA-AAAATAAACAACAACAA-AA-AACAAAAAAAAC 1 AAAAAAACAAA-AAAAAACAACAAAATAAAAAACAA-AATAACAAC-AAAAAAAC 19922 AAAAAAA 1 AAAAAAA 19929 AGAGGAAAAA Statistics Matches: 52, Mismatches: 2, Indels: 9 0.83 0.03 0.14 Matches are distributed among these distances: 50 3 0.06 51 8 0.15 52 31 0.60 53 10 0.19 ACGTcount: A:0.82, C:0.14, G:0.01, T:0.03 Consensus pattern (52 bp): AAAAAAACAAAAAAAAACAACAAAATAAAAAACAAAATAACAACAAAAAAAC Found at i:21538 original size:32 final size:31 Alignment explanation

Indices: 21502--22030 Score: 582 Period size: 32 Copynumber: 16.7 Consensus size: 31 21492 CAAGTGGAGA * 21502 AACCTTCTTCAAAGCCCACACAAGTTGGTGGC 1 AACC-TCTTCAAAGCCCACACAAGTCGGTGGC * 21534 AACCTCTTCAAAAGCCCACACAAGTCAGTGGC 1 AACCTCTTC-AAAGCCCACACAAGTCGGTGGC * * * 21566 AACCCCTTCAAAGCCCACACAAGTTGGTGGT 1 AACCTCTTCAAAGCCCACACAAGTCGGTGGC * 21597 AACCTCTTAAAAAGCCCACACAAGTCGGTGGC 1 AACCTCTT-CAAAGCCCACACAAGTCGGTGGC * * 21629 AACCTCTTGAAAAGCCCACACAAGTCAGTGGC 1 AACCTCTT-CAAAGCCCACACAAGTCGGTGGC * * 21661 AACC-CTTTCAAAGCCCACACAAATTGGTGGC 1 AACCTC-TTCAAAGCCCACACAAGTCGGTGGC * * * 21692 AACCTCTTTAAAAGCCCACACAAGTTGGTAGC 1 AACCTC-TTCAAAGCCCACACAAGTCGGTGGC 21724 AACCTCTTCAAAAGCCCACACAAGTCGGTGGC 1 AACCTCTTC-AAAGCCCACACAAGTCGGTGGC * * 21756 AACCCCTTTAAAAGCCCACACAAGTCGGTGGC 1 AACCTC-TTCAAAGCCCACACAAGTCGGTGGC 21788 AACC-CTTTCAAAGCCCACACAAGTCGGTGGC 1 AACCTC-TTCAAAGCCCACACAAGTCGGTGGC * * * * 21819 AACCCCTTCAAAGCCCACACAAATCAGTGGA 1 AACCTCTTCAAAGCCCACACAAGTCGGTGGC * * 21850 AACCTTTTTCAAAACCCACACAAGTCGGTGGC 1 AACC-TCTTCAAAGCCCACACAAGTCGGTGGC * * 21882 AACCTCTTCAAAAGCCGACACAAGTCCGTGGC 1 AACCTCTTC-AAAGCCCACACAAGTCGGTGGC * 21914 AACCTCTTCAAAAGCCCACACAAG-CTGGTGGT 1 AACCTCTTC-AAAGCCCACACAAGTC-GGTGGC * * * * * 21946 AACCCCTTTAAAGCCCACACAAATTGGTGGT 1 AACCTCTTCAAAGCCCACACAAGTCGGTGGC * * * 21977 AACCAT-TCTCAGAGCCCACAGAAGTCGATGGC 1 AACC-TCT-TCAAAGCCCACACAAGTCGGTGGC 22009 AACC-CTTTCAAAAGCCCACACA 1 AACCTC-TTC-AAAGCCCACACA 22031 TTGTGGTGGC Statistics Matches: 426, Mismatches: 55, Indels: 32 0.83 0.11 0.06 Matches are distributed among these distances: 31 144 0.34 32 280 0.66 33 2 0.00 ACGTcount: A:0.33, C:0.33, G:0.17, T:0.18 Consensus pattern (31 bp): AACCTCTTCAAAGCCCACACAAGTCGGTGGC Found at i:21618 original size:95 final size:95 Alignment explanation

Indices: 21512--22030 Score: 670 Period size: 95 Copynumber: 5.5 Consensus size: 95 21502 AACCTTCTTC * 21512 AAAGCCCACACAAGTTGGTGGCAACCTCTTCAAAAGCCCACACAAGTCAGTGGCAACCCCTTCAA 1 AAAGCCCACACAAGTCGGTGGCAACCTCTTCAAAAGCCCACACAAGTCAGTGGCAACCCCTTCAA * * 21577 AGCCCACACAAGTTGGTGGTAACCTCTTAA 66 AGCCCACACAAGTTGGTGGCAACCTCTTTA * * 21607 AAAGCCCACACAAGTCGGTGGCAACCTCTTGAAAAGCCCACACAAGTCAGTGGCAACCCTTTCAA 1 AAAGCCCACACAAGTCGGTGGCAACCTCTTCAAAAGCCCACACAAGTCAGTGGCAACCCCTTCAA * 21672 AGCCCACACAAATTGGTGGCAACCTCTTTA 66 AGCCCACACAAGTTGGTGGCAACCTCTTTA * * * * 21702 AAAGCCCACACAAGTTGGTAGCAACCTCTTCAAAAGCCCACACAAGTCGGTGGCAACCCCTTTAA 1 AAAGCCCACACAAGTCGGTGGCAACCTCTTCAAAAGCCCACACAAGTCAGTGGCAACCCC-TTCA * * 21767 AAGCCCACACAAGTCGGTGGCAACC-CTTTC 65 AAGCCCACACAAGTTGGTGGCAACCTCTTTA * * * ** 21797 AAAGCCCACACAAGTCGGTGGCAACCCCTTC-AAAGCCCACACAAATCAGTGGAAACCTTTTTCA 1 AAAGCCCACACAAGTCGGTGGCAACCTCTTCAAAAGCCCACACAAGTCAGTGGCAACC-CCTTCA * * * 21861 AAACCCACACAAGTCGGTGGCAACCTCTTCA 65 AAGCCCACACAAGTTGGTGGCAACCTCTTTA * * * * * 21892 AAAGCCGACACAAGTCCGTGGCAACCTCTTCAAAAGCCCACACAAG-CTGGTGGTAACCCCTTTA 1 AAAGCCCACACAAGTCGGTGGCAACCTCTTCAAAAGCCCACACAAGTC-AGTGGCAACCCCTTCA * * * * 21956 AAGCCCACACAAATTGGTGGTAACCAT-TCTC 65 AAGCCCACACAAGTTGGTGGCAACC-TCTTTA * * * 21987 AGAGCCCACAGAAGTCGATGGCAACC-CTTTCAAAAGCCCACACA 1 AAAGCCCACACAAGTCGGTGGCAACCTC-TTCAAAAGCCCACACA 22031 TTGTGGTGGC Statistics Matches: 369, Mismatches: 48, Indels: 14 0.86 0.11 0.03 Matches are distributed among these distances: 94 51 0.14 95 270 0.73 96 48 0.13 ACGTcount: A:0.33, C:0.33, G:0.18, T:0.17 Consensus pattern (95 bp): AAAGCCCACACAAGTCGGTGGCAACCTCTTCAAAAGCCCACACAAGTCAGTGGCAACCCCTTCAA AGCCCACACAAGTTGGTGGCAACCTCTTTA Found at i:21664 original size:127 final size:127 Alignment explanation

Indices: 21502--22030 Score: 664 Period size: 127 Copynumber: 4.2 Consensus size: 127 21492 CAAGTGGAGA * * 21502 AACCTTCTTC-AAAGCCCACACAAGTTGGTGGCAA-CCTCTTCAAAAGCCCACACAAGTCAGTGG 1 AACC-TCTTCAAAAGCCCACACAAGTCGGTGGCAACCCT-TTC-AAAGCCCACACAAGTCGGTGG * * 21565 CAACCCCTTCAAAGCCCACACAAGTTGGTGGTAACC-TCTTAAAAAGCCCACACAAGTCGGTGGC 63 CAACCCCTTCAAAGCCCACACAAATTGGTGGTAACCATCTTCAAAAGCCCACACAAGTCGGTGGC * * * * 21629 AACCTCTTGAAAAGCCCACACAAGTCAGTGGCAACCCTTTCAAAGCCCACACAAATTGGTGGCAA 1 AACCTCTTCAAAAGCCCACACAAGTCGGTGGCAACCCTTTCAAAGCCCACACAAGTCGGTGGCAA * * * * * 21694 CCTCTTTAAAAGCCCACACAAGTTGGTAGCAACC-TCTTCAAAAGCCCACACAAGTCGGTGGC 66 CC-CCTTCAAAGCCCACACAAATTGGTGGTAACCATCTTCAAAAGCCCACACAAGTCGGTGGC * * 21756 AACCCCTTTAAAAGCCCACACAAGTCGGTGGCAACCCTTTCAAAGCCCACACAAGTCGGTGGCAA 1 AACCTCTTCAAAAGCCCACACAAGTCGGTGGCAACCCTTTCAAAGCCCACACAAGTCGGTGGCAA ** * * * 21821 CCCCTTCAAAGCCCACACAAATCAGTGGAAACCTTTTTCAAAA-CCCACACAAGTCGGTGGC 66 CCCCTTCAAAGCCCACACAAATTGGTGGTAACCATCTTCAAAAGCCCACACAAGTCGGTGGC * * 21882 AACCTCTTCAAAAGCCGACACAAGTCCGTGGCAA-CCTCTTCAAAAGCCCACACAAG-CTGGTGG 1 AACCTCTTCAAAAGCCCACACAAGTCGGTGGCAACCCT-TTC-AAAGCCCACACAAGTC-GGTGG * * * * * 21945 TAACCCCTTTAAAGCCCACACAAATTGGTGGTAACCAT-TCTC-AGAGCCCACAGAAGTCGATGG 63 CAACCCCTTCAAAGCCCACACAAATTGGTGGTAACCATCT-TCAAAAGCCCACACAAGTCGGTGG 22008 C 127 C 22009 AACC-CTTTCAAAAGCCCACACA 1 AACCTC-TTCAAAAGCCCACACA 22031 TTGTGGTGGC Statistics Matches: 354, Mismatches: 38, Indels: 20 0.86 0.09 0.05 Matches are distributed among these distances: 125 3 0.01 126 107 0.30 127 241 0.68 128 3 0.01 ACGTcount: A:0.33, C:0.33, G:0.17, T:0.18 Consensus pattern (127 bp): AACCTCTTCAAAAGCCCACACAAGTCGGTGGCAACCCTTTCAAAGCCCACACAAGTCGGTGGCAA CCCCTTCAAAGCCCACACAAATTGGTGGTAACCATCTTCAAAAGCCCACACAAGTCGGTGGC Found at i:22112 original size:43 final size:43 Alignment explanation

Indices: 22064--22190 Score: 128 Period size: 52 Copynumber: 2.7 Consensus size: 43 22054 CCTAATGTCC * 22064 CTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAACATCG 1 CTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAACATCA * * ** 22107 CTGGCCTTGAATTAGCACATTGACACCTTTGCCATCTTCAAGTCCAATGTCA 1 CTGGCCTTGAATCAGCACATTGGCA------CC-T-TT-AAGTCCAACATCA 22159 CTGGCCTTGAATCAGCACATTGGCACCTTTAA 1 CTGGCCTTGAATCAGCACATTGGCACCTTTAA 22191 CTTTAAGTTT Statistics Matches: 68, Mismatches: 7, Indels: 18 0.73 0.08 0.19 Matches are distributed among these distances: 43 25 0.37 44 2 0.03 45 1 0.01 46 2 0.03 49 2 0.03 50 1 0.01 51 2 0.03 52 33 0.49 ACGTcount: A:0.25, C:0.29, G:0.17, T:0.28 Consensus pattern (43 bp): CTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAACATCA Found at i:22288 original size:61 final size:61 Alignment explanation

Indices: 22202--22369 Score: 264 Period size: 61 Copynumber: 2.8 Consensus size: 61 22192 TTTAAGTTTG * * 22202 ATATCGTTGGCCTTGAATCAACATATTGGCACCTTTATCATTCTTTTCATCTTTAAGCCCA 1 ATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTATCATTCTTCTCATCTTTAAGCCCA * 22263 ATATCGTTGGCCTTGAATCAGCATATTAGCACCTTTATCATTCTTCTCATCTTTAAGCCCA 1 ATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTATCATTCTTCTCATCTTTAAGCCCA * ** * * 22324 ATATCGTTGGCCCTGAATTGGCATATTGGCATCTTTATCACTCTTC 1 ATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTATCATTCTTC 22370 CCGTCTTCAT Statistics Matches: 98, Mismatches: 9, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 61 98 1.00 ACGTcount: A:0.23, C:0.25, G:0.13, T:0.39 Consensus pattern (61 bp): ATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTATCATTCTTCTCATCTTTAAGCCCA Found at i:23002 original size:31 final size:31 Alignment explanation

Indices: 22967--23064 Score: 133 Period size: 31 Copynumber: 3.2 Consensus size: 31 22957 CATTGTATAA * * 22967 ATACATTTTAAGTTTTTACCCAGATGTATCG 1 ATACATTCTAGGTTTTTACCCAGATGTATCG * 22998 ATACATTCTAGGTTTTCACCCAGATGTATCG 1 ATACATTCTAGGTTTTTACCCAGATGTATCG * * * * 23029 ATACATTCTGGGTTTGTACCCAGATGTTTCA 1 ATACATTCTAGGTTTTTACCCAGATGTATCG 23060 ATACA 1 ATACA 23065 CTATCTAATG Statistics Matches: 59, Mismatches: 8, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 31 59 1.00 ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38 Consensus pattern (31 bp): ATACATTCTAGGTTTTTACCCAGATGTATCG Found at i:31028 original size:13 final size:13 Alignment explanation

Indices: 31010--31034 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 31000 CATGGCACAT 31010 TGTATCGATACAA 1 TGTATCGATACAA 31023 TGTATCGATACA 1 TGTATCGATACA 31035 CGATGAATTG Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32 Consensus pattern (13 bp): TGTATCGATACAA Found at i:32663 original size:3 final size:3 Alignment explanation

Indices: 32655--32685 Score: 62 Period size: 3 Copynumber: 10.3 Consensus size: 3 32645 AGATGATAAA 32655 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G 1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G 32686 GTGACTTTAA Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 28 1.00 ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32 Consensus pattern (3 bp): GAT Found at i:36969 original size:20 final size:20 Alignment explanation

Indices: 36944--36999 Score: 85 Period size: 20 Copynumber: 2.8 Consensus size: 20 36934 TTTTTTCCCA * 36944 AATGTATCGATACATTTTTC 1 AATGTATCGATACATTTATC * * 36964 AATGTATCGATACATGTATG 1 AATGTATCGATACATTTATC 36984 AATGTATCGATACATT 1 AATGTATCGATACATT 37000 ATGTCTTTTT Statistics Matches: 32, Mismatches: 4, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 20 32 1.00 ACGTcount: A:0.34, C:0.12, G:0.14, T:0.39 Consensus pattern (20 bp): AATGTATCGATACATTTATC Found at i:37041 original size:20 final size:20 Alignment explanation

Indices: 37016--37071 Score: 69 Period size: 20 Copynumber: 2.8 Consensus size: 20 37006 TTTTACCCAG * 37016 ATGTATCGATACATGT-ATGA 1 ATGTATCGATACAT-TCATCA * * 37036 ATGTATCGATGCATTCTTCA 1 ATGTATCGATACATTCATCA 37056 ATGTATCGATACATTC 1 ATGTATCGATACATTC 37072 TGTCTTTTTA Statistics Matches: 31, Mismatches: 4, Indels: 2 0.84 0.11 0.05 Matches are distributed among these distances: 19 1 0.03 20 30 0.97 ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38 Consensus pattern (20 bp): ATGTATCGATACATTCATCA Found at i:37059 original size:71 final size:70 Alignment explanation

Indices: 36862--37120 Score: 331 Period size: 71 Copynumber: 3.6 Consensus size: 70 36852 AAAAGCCACA * * * * 36862 TTTTTACCCAGATGTATTGATACATTGAAAAATGTATCGATACATGTATGAATGCATCGATACAT 1 TTTTTACCCAGATGTATCGATACA-TGTATAATGTATCGATACATGTATGAATGTATCGATACAT 36927 TCTGTC 65 TCTGTC * * * * 36933 TTTTTTTCCCAAATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACA 1 -TTTTTACCCAGATGTATCGATACATGTAT-AATGTATCGATACATGTATGAATGTATCGATACA * 36998 TTATGTC 64 TTCTGTC * * * 37005 TTTTTACCCAGATGTATCGATACATGTATGAATGTATCGATGCAT-TCTTCAATGTATCGATACA 1 TTTTTACCCAGATGTATCGATACATGTAT-AATGTATCGATACATGT-ATGAATGTATCGATACA 37069 TTCTGTC 64 TTCTGTC * * 37076 TTTTTACCTAGATGTATCGATACATTGAATAATGTATCGATACAT 1 TTTTTACCCAGATGTATCGATACA-TGTATAATGTATCGATACAT 37121 CTAGTTAAAA Statistics Matches: 163, Mismatches: 21, Indels: 7 0.85 0.11 0.04 Matches are distributed among these distances: 70 1 0.01 71 98 0.60 72 64 0.39 ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40 Consensus pattern (70 bp): TTTTTACCCAGATGTATCGATACATGTATAATGTATCGATACATGTATGAATGTATCGATACATT CTGTC Found at i:49772 original size:20 final size:20 Alignment explanation

Indices: 49747--49802 Score: 85 Period size: 20 Copynumber: 2.8 Consensus size: 20 49737 TTTTTTCCCA * 49747 AATGTATCGATACATTTTTC 1 AATGTATCGATACATTTATC * * 49767 AATGTATCGATACATGTATG 1 AATGTATCGATACATTTATC 49787 AATGTATCGATACATT 1 AATGTATCGATACATT 49803 ATGTCTTTTT Statistics Matches: 32, Mismatches: 4, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 20 32 1.00 ACGTcount: A:0.34, C:0.12, G:0.14, T:0.39 Consensus pattern (20 bp): AATGTATCGATACATTTATC Found at i:49782 original size:71 final size:70 Alignment explanation

Indices: 49666--49923 Score: 338 Period size: 71 Copynumber: 3.6 Consensus size: 70 49656 AAAAACCACA * * * * 49666 TTTTTACCCAGATGTATTGATACATTGAAAAATGTATCGATACATGTATGAATGCATCGATACAT 1 TTTTTACCCAGATGTATCGATACATT-TATAATGTATCGATACATGTATGAATGTATCGATACAT 49731 TCTGTC 65 TCTGTC * * * 49737 TTTTTTCCCAAATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT 1 TTTTTACCCAGATGTATCGATACATTTAT-AATGTATCGATACATGTATGAATGTATCGATACAT * 49802 TATGTC 65 TCTGTC * * * * 49808 TTTTTACCCAGATGTATCGATACATGTATGAATGTATCGATGCAT-TCTTCAATGTATCGATACA 1 TTTTTACCCAGATGTATCGATACATTTAT-AATGTATCGATACATGT-ATGAATGTATCGATACA 49872 TTCTGTC 64 TTCTGTC * * 49879 TTTTTACCTAGATGTATCGATACATTGAATAATGTATCGATACAT 1 TTTTTACCCAGATGTATCGATACATT-TATAATGTATCGATACAT 49924 CTAGTTAAAA Statistics Matches: 163, Mismatches: 21, Indels: 6 0.86 0.11 0.03 Matches are distributed among these distances: 70 1 0.01 71 160 0.98 72 2 0.01 ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40 Consensus pattern (70 bp): TTTTTACCCAGATGTATCGATACATTTATAATGTATCGATACATGTATGAATGTATCGATACATT CTGTC Found at i:49844 original size:20 final size:20 Alignment explanation

Indices: 49819--49874 Score: 69 Period size: 20 Copynumber: 2.8 Consensus size: 20 49809 TTTTACCCAG * 49819 ATGTATCGATACATGT-ATGA 1 ATGTATCGATACAT-TCATCA * * 49839 ATGTATCGATGCATTCTTCA 1 ATGTATCGATACATTCATCA 49859 ATGTATCGATACATTC 1 ATGTATCGATACATTC 49875 TGTCTTTTTA Statistics Matches: 31, Mismatches: 4, Indels: 2 0.84 0.11 0.05 Matches are distributed among these distances: 19 1 0.03 20 30 0.97 ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38 Consensus pattern (20 bp): ATGTATCGATACATTCATCA Found at i:62564 original size:20 final size:20 Alignment explanation

Indices: 62539--62594 Score: 85 Period size: 20 Copynumber: 2.8 Consensus size: 20 62529 TTTTTTCCCA * 62539 AATGTATCGATACATTTTTC 1 AATGTATCGATACATTTATC * * 62559 AATGTATCGATACATGTATG 1 AATGTATCGATACATTTATC 62579 AATGTATCGATACATT 1 AATGTATCGATACATT 62595 ATGTCTTTTT Statistics Matches: 32, Mismatches: 4, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 20 32 1.00 ACGTcount: A:0.34, C:0.12, G:0.14, T:0.39 Consensus pattern (20 bp): AATGTATCGATACATTTATC Found at i:62574 original size:71 final size:70 Alignment explanation

Indices: 62458--62715 Score: 338 Period size: 71 Copynumber: 3.6 Consensus size: 70 62448 GAAAACCACA * * * * 62458 TTTTTACCCAGATGTATTGATACATTGAAAAATGTATCGATACATGTATGAATGCATCGATACAT 1 TTTTTACCCAGATGTATCGATACATT-TATAATGTATCGATACATGTATGAATGTATCGATACAT 62523 TCTGTC 65 TCTGTC * * * 62529 TTTTTTCCCAAATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT 1 TTTTTACCCAGATGTATCGATACATTTAT-AATGTATCGATACATGTATGAATGTATCGATACAT * 62594 TATGTC 65 TCTGTC * * * * 62600 TTTTTACCCAGATGTATCGATACATGTATGAATGTATCGATGCAT-TCTTCAATGTATCGATACA 1 TTTTTACCCAGATGTATCGATACATTTAT-AATGTATCGATACATGT-ATGAATGTATCGATACA 62664 TTCTGTC 64 TTCTGTC * * 62671 TTTTTACCTAGATGTATCGATACATTGAATAATGTATCGATACAT 1 TTTTTACCCAGATGTATCGATACATT-TATAATGTATCGATACAT 62716 CTAGTTAAAA Statistics Matches: 163, Mismatches: 21, Indels: 6 0.86 0.11 0.03 Matches are distributed among these distances: 70 1 0.01 71 160 0.98 72 2 0.01 ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40 Consensus pattern (70 bp): TTTTTACCCAGATGTATCGATACATTTATAATGTATCGATACATGTATGAATGTATCGATACATT CTGTC Found at i:62636 original size:20 final size:20 Alignment explanation

Indices: 62611--62666 Score: 69 Period size: 20 Copynumber: 2.8 Consensus size: 20 62601 TTTTACCCAG * 62611 ATGTATCGATACATGT-ATGA 1 ATGTATCGATACAT-TCATCA * * 62631 ATGTATCGATGCATTCTTCA 1 ATGTATCGATACATTCATCA 62651 ATGTATCGATACATTC 1 ATGTATCGATACATTC 62667 TGTCTTTTTA Statistics Matches: 31, Mismatches: 4, Indels: 2 0.84 0.11 0.05 Matches are distributed among these distances: 19 1 0.03 20 30 0.97 ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38 Consensus pattern (20 bp): ATGTATCGATACATTCATCA Done.