Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold100

Parameters: 2 7 7 80 10 50 500

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500

Length: 1174989
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29

Warning! 153044 characters in sequence are not A, C, G, or T


File 5 of 4

Found at i:1081336 original size:21 final size:21

Alignment explanation

Indices: 1081310--1081540 Score: 265 Period size: 21 Copynumber: 10.9 Consensus size: 21 1081300 ATATAGACCA * 1081310 TTTCTCGTAATTACGAGATCT 1 TTTCTCGTAATAACGAGATCT * 1081331 TTTCTCGTAATAACGATATCT 1 TTTCTCGTAATAACGAGATCT 1081352 TTTC-CTGTAATAACGAGATCT 1 TTTCTC-GTAATAACGAGATCT * 1081373 TTTCTCGTAATTAA-GAGATAAT 1 TTTCTCGTAA-TAACGAGAT-CT ** * 1081395 TAACTCGTAATAACGATATCT 1 TTTCTCGTAATAACGAGATCT 1081416 TTTC-CTGTAATAACGAGATCT 1 TTTCTC-GTAATAACGAGATCT * 1081437 TTTCTCGTAATTAA-GAGATAAT 1 TTTCTCGTAA-TAACGAGAT-CT ** * 1081459 TAACTCGTAATAACGATATCT 1 TTTCTCGTAATAACGAGATCT 1081480 TTTC-CTGTAATAACGAGATCT 1 TTTCTC-GTAATAACGAGATCT 1081501 TTTCTCGTAATAACGAGATCT 1 TTTCTCGTAATAACGAGATCT * 1081522 TTTCTCATAATAACGAGAT 1 TTTCTCGTAATAACGAGAT 1081541 AATTTACCCG Statistics Matches: 178, Mismatches: 20, Indels: 24 0.80 0.09 0.11 Matches are distributed among these distances: 20 3 0.02 21 140 0.79 22 35 0.20 ACGTcount: A:0.32, C:0.17, G:0.13, T:0.39 Consensus pattern (21 bp): TTTCTCGTAATAACGAGATCT Found at i:1081404 original size:22 final size:23 Alignment explanation

Indices: 1081376--1081474 Score: 77 Period size: 22 Copynumber: 4.6 Consensus size: 23 1081366 GAGATCTTTT 1081376 CTCGTAATTAA-GAGATAATTAA 1 CTCGTAATTAACGAGATAATTAA * ** ** 1081398 CTCGTAA-TAACGATATCTTTTC 1 CTCGTAATTAACGAGATAATTAA * ** 1081420 CT-GTAA-TAACGAGAT-CTTTT 1 CTCGTAATTAACGAGATAATTAA 1081440 CTCGTAATTAA-GAGATAATTAA 1 CTCGTAATTAACGAGATAATTAA 1081462 CTCGTAA-TAACGA 1 CTCGTAATTAACGA 1081475 TATCTTTTCC Statistics Matches: 61, Mismatches: 11, Indels: 10 0.74 0.13 0.12 Matches are distributed among these distances: 20 5 0.08 21 27 0.44 22 29 0.48 ACGTcount: A:0.37, C:0.15, G:0.13, T:0.34 Consensus pattern (23 bp): CTCGTAATTAACGAGATAATTAA Found at i:1081490 original size:85 final size:85 Alignment explanation

Indices: 1081316--1081562 Score: 261 Period size: 85 Copynumber: 2.9 Consensus size: 85 1081306 ACCATTTCTC * * * * ** * 1081316 GTAATTACGAGATCTTTTCTCGTAATAACGATATCTTTTC-CTGTAATAACGAGAT-CTTTTCTC 1 GTAATAACGAGATCTTTTCTCGTAATAACGAGATCTTTTCTC-ATAATAACGAGATAATTAACCC * ** ** 1081379 GTAATTAA-GAGATAATTAACT 65 GTAA-TAACGATATCTTTTCCT * * 1081400 CGTAATAACGATATCTTTTC-CTGTAATAACGAGATCTTTTCTCGTAATTAA-GAGATAATTAAC 1 -GTAATAACGAGATCTTTTCTC-GTAATAACGAGATCTTTTCTCATAA-TAACGAGATAATTAAC * 1081463 TCGTAATAACGATATCTTTTCCT 63 CCGTAATAACGATATCTTTTCCT * 1081486 GTAATAACGAGATCTTTTCTCGTAATAACGAGATCTTTTCTCATAATAACGAGATAATTTACCCG 1 GTAATAACGAGATCTTTTCTCGTAATAACGAGATCTTTTCTCATAATAACGAGATAATTAACCCG * 1081551 TAATTACGATAT 66 TAATAACGATAT 1081563 AATGAAAACT Statistics Matches: 139, Mismatches: 16, Indels: 14 0.82 0.09 0.08 Matches are distributed among these distances: 84 4 0.03 85 113 0.81 86 22 0.16 ACGTcount: A:0.33, C:0.17, G:0.13, T:0.38 Consensus pattern (85 bp): GTAATAACGAGATCTTTTCTCGTAATAACGAGATCTTTTCTCATAATAACGAGATAATTAACCCG TAATAACGATATCTTTTCCT Found at i:1081554 original size:64 final size:64 Alignment explanation

Indices: 1081310--1081519 Score: 361 Period size: 64 Copynumber: 3.3 Consensus size: 64 1081300 ATATAGACCA * * ** 1081310 TTTCTCGTAATTACGAGAT-CTTTTCTCGTAATAACGATATCTTTTCCTGTAATAACGAGATCT 1 TTTCTCGTAATTAAGAGATAATTAACTCGTAATAACGATATCTTTTCCTGTAATAACGAGATCT 1081373 TTTCTCGTAATTAAGAGATAATTAACTCGTAATAACGATATCTTTTCCTGTAATAACGAGATCT 1 TTTCTCGTAATTAAGAGATAATTAACTCGTAATAACGATATCTTTTCCTGTAATAACGAGATCT 1081437 TTTCTCGTAATTAAGAGATAATTAACTCGTAATAACGATATCTTTTCCTGTAATAACGAGATCT 1 TTTCTCGTAATTAAGAGATAATTAACTCGTAATAACGATATCTTTTCCTGTAATAACGAGATCT 1081501 TTTCTCGTAA-TAACGAGAT 1 TTTCTCGTAATTAA-GAGAT 1081520 CTTTTCTCAT Statistics Matches: 141, Mismatches: 4, Indels: 3 0.95 0.03 0.02 Matches are distributed among these distances: 63 21 0.15 64 120 0.85 ACGTcount: A:0.32, C:0.17, G:0.13, T:0.39 Consensus pattern (64 bp): TTTCTCGTAATTAAGAGATAATTAACTCGTAATAACGATATCTTTTCCTGTAATAACGAGATCT Found at i:1083340 original size:19 final size:20 Alignment explanation

Indices: 1083294--1083341 Score: 64 Period size: 21 Copynumber: 2.4 Consensus size: 20 1083284 ATGATATTAG 1083294 GTTTTGCATCGGTGGTCGTTT 1 GTTTTGCATCGGTGGTCG-TT 1083315 GTTTTGCATCGGT-GTC-TT 1 GTTTTGCATCGGTGGTCGTT 1083333 GATTTTGCA 1 G-TTTTGCA 1083342 AAAGAGGGAG Statistics Matches: 26, Mismatches: 0, Indels: 4 0.87 0.00 0.13 Matches are distributed among these distances: 18 3 0.12 19 7 0.27 20 3 0.12 21 13 0.50 ACGTcount: A:0.08, C:0.15, G:0.29, T:0.48 Consensus pattern (20 bp): GTTTTGCATCGGTGGTCGTT Found at i:1083820 original size:2 final size:2 Alignment explanation

Indices: 1083813--1083886 Score: 148 Period size: 2 Copynumber: 37.0 Consensus size: 2 1083803 GTATGAATAT 1083813 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1083855 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1083887 ATATACCCTG Statistics Matches: 72, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 72 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:1086315 original size:33 final size:33 Alignment explanation

Indices: 1086273--1086336 Score: 92 Period size: 33 Copynumber: 1.9 Consensus size: 33 1086263 CGTTACTGAT * 1086273 TCCTTAAGTAAATGAAAACACAAAATCAAATCA 1 TCCTTAAGTAAATGAAAACACAAAATAAAATCA * * * 1086306 TCCTTAAGTAAATTAATACACCAAATAAAAT 1 TCCTTAAGTAAATGAAAACACAAAATAAAAT 1086337 AAAATTATTC Statistics Matches: 27, Mismatches: 4, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 33 27 1.00 ACGTcount: A:0.53, C:0.17, G:0.05, T:0.25 Consensus pattern (33 bp): TCCTTAAGTAAATGAAAACACAAAATAAAATCA Found at i:1098079 original size:127 final size:127 Alignment explanation

Indices: 1097853--1098110 Score: 498 Period size: 127 Copynumber: 2.0 Consensus size: 127 1097843 TTTAAAAATG * * 1097853 TTATCATATACGTACAACATTGTTGAGTATTGCACTTGATTGGCAATGTCCATATCTCTAGTGAG 1 TTATCACATACGTACAACACTGTTGAGTATTGCACTTGATTGGCAATGTCCATATCTCTAGTGAG 1097918 TTCCAGTTGATCTTCTTTTTATGGTAGTTTTGCAGTTTATCTTCCATTTGAATGTAATACAT 66 TTCCAGTTGATCTTCTTTTTATGGTAGTTTTGCAGTTTATCTTCCATTTGAATGTAATACAT 1097980 TTATCACATACGTACAACACTGTTGAGTATTGCACTTGATTGGCAATGTCCATATCTCTAGTGAG 1 TTATCACATACGTACAACACTGTTGAGTATTGCACTTGATTGGCAATGTCCATATCTCTAGTGAG 1098045 TTCCAGTTGATCTTCTTTTTATGGTAGTTTTGCAGTTTATCTTCCATTTGAATGTAATACAT 66 TTCCAGTTGATCTTCTTTTTATGGTAGTTTTGCAGTTTATCTTCCATTTGAATGTAATACAT 1098107 TTAT 1 TTAT 1098111 TTTGGAATTT Statistics Matches: 129, Mismatches: 2, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 127 129 1.00 ACGTcount: A:0.24, C:0.16, G:0.16, T:0.43 Consensus pattern (127 bp): TTATCACATACGTACAACACTGTTGAGTATTGCACTTGATTGGCAATGTCCATATCTCTAGTGAG TTCCAGTTGATCTTCTTTTTATGGTAGTTTTGCAGTTTATCTTCCATTTGAATGTAATACAT Found at i:1105274 original size:2 final size:2 Alignment explanation

Indices: 1105267--1105315 Score: 91 Period size: 2 Copynumber: 25.0 Consensus size: 2 1105257 CAGAAAAGCT 1105267 TC TC TC TC TC TC TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1105308 TC TC TC TC 1 TC TC TC TC 1105316 AAAATTTTCT Statistics Matches: 46, Mismatches: 0, Indels: 2 0.96 0.00 0.04 Matches are distributed among these distances: 1 1 0.02 2 45 0.98 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:1115154 original size:140 final size:145 Alignment explanation

Indices: 1114892--1115179 Score: 433 Period size: 140 Copynumber: 2.0 Consensus size: 145 1114882 CAGTATAAAA * 1114892 TTTGTAGATTACGTGCTTTAGGAAAAGCCTGAAGAAAAAAAAATATATTCTGGATAATATATCAT 1 TTTGTAGATTACGTGCTTTAGGAAAAGCCTGAAGAAAAAAAAATATATTCCGG--AATATATCAT * * * 1114957 AATATCATAAGTTAGTTTTTTACCTCGATAATTTTAATATAAACAACATATATGTTGTTATCGAC 64 AATATCATAAGTTAGTTTTTGACCTCGATAATTTCAATATAAACAACATATATGTTGTAATCGAC * * 1115022 AATGGATGGTTTGAAGC 129 AATGGATAGATTGAAGC * 1115039 TTTGTAGATTACGTGCTTTAGGAAAAGCCTGAAG-AAAAAAAATCTATTCCGG-ATA-AT-AT-A 1 TTTGTAGATTACGTGCTTTAGGAAAAGCCTGAAGAAAAAAAAATATATTCCGGAATATATCATAA * * * 1115099 TATCATAAGTTAGTTTTTGACCTCGATAGTTTCACTATCAACAACATATATGTTGTAATCGACAA 66 TATCATAAGTTAGTTTTTGACCTCGATAATTTCAATATAAACAACATATATGTTGTAATCGACAA 1115164 TGGATAGATTGAAGC 131 TGGATAGATTGAAGC 1115179 T 1 T 1115180 CCTATTTGTC Statistics Matches: 131, Mismatches: 10, Indels: 7 0.89 0.07 0.05 Matches are distributed among these distances: 140 74 0.56 141 2 0.02 142 2 0.02 143 3 0.02 146 16 0.12 147 34 0.26 ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35 Consensus pattern (145 bp): TTTGTAGATTACGTGCTTTAGGAAAAGCCTGAAGAAAAAAAAATATATTCCGGAATATATCATAA TATCATAAGTTAGTTTTTGACCTCGATAATTTCAATATAAACAACATATATGTTGTAATCGACAA TGGATAGATTGAAGC Found at i:1115266 original size:19 final size:18 Alignment explanation

Indices: 1115214--1115257 Score: 79 Period size: 18 Copynumber: 2.4 Consensus size: 18 1115204 GTACTGAATC 1115214 AAAAGTGTATAAAAATAA 1 AAAAGTGTATAAAAATAA 1115232 AAAAGTGTATAAAAATAA 1 AAAAGTGTATAAAAATAA 1115250 AGAAAGTG 1 A-AAAGTG 1115258 ATGGAAAATT Statistics Matches: 25, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 18 19 0.76 19 6 0.24 ACGTcount: A:0.64, C:0.00, G:0.16, T:0.20 Consensus pattern (18 bp): AAAAGTGTATAAAAATAA Found at i:1117867 original size:2 final size:2 Alignment explanation

Indices: 1117860--1117923 Score: 128 Period size: 2 Copynumber: 32.0 Consensus size: 2 1117850 ACCGTCATTT 1117860 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1117902 GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA 1117924 CCTTCTGTTA Statistics Matches: 62, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 62 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:1118469 original size:2 final size:2 Alignment explanation

Indices: 1118462--1118515 Score: 108 Period size: 2 Copynumber: 27.0 Consensus size: 2 1118452 TTTGAAAATT 1118462 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1118504 TC TC TC TC TC TC 1 TC TC TC TC TC TC 1118516 CTTATTTGCT Statistics Matches: 52, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 52 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:1121469 original size:8 final size:8 Alignment explanation

Indices: 1121456--1121489 Score: 52 Period size: 8 Copynumber: 4.4 Consensus size: 8 1121446 GTAACTGAGT 1121456 ATTTATTA 1 ATTTATTA * 1121464 ATTTATTT 1 ATTTATTA 1121472 ATTTATT- 1 ATTTATTA 1121479 ATTTATTA 1 ATTTATTA 1121487 ATT 1 ATT 1121490 AATCAGTATT Statistics Matches: 24, Mismatches: 1, Indels: 2 0.89 0.04 0.07 Matches are distributed among these distances: 7 7 0.29 8 17 0.71 ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68 Consensus pattern (8 bp): ATTTATTA Found at i:1125123 original size:19 final size:20 Alignment explanation

Indices: 1125091--1125130 Score: 55 Period size: 19 Copynumber: 2.0 Consensus size: 20 1125081 AAAGCAATAG ** 1125091 AACTTTTTTTAAAAC-TTTT 1 AACTTTTTCAAAAACATTTT 1125110 AACTTTTTCAAAAACATTTT 1 AACTTTTTCAAAAACATTTT 1125130 A 1 A 1125131 CTCAATGTGA Statistics Matches: 18, Mismatches: 2, Indels: 1 0.86 0.10 0.05 Matches are distributed among these distances: 19 13 0.72 20 5 0.28 ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50 Consensus pattern (20 bp): AACTTTTTCAAAAACATTTT Found at i:1135760 original size:4 final size:4 Alignment explanation

Indices: 1135753--1135826 Score: 51 Period size: 4 Copynumber: 17.8 Consensus size: 4 1135743 TTAGTAAATT * * * 1135753 AGTA AGTA AGTA AGTGCA ACTGCA AGTA AGTA CGTA AGTA AGTA ACTA 1 AGTA AGTA AGTA AGT--A A--GTA AGTA AGTA AGTA AGTA AGTA AGTA * * * 1135801 AGTA AGAA AGGA AGAA AGT- AGTA AGT 1 AGTA AGTA AGTA AGTA AGTA AGTA AGT 1135827 GTGAAGCATA Statistics Matches: 55, Mismatches: 10, Indels: 10 0.73 0.13 0.13 Matches are distributed among these distances: 3 3 0.05 4 47 0.85 6 4 0.07 8 1 0.02 ACGTcount: A:0.47, C:0.07, G:0.26, T:0.20 Consensus pattern (4 bp): AGTA Found at i:1140288 original size:178 final size:178 Alignment explanation

Indices: 1139988--1140337 Score: 666 Period size: 178 Copynumber: 2.0 Consensus size: 178 1139978 GAAAGATGAA 1139988 GTCAGAATGATCTTGATGTAGGGAGAAGGATGAAATAGGCTGTGCCTGCTTGCTGGCTGCTGCCT 1 GTCAGAATGATCTTGATGTAGGGAGAAGGATGAAATAGGCTGTGCCTGCTTGCTGGCTGCTGCCT 1140053 AATCCCATGCATACAATATATGAAGTCAGCCTGTGCTATCCGTGGACTTCGTGCCCTCAATGCAA 66 AATCCCATGCATACAATATATGAAGTCAGCCTGTGCTATCCGTGGACTTCGTGCCCTCAATGCAA 1140118 CTACAGTTCTTATCGACCACATCATACATAG-AGGCGGGGGGGGGGGG 131 CTACAGTTCTTATCGACCACATCATACATAGAAGGCGGGGGGGGGGGG 1140165 GNTCAGAATGATCTTGATGTAGGGAGAAGGATGAAATAGGCTGTGCCTGCTTGCTGGCTGCTGCC 1 G-TCAGAATGATCTTGATGTAGGGAGAAGGATGAAATAGGCTGTGCCTGCTTGCTGGCTGCTGCC 1140230 TAATCCCATGCATACAATATATGAAGTCAGCCTGTGCTATCCGTGGACTTCGTGCCCTCAATGCA 65 TAATCCCATGCATACAATATATGAAGTCAGCCTGTGCTATCCGTGGACTTCGTGCCCTCAATGCA * * 1140295 ACTACAGTTCTTATCGACCACATCATACATAGANGGTGGGGGG 130 ACTACAGTTCTTATCGACCACATCATACATAGAAGGCGGGGGG 1140338 CTTTCAATGC Statistics Matches: 169, Mismatches: 2, Indels: 2 0.98 0.01 0.01 Matches are distributed among these distances: 177 1 0.01 178 160 0.95 179 8 0.05 ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25 Consensus pattern (178 bp): GTCAGAATGATCTTGATGTAGGGAGAAGGATGAAATAGGCTGTGCCTGCTTGCTGGCTGCTGCCT AATCCCATGCATACAATATATGAAGTCAGCCTGTGCTATCCGTGGACTTCGTGCCCTCAATGCAA CTACAGTTCTTATCGACCACATCATACATAGAAGGCGGGGGGGGGGGG Found at i:1147355 original size:12 final size:11 Alignment explanation

Indices: 1147336--1147367 Score: 55 Period size: 12 Copynumber: 2.8 Consensus size: 11 1147326 CTTTAGAAGC 1147336 AAAAAAAACAA 1 AAAAAAAACAA 1147347 AACAAAAAACAA 1 AA-AAAAAACAA 1147359 AAAAAAAAC 1 AAAAAAAAC 1147368 CCGAAAAATC Statistics Matches: 20, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 11 9 0.45 12 11 0.55 ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00 Consensus pattern (11 bp): AAAAAAAACAA Found at i:1148548 original size:12 final size:12 Alignment explanation

Indices: 1148520--1148564 Score: 65 Period size: 12 Copynumber: 3.8 Consensus size: 12 1148510 ATCACATTTT 1148520 GTCTGTC-GTCC 1 GTCTGTCTGTCC * 1148531 GTCTGTCTGTCT 1 GTCTGTCTGTCC * 1148543 GTCTGTCCGTCC 1 GTCTGTCTGTCC 1148555 GTCTGTCTGT 1 GTCTGTCTGT 1148565 AAACTTTTCA Statistics Matches: 29, Mismatches: 4, Indels: 1 0.85 0.12 0.03 Matches are distributed among these distances: 11 7 0.24 12 22 0.76 ACGTcount: A:0.00, C:0.31, G:0.27, T:0.42 Consensus pattern (12 bp): GTCTGTCTGTCC Found at i:1148562 original size:4 final size:4 Alignment explanation

Indices: 1148519--1148564 Score: 58 Period size: 4 Copynumber: 11.8 Consensus size: 4 1148509 GATCACATTT * * * 1148519 TGTC TGTC -GTC CGTC TGTC TGTC TGTC TGTC CGTC CGTC TGTC TGT 1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGT 1148565 AAACTTTTCA Statistics Matches: 38, Mismatches: 3, Indels: 2 0.88 0.07 0.05 Matches are distributed among these distances: 3 3 0.08 4 35 0.92 ACGTcount: A:0.00, C:0.30, G:0.26, T:0.43 Consensus pattern (4 bp): TGTC Found at i:1148794 original size:61 final size:61 Alignment explanation

Indices: 1148729--1148847 Score: 220 Period size: 61 Copynumber: 2.0 Consensus size: 61 1148719 GAAATTTTCA * * 1148729 AAAATCTTCTTCTCATGAACCATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCATCATC 1 AAAATCTTCTTCTCATGAACAATAAAACCAGGAAAGCTGAAACTTGTGTGGAAGCATCATC 1148790 AAAATCTTCTTCTCATGAACAATAAAACCAGGAAAGCTGAAACTTGTGTGGAAGCATC 1 AAAATCTTCTTCTCATGAACAATAAAACCAGGAAAGCTGAAACTTGTGTGGAAGCATC 1148848 CTCAGGTAGT Statistics Matches: 56, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 61 56 1.00 ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24 Consensus pattern (61 bp): AAAATCTTCTTCTCATGAACAATAAAACCAGGAAAGCTGAAACTTGTGTGGAAGCATCATC Found at i:1149461 original size:333 final size:331 Alignment explanation

Indices: 1148790--1149968 Score: 1719 Period size: 333 Copynumber: 3.5 Consensus size: 331 1148780 AAGCATCATC * * 1148790 AAAATCTTCTTCTCATG-AAC-AATAAAACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG 1 AAAATCTTCTTCTCA-GAAACTAAT-CAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG * * * * 1148853 GTAGTGTAGATTCTAATTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGG 64 GTAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAAAGGGGGG * * * * * 1148918 TCGAAGTTTTACATAGGAATATACAGATTAAATCTTTAAAAATCTTCTTCTCATGAACCATAAGG 129 TCGAAATTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCATGAACCATAAGA * * * * * 1148983 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGAAGTGTAGACTTCTAATTTGTGAAAATA 194 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTA-AATTCAAAGTTGTGAAAATC * * 1149048 ATGATCCCCGGTGGTAGGGTGGGGCCACAATGGGGGATCGAAGTTTTACATAGGAATATAAAGAG 258 ATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGG-TCGAAGTTTTACATAGGAATATATAGAG 1149113 TAAATCTTTA 322 TAAATCTTTA * * * 1149123 AAAATCTTCTTCTCATG-AAC-CATAAGACCAGGACAGCTGAAACTTGTGTGGAAGCATCCTCAG 1 AAAATCTTCTTCTCA-GAAACTAATCAG-CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG * * * * * ** 1149186 GAAGTGTAGATTCATAGTTGTGAAAATCATG-GCCTTCGGGGGTAGGGTGGGGCCACGATTGGGG 64 GTAGTGTAGATTCAAAGTTGTGAAAATCATGATCC-CCGGGGGTAGGGTGGGGCCACAAAGGGGG * 1149250 GTCGAAATTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTTATGAACCATAAG 128 GTCGAAATTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCATGAACCATAAG * * 1149315 ACCAGGAAAACTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAAATTAAAAGTTGTGAAAATC 193 ACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAAATTCAAAGTTGTGAAAATC * 1149380 ATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGTAGTCGAAGTTTTACATAGGAATATATAGAG 258 ATGATCCCCGGGGGTAGGGTGGGGCCACAATGGG-GGTCGAAGTTTTACATAGGAATATATAGAG * 1149445 TAAATCTTAAA 322 TAAATCTT-TA * 1149456 AAAATCTTTTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGT 1 AAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGT * * ** 1149521 AGTGTAGATGCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGATGGTC 66 AGTGTAGATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAAAGGGGGGTC * * * * * 1149586 GAACTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTTTTCTCA-GAAAC-TAATCAG 131 GAAATTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCATGAACCATAA-GA- * 1149649 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCA 194 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAAATTCAAAGTTGTGAAAATCA * 1149714 TGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTCGAAGTTTTACATAGGAATATATAGAGT 259 TGATCCCCGGGGGTAGGGTGGGGCCACAAT-GGGGGTCGAAGTTTTACATAGGAATATATAGAGT 1149779 AAATCTTTA 323 AAATCTTTA * * 1149788 AAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTTAAACTTGTGTGGAAGCGTCCTCAGGT 1 AAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGT * * 1149853 AGTGTAAATTCAAAGTTGTGAAAATCATGATCCCCAGGGGTAGGGTGGGGCCACAAAGGGGGGTC 66 AGTGTAGATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAAAGGGGGGTC * 1149918 -AAAGTTTAACAAAGGAATATATATG-GTAAATCTTTAAAAATCTTCTTCTCA 131 GAAA-TTTAACATAGGAATATATA-GAGTAAATCTTTAAAAATCTTCTTCTCA 1149969 GAAACTAATC Statistics Matches: 768, Mismatches: 66, Indels: 25 0.89 0.08 0.03 Matches are distributed among these distances: 331 5 0.01 332 257 0.33 333 497 0.65 334 9 0.01 ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26 Consensus pattern (331 bp): AAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGT AGTGTAGATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAAAGGGGGGTC GAAATTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCATGAACCATAAGACC AGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAAATTCAAAGTTGTGAAAATCATG ATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAA TCTTTA Found at i:1149662 original size:499 final size:499 Alignment explanation

Indices: 1148790--1149984 Score: 1814 Period size: 499 Copynumber: 2.4 Consensus size: 499 1148780 AAGCATCATC * 1148790 AAAATCTTCTTCTCATGAACAATAAAACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGT 1 AAAATCTTCTTCTCATGAACCATAAAACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGT * * * * 1148855 AGTGTAGATTCTAATTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTC 66 AGTGTAAATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTC * * * * 1148920 GAAGTTTTACATAGGAATATACAGATTAAATCTTTAAAAATCTTCTTCTCATGAACCATAA--GG 131 GAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCA-GAAAC-TAATCAG * * * 1148983 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGAAGTGTAGACTTCTAATTTGTGAAAATA 194 CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGAAGTGTAGACTGCAAAGTTGTGAAAATA * * 1149048 ATGATCCCCGGTGGTAGGGTGGGGCCACAATGGGGGATCGAAGTTTTACATAGGAATATAAAGAG 259 ATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGATCGAACTTTTACATAGGAATATAAAGAG * * 1149113 TAAATCTTTAAAAATCTTCTTCTCATGAACCATAAGACCAGGACAGCTGAAACTTGTGTGGAAGC 324 TAAATCTTTAAAAATCTTCTTCTCATGAACAATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGC * * ** * 1149178 ATCCTCAGGAAGTGTAGATTCATAGTTGTGAAAATCATGGCCTTCGGGGGTAGGGTGGGGCCACG 389 ATCCTCAGGAAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACA * 1149243 ATTGGGGGTCGAAATTTAACATAGGAATATATAGAGTAAATCTTTA 454 ATGGGGGGTCGAAATTTAACATAGGAATATATAGAGTAAATCTTTA * * * 1149289 AAAATCTTCTTCTTATGAACCATAAGACCAGGAAAACTGAAACTTGTGTGGAAGCATCCTCAGGT 1 AAAATCTTCTTCTCATGAACCATAAAACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGT * ** 1149354 AGTGTAAATTAAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGTAGTC 66 AGTGTAAATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTC * * 1149419 GAAGTTTTACATAGGAATATATAGAGTAAATCTTAAAAAAATCTTTTTCTCAGAAACTAATCAGC 131 GAAGTTTTACATAGGAATATATAGAGTAAATCTT-TAAAAATCTTCTTCTCAGAAACTAATCAGC * * 1149484 CAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGA-TGCAAAGTTGTGAAAATCA 195 CAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGAAGTGTAGACTGCAAAGTTGTGAAAATAA * * 1149548 TGATCCCCGGGGGTAGGGTGGGGCCACAATGGATGG-TCGAACTTTTACATAGGAATATATAGAG 260 TGATCCCCGGGGGTAGGGTGGGGCCACAATGG-GGGATCGAACTTTTACATAGGAATATAAAGAG * * 1149612 TAAATCTTTAAAAATCTTTTTCTCA-GAAACTAATCAG-CCAGGAAAGCTGAAACTTGTGTGGAA 324 TAAATCTTTAAAAATCTTCTTCTCATG-AAC-AATAAGACCAGGAAAGCTGAAACTTGTGTGGAA * 1149675 GCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCA 387 GCATCCTCAGGAAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCA * * 1149740 CAATGGGGGGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTA 452 CAATGGGGGGTCGAAATTTAACATAGGAATATATAGAGTAAATCTTTA * * * * 1149788 AAAATCTTCTTCTCA-GAAAC-TAATCAGCCAGGAAAGCTTAAACTTGTGTGGAAGCGTCCTCAG 1 AAAATCTTCTTCTCATGAACCATAA--AACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG * * 1149851 GTAGTGTAAATTCAAAGTTGTGAAAATCATGATCCCCAGGGGTAGGGTGGGGCCACAAAGGGGGG 64 GTAGTGTAAATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGG * * * 1149916 TCAAAGTTTAACAAAGGAATATATATG-GTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCA 129 TCGAAGTTTTACATAGGAATATATA-GAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCA 1149980 GCCAG 193 GCCAG 1149985 ATGATTCTTT Statistics Matches: 631, Mismatches: 56, Indels: 19 0.89 0.08 0.03 Matches are distributed among these distances: 497 3 0.00 498 39 0.06 499 521 0.83 500 68 0.11 ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26 Consensus pattern (499 bp): AAAATCTTCTTCTCATGAACCATAAAACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGT AGTGTAAATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGTC GAAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCC AGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGAAGTGTAGACTGCAAAGTTGTGAAAATAAT GATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGATCGAACTTTTACATAGGAATATAAAGAGTA AATCTTTAAAAATCTTCTTCTCATGAACAATAAGACCAGGAAAGCTGAAACTTGTGTGGAAGCAT CCTCAGGAAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAAT GGGGGGTCGAAATTTAACATAGGAATATATAGAGTAAATCTTTA Found at i:1149969 original size:166 final size:167 Alignment explanation

Indices: 1148790--1149984 Score: 1761 Period size: 166 Copynumber: 7.2 Consensus size: 167 1148780 AAGCATCATC * * 1148790 AAAATCTTCTTCTCATG-AAC-AATAAAACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG 1 AAAATCTTCTTCTCATGAAACTAAT-CAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG * * * 1148853 GTAGTGTAGATTCTAATTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGG 65 GTAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGG * * 1148918 TCGAAGTTTTACATAGGAATATACAGATTAAATCTTTA 130 TCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTA * * 1148956 AAAATCTTCTTCTCATGAACCATAA--GGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG 1 AAAATCTTCTTCTCATGAAAC-TAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG * * * * * 1149019 GAAGTGTAGACTTCTAATTTGTGAAAATAATGATCCCCGGTGGTAGGGTGGGGCCACAATGGGGG 65 GTAGTGTAGA-TTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGG * * 1149084 ATCGAAGTTTTACATAGGAATATAAAGAGTAAATCTTTA 129 GTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTA * * * 1149123 AAAATCTTCTTCTCATG-AAC-CATAAGACCAGGACAGCTGAAACTTGTGTGGAAGCATCCTCAG 1 AAAATCTTCTTCTCATGAAACTAATCAG-CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG * * * * * * 1149186 GAAGTGTAGATTCATAGTTGTGAAAATCATG-GCCTTCGGGGGTAGGGTGGGGCCACGATTGGGG 65 GTAGTGTAGATTCAAAGTTGTGAAAATCATGATCC-CCGGGGGTAGGGTGGGGCCACAATGGGGG * * 1149250 GTCGAAATTTAACATAGGAATATATAGAGTAAATCTTTA 129 GTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTTA * * * * 1149289 AAAATCTTCTTCTTATG-AAC-CATAAGACCAGGAAAACTGAAACTTGTGTGGAAGCATCCTCAG 1 AAAATCTTCTTCTCATGAAACTAATCAG-CCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG * * ** 1149352 GTAGTGTAAATTAAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGTAG 65 GTAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGG * 1149417 TCGAAGTTTTACATAGGAATATATAGAGTAAATCTTAAA 130 TCGAAGTTTTACATAGGAATATATAGAGTAAATCTT-TA * 1149456 AAAATCTTTTTCTCA-GAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG 1 AAAATCTTCTTCTCATGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG * ** 1149520 TAGTGTAGATGCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGATGGT 66 TAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT * 1149585 CGAACTTTTACATAGGAATATATAGAGTAAATCTTTA 131 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTTA * 1149622 AAAATCTTTTTCTCA-GAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG 1 AAAATCTTCTTCTCATGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG * 1149686 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT 66 TAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT 1149751 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTTA 131 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTTA * * 1149788 AAAATCTTCTTCTCA-GAAACTAATCAGCCAGGAAAGCTTAAACTTGTGTGGAAGCGTCCTCAGG 1 AAAATCTTCTTCTCATGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG * * * 1149852 TAGTGTAAATTCAAAGTTGTGAAAATCATGATCCCCAGGGGTAGGGTGGGGCCACAAAGGGGGGT 66 TAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT * * * 1149917 CAAAGTTTAACAAAGGAATATATATG-GTAAATCTTTA 131 CGAAGTTTTACATAGGAATATATA-GAGTAAATCTTTA 1149954 AAAATCTTCTTCTCA-GAAACTAATCAGCCAG 1 AAAATCTTCTTCTCATGAAACTAATCAGCCAG 1149985 ATGATTCTTT Statistics Matches: 946, Mismatches: 70, Indels: 26 0.91 0.07 0.02 Matches are distributed among these distances: 164 1 0.00 165 2 0.00 166 636 0.67 167 301 0.32 168 4 0.00 169 2 0.00 ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26 Consensus pattern (167 bp): AAAATCTTCTTCTCATGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG TAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGT CGAAGTTTTACATAGGAATATATAGAGTAAATCTTTA Found at i:1151248 original size:2 final size:2 Alignment explanation

Indices: 1151241--1151276 Score: 72 Period size: 2 Copynumber: 18.0 Consensus size: 2 1151231 TTGTTAGCAC 1151241 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1151277 GGGGGAGGGT 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:0.50, T:0.00 Consensus pattern (2 bp): AG Found at i:1157320 original size:3 final size:3 Alignment explanation

Indices: 1157305--1157334 Score: 51 Period size: 3 Copynumber: 10.0 Consensus size: 3 1157295 GACTTTCTCA * 1157305 TTC TTC TTA TTC TTC TTC TTC TTC TTC TTC 1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC 1157335 ATCCAAATTT Statistics Matches: 25, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 3 25 1.00 ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67 Consensus pattern (3 bp): TTC Found at i:1158182 original size:437 final size:438 Alignment explanation

Indices: 1157355--1158610 Score: 2108 Period size: 437 Copynumber: 2.9 Consensus size: 438 1157345 GTCCAGGCCG * * 1157355 TAACTTAAATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTAAGAAGG 1 TAACTTTAATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTGAGAAGG * * * * 1157420 AGTGCACGCCACCAAAAGTTTTGACCTTGACCTGTTTAGTTCTTCAAGGTCAGGCTTTTGATAAA 66 AGTGCACGCCACCAAAAGTTTTGACCTTGACCTATTTTGTTTTTCAAGGTCAAGCTTTTGATAAA * 1157485 AAATATTGTCGGGACCATAACACAATACTCCTTTAACATACAGACTTTTAACTTGTATCATAGAT 131 AAATATTGTCGGGACCATAACACAAGA--CCTTTAACATACAGACTTTTAACTTGTATCATAGAT * 1157550 AGATGGTATATAACCTAGTTCAACCTTACCAAAATTTTTGACCTTGACCTAGAATTTTTATTTCA 194 AGATGGTATATAACCTAGTTGAACCTTACCAAAATTTTTGACCTTGACCTAGAA-TTTTATTTCA * 1157615 AGGTCATATTTGAAAAAACTTCATTGTTCAACTT-CTGAATATACTTTGACAGAAGGACTTCAAA 258 AGGTCATATTAGAAAAAACTTCATTGTTCAA-TTCCTGAATATACTTTGACAGAAGGACTTCAAA * * 1157679 CTTGAAACAAAGAACAACAATAATACACTTAGGTGTACTATT-AATTAATATTTGACATTGACCT 322 CTTTAAACAAAGAACAATAATAATACACTTAGGTGTACTATTGAA-TAATATTTGACATTGACCT 1157743 TGTTTTACTCAAGGTCAAATTAAGAAAAAAGTAATAAAATTTTGTCTGGGTCA 386 TGTTTTACTCAAGGTCAAATTAAGAAAAAAGTAATAAAATTTTGTCTGGGTCA * * * 1157796 TAACTTTATTACCCTTTGACATTAAGACTTCAAACGTAGAACATAGGTAGATGGTATTGAGAAGG 1 TAACTTTAATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTGAGAAGG ** 1157861 AGTGCACGAGACCAAAAGTTTTGACCTTGACCTATTTTGTTTTTCAAGGTCAAGCTTTTGATAAA 66 AGTGCACGCCACCAAAAGTTTTGACCTTGACCTATTTTGTTTTTCAAGGTCAAGCTTTTGATAAA * * * 1157926 AAATAATGTCCGGACCATAACACAAGA-CTTTAACATACAGACTTTTAACTTGTATCATAGATAA 131 AAATATTGTCGGGACCATAACACAAGACCTTTAACATACAGACTTTTAACTTGTATCATAGATAG 1157990 ATGGTATATAACCTAGTTGAACCTTACCAAAA-TTTTGACCTTGACCTAGAATTTTCATTTCAAG 196 ATGGTATATAACCTAGTTGAACCTTACCAAAATTTTTGACCTTGACCTAGAATTTT-ATTTCAAG 1158054 GTCATATTAGAAAAAACTTCATTGTTCAATTCCTGAATATACTTTGACAGAAGGACTTCAAACTT 260 GTCATATTAGAAAAAACTTCATTGTTCAATTCCTGAATATACTTTGACAGAAGGACTTCAAACTT * 1158119 TAAACAAAGAACAATAATAATACACTTAGGTGTACTATTGAATACTATTTGACATTGACCTTGTT 325 TAAACAAAGAACAATAATAATACACTTAGGTGTACTATTGAATAATATTTGACATTGACCTTGTT * 1158184 TTACTCAAGGTCAAATTAAGATAAAAGTAATAAAATTTTGTCTGGGTCA 390 TTACTCAAGGTCAAATTAAGAAAAAAGTAATAAAATTTTGTCTGGGTCA * * 1158233 TAACTTTAATACCCTTTGACATTAAGACTTCAATCTTGGAACATAGGTATATGGTATTGAGAAGG 1 TAACTTTAATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTGAGAAGG * * 1158298 AGTGCACGCCACCAAAAGTTTTGACCTTGACCTATTTTGTATTTCAAGGTCAAGCTTTTCATAAA 66 AGTGCACGCCACCAAAAGTTTTGACCTTGACCTATTTTGTTTTTCAAGGTCAAGCTTTTGATAAA 1158363 AAATATTGTCGGGACCATAACACAAGACTCCTTTAACATACAGACTTTTAACTTGTATCAT-GAA 131 AAATATTGTCGGGACCATAACACAAGA--CCTTTAACATACAGACTTTTAACTTGTATCATAG-A * * 1158427 TAGATGGTATATTACCTAGTTGAACCTTACCAAAATTTTTGACCTTGACCTAAAAATTTTATTTC 193 TAGATGGTATATAACCTAGTTGAACCTTACCAAAATTTTTGACCTTGACCT-AGAATTTTATTTC * * * * 1158492 AAAGTCAAATTAGAAAAAACTTCATTGTTCAACTCCTGAATATGCTTTGACAGAAGGACTTCAAA 257 AAGGTCATATTAGAAAAAACTTCATTGTTCAATTCCTGAATATACTTTGACAGAAGGACTTCAAA 1158557 CTTTAAACAAAGAACAATAATAATACACTTAGGTGTACTATTGAATAATATTTG 322 CTTTAAACAAAGAACAATAATAATACACTTAGGTGTACTATTGAATAATATTTG 1158611 TTAAATTTGC Statistics Matches: 766, Mismatches: 40, Indels: 18 0.93 0.05 0.02 Matches are distributed among these distances: 436 6 0.01 437 341 0.45 438 69 0.09 439 1 0.00 440 65 0.08 441 277 0.36 442 7 0.01 ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33 Consensus pattern (438 bp): TAACTTTAATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTATTGAGAAGG AGTGCACGCCACCAAAAGTTTTGACCTTGACCTATTTTGTTTTTCAAGGTCAAGCTTTTGATAAA AAATATTGTCGGGACCATAACACAAGACCTTTAACATACAGACTTTTAACTTGTATCATAGATAG ATGGTATATAACCTAGTTGAACCTTACCAAAATTTTTGACCTTGACCTAGAATTTTATTTCAAGG TCATATTAGAAAAAACTTCATTGTTCAATTCCTGAATATACTTTGACAGAAGGACTTCAAACTTT AAACAAAGAACAATAATAATACACTTAGGTGTACTATTGAATAATATTTGACATTGACCTTGTTT TACTCAAGGTCAAATTAAGAAAAAAGTAATAAAATTTTGTCTGGGTCA Found at i:1159657 original size:2 final size:2 Alignment explanation

Indices: 1159650--1159693 Score: 70 Period size: 2 Copynumber: 22.0 Consensus size: 2 1159640 AGCTGCACCA * * 1159650 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TT TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1159692 TC 1 TC 1159694 ATGTTTGTAT Statistics Matches: 38, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 2 38 1.00 ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55 Consensus pattern (2 bp): TC Found at i:1167268 original size:2 final size:2 Alignment explanation

Indices: 1167263--1167295 Score: 50 Period size: 2 Copynumber: 17.0 Consensus size: 2 1167253 GACCCCCCCC * 1167263 CT CT CT CT CT CT CT -T TT 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 1167296 TTTCTCTATG Statistics Matches: 29, Mismatches: 1, Indels: 2 0.91 0.03 0.06 Matches are distributed among these distances: 1 1 0.03 2 28 0.97 ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55 Consensus pattern (2 bp): CT Found at i:1167285 original size:17 final size:18 Alignment explanation

Indices: 1167263--1167302 Score: 66 Period size: 17 Copynumber: 2.3 Consensus size: 18 1167253 GACCCCCCCC 1167263 CTCTCTCTCTCTCT-TTT 1 CTCTCTCTCTCTCTCTTT 1167280 CTCTCTCTCTCTCTCTTT 1 CTCTCTCTCTCTCTCTTT 1167298 -TCTCT 1 CTCTCT 1167303 ATGTATGTGC Statistics Matches: 22, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 17 19 0.86 18 3 0.14 ACGTcount: A:0.00, C:0.42, G:0.00, T:0.57 Consensus pattern (18 bp): CTCTCTCTCTCTCTCTTT Found at i:1167287 original size:19 final size:19 Alignment explanation

Indices: 1167263--1167302 Score: 80 Period size: 19 Copynumber: 2.1 Consensus size: 19 1167253 GACCCCCCCC 1167263 CTCTCTCTCTCTCTTTTCT 1 CTCTCTCTCTCTCTTTTCT 1167282 CTCTCTCTCTCTCTTTTCT 1 CTCTCTCTCTCTCTTTTCT 1167301 CT 1 CT 1167303 ATGTATGTGC Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 21 1.00 ACGTcount: A:0.00, C:0.42, G:0.00, T:0.57 Consensus pattern (19 bp): CTCTCTCTCTCTCTTTTCT Found at i:1173968 original size:16 final size:14 Alignment explanation

Indices: 1173936--1173962 Score: 54 Period size: 14 Copynumber: 1.9 Consensus size: 14 1173926 AGAGTTTATA 1173936 ATATATAACATGTT 1 ATATATAACATGTT 1173950 ATATATAACATGT 1 ATATATAACATGT 1173963 ATTATAGGAT Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 13 1.00 ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41 Consensus pattern (14 bp): ATATATAACATGTT Done.