TRAP (Tandem Repeats Analysis Program)

TRF Version 4.00

Sequence: contig00000153

tutorial_data.fasta.s5.2.5.7.80.10.25.1000.txt.html

Found at i: i:253 original size:6 final size:6

Alignment explanation

Indices: 242--276 Score: 42 Period size: 6 Copynumber: 5.8 Consensus size: 6 232 TACTCGGTTT * * * * 242 GCTGCA GCTGCA GCAGCA GCGGCA GCAGCT GCTGC 1 GCTGCA GCTGCA GCTGCA GCTGCA GCTGCA GCTGC 277 TCTGCTGCAG Statistics Matches: 24, Mismatches: 5, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 6 24 1.00 ACGTcount: A:0.17, C:0.34, G:0.37, T:0.11 Consensus pattern (6 bp): GCTGCA Left flanking sequence: Indices 1 -- 241 GTCTCGGGTTTGGAACTATCNTCTTAGATGGGAGCNTGAAACCTCCCCCTCCCCCTANCCTGCGT AGNCCTTGCTGCTGCTGTTGCTGCTTCTGTTGCNTGCTGCTGCTGTTGCTGCTGCTGCTCTTGCT GCTGCTGCTCTTGCTGCTGCTGCTCTTGCTGCTGCCGCTGCTGCTGCTGCGCCTTTGCAATTGGG ATTCGCCACAGCTCTTCGTTTTTTTTCATCTCTTCATACTCGGTTT Right flanking sequence: Indices 277 -- 776 TCTGCTGCAGCACAGTAGCGTTCTGCTGCTGCAATGTCTTTTCTTTCTTTCACAAAGCAAAGCAA CGCCGACCTGCATGCGCCCAGAAGTCTAGGGTTTAGGGTTTAGGGTTTGGGGCTTGGTAGCTGCG GAGCCAGAGGGGCGCAACAGAGCAAGGGTTTAGGGTCTAGGGTTTGGGGTTTTGCAGCTCACTCG TGTTCTCCCGCTTTCCCGTGCAGTATGGCCTTTTCCTCTACCAACTCCGAGCCTGCCACCTGCAG CAGCAGCAGCAGCAGCAACAACAACAGCAACATAAGAGAACGACAGCTCTTCCAGCACCAGGGTT TGGGATCGAGGGTTTAGGGTTTAGGGTTTACTNTTCTTAAGAAGGCTCTGGACATCGTAGCTGCT CTGCTGCTCCAGGAATCGCCGTAGCTGACTGCGCTGCTCTTCTGCTGCTGCTGCTGCTGCTGTCG CTGCTGCGGGTGTTGCTGCTGCTGCTGCTGCTGCTGCTGTCCCTG Found at i:259 original size:3 final size:3 Alignment explanation

Indices: 245--270 Score: 38 Period size: 3 Copynumber: 8.7 Consensus size: 3 235 TCGGTTTGCT * * 245 GCA GCT GCA GCA GCA GCG GCA GCA GC 1 GCA GCA GCA GCA GCA GCA GCA GCA GC 271 TGCTGCTCTG Statistics Matches: 19, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 3 19 1.00 ACGTcount: A:0.23, C:0.35, G:0.38, T:0.04 Consensus pattern (3 bp): GCA Left flanking sequence: Indices 1 -- 244 GTCTCGGGTTTGGAACTATCNTCTTAGATGGGAGCNTGAAACCTCCCCCTCCCCCTANCCTGCGT AGNCCTTGCTGCTGCTGTTGCTGCTTCTGTTGCNTGCTGCTGCTGTTGCTGCTGCTGCTCTTGCT GCTGCTGCTCTTGCTGCTGCTGCTCTTGCTGCTGCCGCTGCTGCTGCTGCGCCTTTGCAATTGGG ATTCGCCACAGCTCTTCGTTTTTTTTCATCTCTTCATACTCGGTTTGCT Right flanking sequence: Indices 271 -- 770 TGCTGCTCTGCTGCAGCACAGTAGCGTTCTGCTGCTGCAATGTCTTTTCTTTCTTTCACAAAGCA AAGCAACGCCGACCTGCATGCGCCCAGAAGTCTAGGGTTTAGGGTTTAGGGTTTGGGGCTTGGTA GCTGCGGAGCCAGAGGGGCGCAACAGAGCAAGGGTTTAGGGTCTAGGGTTTGGGGTTTTGCAGCT CACTCGTGTTCTCCCGCTTTCCCGTGCAGTATGGCCTTTTCCTCTACCAACTCCGAGCCTGCCAC CTGCAGCAGCAGCAGCAGCAGCAACAACAACAGCAACATAAGAGAACGACAGCTCTTCCAGCACC AGGGTTTGGGATCGAGGGTTTAGGGTTTAGGGTTTACTNTTCTTAAGAAGGCTCTGGACATCGTA GCTGCTCTGCTGCTCCAGGAATCGCCGTAGCTGACTGCGCTGCTCTTCTGCTGCTGCTGCTGCTG CTGTCGCTGCTGCGGGTGTTGCTGCTGCTGCTGCTGCTGCTGCTG Found at i:275 original size:3 final size:3 Alignment explanation

Indices: 241--284 Score: 32 Period size: 3 Copynumber: 15.0 Consensus size: 3 231 ATACTCGGTT * * * * * * * 241 TGC TGC AGC TGC AGC AGC AGC GGC AGC AGC TGC TGC T-C TGC TGC 1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC 285 AGCACAGTAG Statistics Matches: 34, Mismatches: 6, Indels: 2 0.81 0.14 0.05 Matches are distributed among these distances: 2 2 0.06 3 32 0.94 ACGTcount: A:0.14, C:0.34, G:0.34, T:0.18 Consensus pattern (3 bp): TGC Left flanking sequence: Indices 1 -- 240 GTCTCGGGTTTGGAACTATCNTCTTAGATGGGAGCNTGAAACCTCCCCCTCCCCCTANCCTGCGT AGNCCTTGCTGCTGCTGTTGCTGCTTCTGTTGCNTGCTGCTGCTGTTGCTGCTGCTGCTCTTGCT GCTGCTGCTCTTGCTGCTGCTGCTCTTGCTGCTGCCGCTGCTGCTGCTGCGCCTTTGCAATTGGG ATTCGCCACAGCTCTTCGTTTTTTTTCATCTCTTCATACTCGGTT Right flanking sequence: Indices 285 -- 784 AGCACAGTAGCGTTCTGCTGCTGCAATGTCTTTTCTTTCTTTCACAAAGCAAAGCAACGCCGACC TGCATGCGCCCAGAAGTCTAGGGTTTAGGGTTTAGGGTTTGGGGCTTGGTAGCTGCGGAGCCAGA GGGGCGCAACAGAGCAAGGGTTTAGGGTCTAGGGTTTGGGGTTTTGCAGCTCACTCGTGTTCTCC CGCTTTCCCGTGCAGTATGGCCTTTTCCTCTACCAACTCCGAGCCTGCCACCTGCAGCAGCAGCA GCAGCAGCAACAACAACAGCAACATAAGAGAACGACAGCTCTTCCAGCACCAGGGTTTGGGATCG AGGGTTTAGGGTTTAGGGTTTACTNTTCTTAAGAAGGCTCTGGACATCGTAGCTGCTCTGCTGCT CCAGGAATCGCCGTAGCTGACTGCGCTGCTCTTCTGCTGCTGCTGCTGCTGCTGTCGCTGCTGCG GGTGTTGCTGCTGCTGCTGCTGCTGCTGCTGTCCCTGTTGCTGGC Found at i:541 original size:3 final size:3 Alignment explanation

Indices: 533--565 Score: 45 Period size: 3 Copynumber: 11.0 Consensus size: 3 523 CCTGCCACCT * * * 533 GCA GCA GCA GCA GCA GCA GCA ACA ACA ACA GCA 1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA 566 ACATAAGAGA Statistics Matches: 28, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 3 28 1.00 ACGTcount: A:0.42, C:0.33, G:0.24, T:0.00 Consensus pattern (3 bp): GCA Left flanking sequence: Indices 33 -- 532 AGCNTGAAACCTCCCCCTCCCCCTANCCTGCGTAGNCCTTGCTGCTGCTGTTGCTGCTTCTGTTG CNTGCTGCTGCTGTTGCTGCTGCTGCTCTTGCTGCTGCTGCTCTTGCTGCTGCTGCTCTTGCTGC TGCCGCTGCTGCTGCTGCGCCTTTGCAATTGGGATTCGCCACAGCTCTTCGTTTTTTTTCATCTC TTCATACTCGGTTTGCTGCAGCTGCAGCAGCAGCGGCAGCAGCTGCTGCTCTGCTGCAGCACAGT AGCGTTCTGCTGCTGCAATGTCTTTTCTTTCTTTCACAAAGCAAAGCAACGCCGACCTGCATGCG CCCAGAAGTCTAGGGTTTAGGGTTTAGGGTTTGGGGCTTGGTAGCTGCGGAGCCAGAGGGGCGCA ACAGAGCAAGGGTTTAGGGTCTAGGGTTTGGGGTTTTGCAGCTCACTCGTGTTCTCCCGCTTTCC CGTGCAGTATGGCCTTTTCCTCTACCAACTCCGAGCCTGCCACCT Right flanking sequence: Indices 566 -- 1065 ACATAAGAGAACGACAGCTCTTCCAGCACCAGGGTTTGGGATCGAGGGTTTAGGGTTTAGGGTTT ACTNTTCTTAAGAAGGCTCTGGACATCGTAGCTGCTCTGCTGCTCCAGGAATCGCCGTAGCTGAC TGCGCTGCTCTTCTGCTGCTGCTGCTGCTGCTGTCGCTGCTGCGGGTGTTGCTGCTGCTGCTGCT GCTGCTGCTGTCCCTGTTGCTGGCACGGCTGCTGGCGCTGCTGCGNGCTGCTGCTGCTGCTGCCA GNCGCTGAGCACACAGGCACANCNTTTGGGGACTACTGTAAGTTGTTAGNGGTTTANAGGTTTAG GGTTTAGGGTTTAGGGTTCAGGGTTTAGAGCTCAGACTGAGGAGGAGCGGTTTACTGGCAGCTTG AGGGTTTACGATTTATGTTTTAGGGTTTAGGGCATAGAGTTCAAAATGGCATTGAAGGGAAATAG CAAAGAAAAAAAATACCGAACAAAAAACGGGCGCTCCCACCAAAC Found at i:896 original size:7 final size:7 Alignment explanation

Indices: 871--918 Score: 64 Period size: 7 Copynumber: 6.6 Consensus size: 7 861 CTGTAAGTTG 871 TTAGNGGT 1 TTAG-GGT * 879 TTANAGGT 1 TTA-GGGT 887 TTAGGGT 1 TTAGGGT 894 TTAGGGT 1 TTAGGGT 901 TTAGGGT 1 TTAGGGT * 908 TCAGGGT 1 TTAGGGT 915 TTAG 1 TTAG 919 AGCTCAGACT Statistics Matches: 35, Mismatches: 4, Indels: 3 0.83 0.10 0.07 Matches are distributed among these distances: 7 26 0.74 8 9 0.26 ACGTcount: A:0.17, C:0.02, G:0.38, T:0.40 Consensus pattern (7 bp): TTAGGGT Left flanking sequence: Indices 371 -- 870 GGTTTAGGGTTTAGGGTTTGGGGCTTGGTAGCTGCGGAGCCAGAGGGGCGCAACAGAGCAAGGGT TTAGGGTCTAGGGTTTGGGGTTTTGCAGCTCACTCGTGTTCTCCCGCTTTCCCGTGCAGTATGGC CTTTTCCTCTACCAACTCCGAGCCTGCCACCTGCAGCAGCAGCAGCAGCAGCAACAACAACAGCA ACATAAGAGAACGACAGCTCTTCCAGCACCAGGGTTTGGGATCGAGGGTTTAGGGTTTAGGGTTT ACTNTTCTTAAGAAGGCTCTGGACATCGTAGCTGCTCTGCTGCTCCAGGAATCGCCGTAGCTGAC TGCGCTGCTCTTCTGCTGCTGCTGCTGCTGCTGTCGCTGCTGCGGGTGTTGCTGCTGCTGCTGCT GCTGCTGCTGTCCCTGTTGCTGGCACGGCTGCTGGCGCTGCTGCGNGCTGCTGCTGCTGCTGCCA GNCGCTGAGCACACAGGCACANCNTTTGGGGACTACTGTAAGTTG Right flanking sequence: Indices 919 -- 1418 AGCTCAGACTGAGGAGGAGCGGTTTACTGGCAGCTTGAGGGTTTACGATTTATGTTTTAGGGTTT AGGGCATAGAGTTCAAAATGGCATTGAAGGGAAATAGCAAAGAAAAAAAATACCGAACAAAAAAC GGGCGCTCCCACCAAACCCTAAACCCTAAACCCTAAACCCTGATTTGTGCACCTCGATCAATGTA GATGGAGGCTAACTCCGTTTCTATTTGAGGGTCGTGCAGCAAACCCTGCAGCAGCAAATGCTCCA GGTAGAGCTCCCGCAGCTGCTGCTGCAGCTGCTTCTGCTGCGGCGGGAGCTGCTGCAGCAGCTGC AGCACCTCAGCAGCAGGCAGCGGGCTGCAGCTCTTCTGCATGAANAAGCTCTATCGCTGCACACC AAAACAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAGCGCTAACCAGCTGGC GAGCCTGGCCACCTGCGAGTTAGGGTTTAGGGTTTAGGGTTTGTC Found at i:1202 original size:3 final size:3 Alignment explanation

Indices: 1194--1243 Score: 44 Period size: 3 Copynumber: 16.7 Consensus size: 3 1184 AGCTCCCGCA * * * * ** * * 1194 GCT GCT GCT GCA GCT GCT TCT GCT GCG GCG GGA GCT GCT GCA GCA GCT 1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT 1242 GC 1 GC 1244 AGCACCTCAG Statistics Matches: 36, Mismatches: 11, Indels: 0 0.77 0.23 0.00 Matches are distributed among these distances: 3 36 1.00 ACGTcount: A:0.08, C:0.32, G:0.38, T:0.22 Consensus pattern (3 bp): GCT Left flanking sequence: Indices 694 -- 1193 ACTGCGCTGCTCTTCTGCTGCTGCTGCTGCTGCTGTCGCTGCTGCGGGTGTTGCTGCTGCTGCTG CTGCTGCTGCTGTCCCTGTTGCTGGCACGGCTGCTGGCGCTGCTGCGNGCTGCTGCTGCTGCTGC CAGNCGCTGAGCACACAGGCACANCNTTTGGGGACTACTGTAAGTTGTTAGNGGTTTANAGGTTT AGGGTTTAGGGTTTAGGGTTCAGGGTTTAGAGCTCAGACTGAGGAGGAGCGGTTTACTGGCAGCT TGAGGGTTTACGATTTATGTTTTAGGGTTTAGGGCATAGAGTTCAAAATGGCATTGAAGGGAAAT AGCAAAGAAAAAAAATACCGAACAAAAAACGGGCGCTCCCACCAAACCCTAAACCCTAAACCCTA AACCCTGATTTGTGCACCTCGATCAATGTAGATGGAGGCTAACTCCGTTTCTATTTGAGGGTCGT GCAGCAAACCCTGCAGCAGCAAATGCTCCAGGTAGAGCTCCCGCA Right flanking sequence: Indices 1244 -- 1743 AGCACCTCAGCAGCAGGCAGCGGGCTGCAGCTCTTCTGCATGAANAAGCTCTATCGCTGCACACC AAAACAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAGCGCTAACCAGCTGGC GAGCCTGGCCACCTGCGAGTTAGGGTTTAGGGTTTAGGGTTTGTCTCACTCTTCCTTGGATTCTC AAGCAGCACGAGAGGAGCAAAGCGCCGCAGCAACGCTGCCTGCTGCTGTTGCTGCTGCTGCTGCT GCTCCTGCTGTTGCTGCTGTTGCTCCTGCTGTTGCTGCTGCTGCTGCTGCTGCTGCACCACCTGC TGCAGAATCAGCAGCATCTGATCCGAAGGGGACAATGCGGTTTCTGCCTTTGCCGGAGAGCCTGC AGAGTCTGCATGCAAAACAAACCCTAAACCCTAAACTCTAAACCCTAAACCCTCGCGNAAATAAC GCAAGGGGGAGGNCGGGAAAGGGNCCAAAANGAAGCAGNCAACAA Found at i:1257 original size:3 final size:3 Alignment explanation

Indices: 1233--1264 Score: 27 Period size: 3 Copynumber: 10.7 Consensus size: 3 1223 GGGAGCTGCT * * * 1233 GCA GCA GCT GCA GCA -CC TCA GCA GCA GGCA GC 1 GCA GCA GCA GCA GCA GCA GCA GCA GCA -GCA GC 1265 GGGCTGCAGC Statistics Matches: 22, Mismatches: 5, Indels: 4 0.71 0.16 0.13 Matches are distributed among these distances: 2 1 0.05 3 18 0.82 4 3 0.14 ACGTcount: A:0.25, C:0.38, G:0.31, T:0.06 Consensus pattern (3 bp): GCA Left flanking sequence: Indices 733 -- 1232 TGCTGCGGGTGTTGCTGCTGCTGCTGCTGCTGCTGCTGTCCCTGTTGCTGGCACGGCTGCTGGCG CTGCTGCGNGCTGCTGCTGCTGCTGCCAGNCGCTGAGCACACAGGCACANCNTTTGGGGACTACT GTAAGTTGTTAGNGGTTTANAGGTTTAGGGTTTAGGGTTTAGGGTTCAGGGTTTAGAGCTCAGAC TGAGGAGGAGCGGTTTACTGGCAGCTTGAGGGTTTACGATTTATGTTTTAGGGTTTAGGGCATAG AGTTCAAAATGGCATTGAAGGGAAATAGCAAAGAAAAAAAATACCGAACAAAAAACGGGCGCTCC CACCAAACCCTAAACCCTAAACCCTAAACCCTGATTTGTGCACCTCGATCAATGTAGATGGAGGC TAACTCCGTTTCTATTTGAGGGTCGTGCAGCAAACCCTGCAGCAGCAAATGCTCCAGGTAGAGCT CCCGCAGCTGCTGCTGCAGCTGCTTCTGCTGCGGCGGGAGCTGCT Right flanking sequence: Indices 1265 -- 1764 GGGCTGCAGCTCTTCTGCATGAANAAGCTCTATCGCTGCACACCAAAACAAACCCTAAACCCTAA ACCCTAAACCCTAAACCCTAAACCCTAAGCGCTAACCAGCTGGCGAGCCTGGCCACCTGCGAGTT AGGGTTTAGGGTTTAGGGTTTGTCTCACTCTTCCTTGGATTCTCAAGCAGCACGAGAGGAGCAAA GCGCCGCAGCAACGCTGCCTGCTGCTGTTGCTGCTGCTGCTGCTGCTCCTGCTGTTGCTGCTGTT GCTCCTGCTGTTGCTGCTGCTGCTGCTGCTGCTGCACCACCTGCTGCAGAATCAGCAGCATCTGA TCCGAAGGGGACAATGCGGTTTCTGCCTTTGCCGGAGAGCCTGCAGAGTCTGCATGCAAAACAAA CCCTAAACCCTAAACTCTAAACCCTAAACCCTCGCGNAAATAACGCAAGGGGGAGGNCGGGAAAG GGNCCAAAANGAAGCAGNCAACAACAGCAGNCNAAAAGCAGCAAA Found at i:1326 original size:7 final size:7 Alignment explanation

Indices: 1314--1357 Score: 88 Period size: 7 Copynumber: 6.3 Consensus size: 7 1304 ACACCAAAAC 1314 AAACCCT 1 AAACCCT 1321 AAACCCT 1 AAACCCT 1328 AAACCCT 1 AAACCCT 1335 AAACCCT 1 AAACCCT 1342 AAACCCT 1 AAACCCT 1349 AAACCCT 1 AAACCCT 1356 AA 1 AA 1358 GCGCTAACCA Statistics Matches: 37, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 37 1.00 ACGTcount: A:0.45, C:0.41, G:0.00, T:0.14 Consensus pattern (7 bp): AAACCCT Left flanking sequence: Indices 814 -- 1313 CTGCTGCTGCCAGNCGCTGAGCACACAGGCACANCNTTTGGGGACTACTGTAAGTTGTTAGNGGT TTANAGGTTTAGGGTTTAGGGTTTAGGGTTCAGGGTTTAGAGCTCAGACTGAGGAGGAGCGGTTT ACTGGCAGCTTGAGGGTTTACGATTTATGTTTTAGGGTTTAGGGCATAGAGTTCAAAATGGCATT GAAGGGAAATAGCAAAGAAAAAAAATACCGAACAAAAAACGGGCGCTCCCACCAAACCCTAAACC CTAAACCCTAAACCCTGATTTGTGCACCTCGATCAATGTAGATGGAGGCTAACTCCGTTTCTATT TGAGGGTCGTGCAGCAAACCCTGCAGCAGCAAATGCTCCAGGTAGAGCTCCCGCAGCTGCTGCTG CAGCTGCTTCTGCTGCGGCGGGAGCTGCTGCAGCAGCTGCAGCACCTCAGCAGCAGGCAGCGGGC TGCAGCTCTTCTGCATGAANAAGCTCTATCGCTGCACACCAAAAC Right flanking sequence: Indices 1358 -- 1857 GCGCTAACCAGCTGGCGAGCCTGGCCACCTGCGAGTTAGGGTTTAGGGTTTAGGGTTTGTCTCAC TCTTCCTTGGATTCTCAAGCAGCACGAGAGGAGCAAAGCGCCGCAGCAACGCTGCCTGCTGCTGT TGCTGCTGCTGCTGCTGCTCCTGCTGTTGCTGCTGTTGCTCCTGCTGTTGCTGCTGCTGCTGCTG CTGCTGCACCACCTGCTGCAGAATCAGCAGCATCTGATCCGAAGGGGACAATGCGGTTTCTGCCT TTGCCGGAGAGCCTGCAGAGTCTGCATGCAAAACAAACCCTAAACCCTAAACTCTAAACCCTAAA CCCTCGCGNAAATAACGCAAGGGGGAGGNCGGGAAAGGGNCCAAAANGAAGCAGNCAACAACAGC AGNCNAAAAGCAGCAAANAGGAGACATGCCTTGCTGCTGCTGCGTCAGGAGCTCAAGGGCCTCTT CAGTTTGCCCACAGTGCTGCAGAGACACAGCAGCACAACCACTCC Found at i:1338 original size:21 final size:21 Alignment explanation

Indices: 1314--1364 Score: 88 Period size: 21 Copynumber: 2.4 Consensus size: 21 1304 ACACCAAAAC 1314 AAACCCTAAACCCTAAACCCT 1 AAACCCTAAACCCTAAACCCT 1335 AAACCCTAAACCCTAAACCCT 1 AAACCCTAAACCCTAAACCCT * * 1356 AAGCGCTAA 1 AAACCCTAA 1365 CCAGCTGGCG Statistics Matches: 28, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 21 28 1.00 ACGTcount: A:0.43, C:0.39, G:0.04, T:0.14 Consensus pattern (21 bp): AAACCCTAAACCCTAAACCCT Left flanking sequence: Indices 814 -- 1313 CTGCTGCTGCCAGNCGCTGAGCACACAGGCACANCNTTTGGGGACTACTGTAAGTTGTTAGNGGT TTANAGGTTTAGGGTTTAGGGTTTAGGGTTCAGGGTTTAGAGCTCAGACTGAGGAGGAGCGGTTT ACTGGCAGCTTGAGGGTTTACGATTTATGTTTTAGGGTTTAGGGCATAGAGTTCAAAATGGCATT GAAGGGAAATAGCAAAGAAAAAAAATACCGAACAAAAAACGGGCGCTCCCACCAAACCCTAAACC CTAAACCCTAAACCCTGATTTGTGCACCTCGATCAATGTAGATGGAGGCTAACTCCGTTTCTATT TGAGGGTCGTGCAGCAAACCCTGCAGCAGCAAATGCTCCAGGTAGAGCTCCCGCAGCTGCTGCTG CAGCTGCTTCTGCTGCGGCGGGAGCTGCTGCAGCAGCTGCAGCACCTCAGCAGCAGGCAGCGGGC TGCAGCTCTTCTGCATGAANAAGCTCTATCGCTGCACACCAAAAC Right flanking sequence: Indices 1365 -- 1864 CCAGCTGGCGAGCCTGGCCACCTGCGAGTTAGGGTTTAGGGTTTAGGGTTTGTCTCACTCTTCCT TGGATTCTCAAGCAGCACGAGAGGAGCAAAGCGCCGCAGCAACGCTGCCTGCTGCTGTTGCTGCT GCTGCTGCTGCTCCTGCTGTTGCTGCTGTTGCTCCTGCTGTTGCTGCTGCTGCTGCTGCTGCTGC ACCACCTGCTGCAGAATCAGCAGCATCTGATCCGAAGGGGACAATGCGGTTTCTGCCTTTGCCGG AGAGCCTGCAGAGTCTGCATGCAAAACAAACCCTAAACCCTAAACTCTAAACCCTAAACCCTCGC GNAAATAACGCAAGGGGGAGGNCGGGAAAGGGNCCAAAANGAAGCAGNCAACAACAGCAGNCNAA AAGCAGCAAANAGGAGACATGCCTTGCTGCTGCTGCGTCAGGAGCTCAAGGGCCTCTTCAGTTTG CCCACAGTGCTGCAGAGACACAGCAGCACAACCACTCCGAAATAA Found at i:1664 original size:7 final size:7 Alignment explanation

Indices: 1652--1686 Score: 63 Period size: 7 Copynumber: 5.0 Consensus size: 7 1642 CATGCAAAAC 1652 AAACCCT 1 AAACCCT 1659 AAACCCT 1 AAACCCT * 1666 AAACTCT 1 AAACCCT 1673 AAACCCT 1 AAACCCT 1680 AAACCCT 1 AAACCCT 1687 CGCGNAAATA Statistics Matches: 26, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 7 26 1.00 ACGTcount: A:0.43, C:0.40, G:0.00, T:0.17 Consensus pattern (7 bp): AAACCCT Left flanking sequence: Indices 1152 -- 1651 GCAAACCCTGCAGCAGCAAATGCTCCAGGTAGAGCTCCCGCAGCTGCTGCTGCAGCTGCTTCTGC TGCGGCGGGAGCTGCTGCAGCAGCTGCAGCACCTCAGCAGCAGGCAGCGGGCTGCAGCTCTTCTG CATGAANAAGCTCTATCGCTGCACACCAAAACAAACCCTAAACCCTAAACCCTAAACCCTAAACC CTAAACCCTAAGCGCTAACCAGCTGGCGAGCCTGGCCACCTGCGAGTTAGGGTTTAGGGTTTAGG GTTTGTCTCACTCTTCCTTGGATTCTCAAGCAGCACGAGAGGAGCAAAGCGCCGCAGCAACGCTG CCTGCTGCTGTTGCTGCTGCTGCTGCTGCTCCTGCTGTTGCTGCTGTTGCTCCTGCTGTTGCTGC TGCTGCTGCTGCTGCTGCACCACCTGCTGCAGAATCAGCAGCATCTGATCCGAAGGGGACAATGC GGTTTCTGCCTTTGCCGGAGAGCCTGCAGAGTCTGCATGCAAAAC Right flanking sequence: Indices 1687 -- 2186 CGCGNAAATAACGCAAGGGGGAGGNCGGGAAAGGGNCCAAAANGAAGCAGNCAACAACAGCAGNC NAAAAGCAGCAAANAGGAGACATGCCTTGCTGCTGCTGCGTCAGGAGCTCAAGGGCCTCTTCAGT TTGCCCACAGTGCTGCAGAGACACAGCAGCACAACCACTCCGAAATAAGGGTTTAGGGTTTAGGG TTTGGGGCTCAGTCTTGCAGCTAGCGCTGGGCATTCGGGCGCGGACTGGCTTGGATACGCTGCAG CAGTTTTTGAGGCTGAGACTCTGCTGAGGGTTTAGGGCTTAGGGTTTAAGGTTTGCAGCAGACCT TAAACCCAAAACCCTAAGCTGAGGGTTTAGGGTTTAGGGTTTGAAGCAAACCTGCAACAACGCAG CTAGGGCATCTGTGCGGCCCAAATACAGCAAAAATAAACNGGCAGTCTTCCACACTGCNAAGTGC ACCCCAGGNAACTGCTCCTCTCGNCTGCTGCTGNCTGCTGCTGCN Found at i:2174 original size:3 final size:3 Alignment explanation

Indices: 2166--2204 Score: 60 Period size: 3 Copynumber: 12.3 Consensus size: 3 2156 CTCCTCTCGN 2166 CTG CTG CTG NCTG CTG CTG CNTG CTG CTG CTG CTG CTG C 1 CTG CTG CTG -CTG CTG CTG C-TG CTG CTG CTG CTG CTG C 2205 AGAGCTTCCG Statistics Matches: 34, Mismatches: 0, Indels: 4 0.89 0.00 0.11 Matches are distributed among these distances: 3 28 0.82 4 6 0.18 ACGTcount: A:0.00, C:0.33, G:0.31, T:0.31 Consensus pattern (3 bp): CTG Left flanking sequence: Indices 1666 -- 2165 AAACTCTAAACCCTAAACCCTCGCGNAAATAACGCAAGGGGGAGGNCGGGAAAGGGNCCAAAANG AAGCAGNCAACAACAGCAGNCNAAAAGCAGCAAANAGGAGACATGCCTTGCTGCTGCTGCGTCAG GAGCTCAAGGGCCTCTTCAGTTTGCCCACAGTGCTGCAGAGACACAGCAGCACAACCACTCCGAA ATAAGGGTTTAGGGTTTAGGGTTTGGGGCTCAGTCTTGCAGCTAGCGCTGGGCATTCGGGCGCGG ACTGGCTTGGATACGCTGCAGCAGTTTTTGAGGCTGAGACTCTGCTGAGGGTTTAGGGCTTAGGG TTTAAGGTTTGCAGCAGACCTTAAACCCAAAACCCTAAGCTGAGGGTTTAGGGTTTAGGGTTTGA AGCAAACCTGCAACAACGCAGCTAGGGCATCTGTGCGGCCCAAATACAGCAAAAATAAACNGGCA GTCTTCCACACTGCNAAGTGCACCCCAGGNAACTGCTCCTCTCGN Right flanking sequence: Indices 2205 -- 2483 AGAGCTTCCGGAGGAAGCAGCAGCTGCTGCCACCGAGGGTCATCTGCTTCTACCTACACCAAACA CACCTTCAACACTAAACCCTAGAAAAAAACCCAAACCACAAACCCTAGACTCAAACCCTAACCCT AAACCTTAGGGCCAGCCCTAAGGAAAATACACAGAGGGTCCCCAAGCGCCCAAATTGNNAGGGTN NTTAGGGTTTGAGGGTNTTAGGGTNTTGGGTTGAGGGCNTTAGAGGACTTACGAGGAGCTTGAGA AGAATCGTGTCAATGGCCT Found at i:2181 original size:10 final size:9 Alignment explanation

Indices: 2166--2204 Score: 60 Period size: 10 Copynumber: 4.1 Consensus size: 9 2156 CTCCTCTCGN 2166 CTGCTGCTG 1 CTGCTGCTG 2175 NCTGCTGCTG 1 -CTGCTGCTG 2185 CNTGCTGCTG 1 C-TGCTGCTG 2195 CTGCTGCTG 1 CTGCTGCTG 2204 C 1 C 2205 AGAGCTTCCG Statistics Matches: 28, Mismatches: 0, Indels: 3 0.90 0.00 0.10 Matches are distributed among these distances: 9 10 0.36 10 18 0.64 ACGTcount: A:0.00, C:0.33, G:0.31, T:0.31 Consensus pattern (9 bp): CTGCTGCTG Left flanking sequence: Indices 1666 -- 2165 AAACTCTAAACCCTAAACCCTCGCGNAAATAACGCAAGGGGGAGGNCGGGAAAGGGNCCAAAANG AAGCAGNCAACAACAGCAGNCNAAAAGCAGCAAANAGGAGACATGCCTTGCTGCTGCTGCGTCAG GAGCTCAAGGGCCTCTTCAGTTTGCCCACAGTGCTGCAGAGACACAGCAGCACAACCACTCCGAA ATAAGGGTTTAGGGTTTAGGGTTTGGGGCTCAGTCTTGCAGCTAGCGCTGGGCATTCGGGCGCGG ACTGGCTTGGATACGCTGCAGCAGTTTTTGAGGCTGAGACTCTGCTGAGGGTTTAGGGCTTAGGG TTTAAGGTTTGCAGCAGACCTTAAACCCAAAACCCTAAGCTGAGGGTTTAGGGTTTAGGGTTTGA AGCAAACCTGCAACAACGCAGCTAGGGCATCTGTGCGGCCCAAATACAGCAAAAATAAACNGGCA GTCTTCCACACTGCNAAGTGCACCCCAGGNAACTGCTCCTCTCGN Right flanking sequence: Indices 2205 -- 2483 AGAGCTTCCGGAGGAAGCAGCAGCTGCTGCCACCGAGGGTCATCTGCTTCTACCTACACCAAACA CACCTTCAACACTAAACCCTAGAAAAAAACCCAAACCACAAACCCTAGACTCAAACCCTAACCCT AAACCTTAGGGCCAGCCCTAAGGAAAATACACAGAGGGTCCCCAAGCGCCCAAATTGNNAGGGTN NTTAGGGTTTGAGGGTNTTAGGGTNTTGGGTTGAGGGCNTTAGAGGACTTACGAGGAGCTTGAGA AGAATCGTGTCAATGGCCT Found at i:2182 original size:13 final size:12 Alignment explanation

Indices: 2166--2204 Score: 60 Period size: 13 Copynumber: 3.1 Consensus size: 12 2156 CTCCTCTCGN 2166 CTGCTGCTGNCTG 1 CTGCTGCTG-CTG 2179 CTGCTGCNTGCTG 1 CTGCTGC-TGCTG 2192 CTGCTGCTGCTG 1 CTGCTGCTGCTG 2204 C 1 C 2205 AGAGCTTCCG Statistics Matches: 25, Mismatches: 0, Indels: 3 0.89 0.00 0.11 Matches are distributed among these distances: 12 6 0.24 13 17 0.68 14 2 0.08 ACGTcount: A:0.00, C:0.33, G:0.31, T:0.31 Consensus pattern (12 bp): CTGCTGCTGCTG Left flanking sequence: Indices 1666 -- 2165 AAACTCTAAACCCTAAACCCTCGCGNAAATAACGCAAGGGGGAGGNCGGGAAAGGGNCCAAAANG AAGCAGNCAACAACAGCAGNCNAAAAGCAGCAAANAGGAGACATGCCTTGCTGCTGCTGCGTCAG GAGCTCAAGGGCCTCTTCAGTTTGCCCACAGTGCTGCAGAGACACAGCAGCACAACCACTCCGAA ATAAGGGTTTAGGGTTTAGGGTTTGGGGCTCAGTCTTGCAGCTAGCGCTGGGCATTCGGGCGCGG ACTGGCTTGGATACGCTGCAGCAGTTTTTGAGGCTGAGACTCTGCTGAGGGTTTAGGGCTTAGGG TTTAAGGTTTGCAGCAGACCTTAAACCCAAAACCCTAAGCTGAGGGTTTAGGGTTTAGGGTTTGA AGCAAACCTGCAACAACGCAGCTAGGGCATCTGTGCGGCCCAAATACAGCAAAAATAAACNGGCA GTCTTCCACACTGCNAAGTGCACCCCAGGNAACTGCTCCTCTCGN Right flanking sequence: Indices 2205 -- 2483 AGAGCTTCCGGAGGAAGCAGCAGCTGCTGCCACCGAGGGTCATCTGCTTCTACCTACACCAAACA CACCTTCAACACTAAACCCTAGAAAAAAACCCAAACCACAAACCCTAGACTCAAACCCTAACCCT AAACCTTAGGGCCAGCCCTAAGGAAAATACACAGAGGGTCCCCAAGCGCCCAAATTGNNAGGGTN NTTAGGGTTTGAGGGTNTTAGGGTNTTGGGTTGAGGGCNTTAGAGGACTTACGAGGAGCTTGAGA AGAATCGTGTCAATGGCCT Found at i:2313 original size:7 final size:6 Alignment explanation

Indices: 2296--2339 Score: 40 Period size: 6 Copynumber: 6.8 Consensus size: 6 2286 CCCTAGAAAA * * * 2296 AAACCC AAACCAC AAACCC TAGACTC AAACCC TAACCC TAAACC 1 AAACCC AAACC-C AAACCC -AAACCC AAACCC AAACCC -AAACC 2340 TTAGGGCCAG Statistics Matches: 29, Mismatches: 6, Indels: 5 0.72 0.15 0.12 Matches are distributed among these distances: 6 15 0.52 7 14 0.48 ACGTcount: A:0.45, C:0.43, G:0.02, T:0.09 Consensus pattern (6 bp): AAACCC Left flanking sequence: Indices 1796 -- 2295 GAGCTCAAGGGCCTCTTCAGTTTGCCCACAGTGCTGCAGAGACACAGCAGCACAACCACTCCGAA ATAAGGGTTTAGGGTTTAGGGTTTGGGGCTCAGTCTTGCAGCTAGCGCTGGGCATTCGGGCGCGG ACTGGCTTGGATACGCTGCAGCAGTTTTTGAGGCTGAGACTCTGCTGAGGGTTTAGGGCTTAGGG TTTAAGGTTTGCAGCAGACCTTAAACCCAAAACCCTAAGCTGAGGGTTTAGGGTTTAGGGTTTGA AGCAAACCTGCAACAACGCAGCTAGGGCATCTGTGCGGCCCAAATACAGCAAAAATAAACNGGCA GTCTTCCACACTGCNAAGTGCACCCCAGGNAACTGCTCCTCTCGNCTGCTGCTGNCTGCTGCTGC NTGCTGCTGCTGCTGCTGCAGAGCTTCCGGAGGAAGCAGCAGCTGCTGCCACCGAGGGTCATCTG CTTCTACCTACACCAAACACACCTTCAACACTAAACCCTAGAAAA Right flanking sequence: Indices 2340 -- 2483 TTAGGGCCAGCCCTAAGGAAAATACACAGAGGGTCCCCAAGCGCCCAAATTGNNAGGGTNNTTAG GGTTTGAGGGTNTTAGGGTNTTGGGTTGAGGGCNTTAGAGGACTTACGAGGAGCTTGAGAAGAAT CGTGTCAATGGCCT Found at