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:1876 original size:7 final size:7

Alignment explanation

Indices: 1864--1888 Score: 43 Period size: 7 Copynumber: 3.6 Consensus size: 7 1854 CTCCGAAATA 1864 AGGGTTT 1 AGGGTTT 1871 AGGGTTT 1 AGGGTTT 1878 AGGGTTT 1 AGGGTTT * 1885 GGGG 1 AGGG 1889 CTCAGTCTTG Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 7 17 1.00 ACGTcount: A:0.12, C:0.00, G:0.52, T:0.36 Consensus pattern (7 bp): AGGGTTT Left flanking sequence: Indices 1364 -- 1863 ACCAGCTGGCGAGCCTGGCCACCTGCGAGTTAGGGTTTAGGGTTTAGGGTTTGTCTCACTCTTCC TTGGATTCTCAAGCAGCACGAGAGGAGCAAAGCGCCGCAGCAACGCTGCCTGCTGCTGTTGCTGC TGCTGCTGCTGCTCCTGCTGTTGCTGCTGTTGCTCCTGCTGTTGCTGCTGCTGCTGCTGCTGCTG CACCACCTGCTGCAGAATCAGCAGCATCTGATCCGAAGGGGACAATGCGGTTTCTGCCTTTGCCG GAGAGCCTGCAGAGTCTGCATGCAAAACAAACCCTAAACCCTAAACTCTAAACCCTAAACCCTCG CGNAAATAACGCAAGGGGGAGGNCGGGAAAGGGNCCAAAANGAAGCAGNCAACAACAGCAGNCNA AAAGCAGCAAANAGGAGACATGCCTTGCTGCTGCTGCGTCAGGAGCTCAAGGGCCTCTTCAGTTT GCCCACAGTGCTGCAGAGACACAGCAGCACAACCACTCCGAAATA Right flanking sequence: Indices 1889 -- 2388 CTCAGTCTTGCAGCTAGCGCTGGGCATTCGGGCGCGGACTGGCTTGGATACGCTGCAGCAGTTTT TGAGGCTGAGACTCTGCTGAGGGTTTAGGGCTTAGGGTTTAAGGTTTGCAGCAGACCTTAAACCC AAAACCCTAAGCTGAGGGTTTAGGGTTTAGGGTTTGAAGCAAACCTGCAACAACGCAGCTAGGGC ATCTGTGCGGCCCAAATACAGCAAAAATAAACNGGCAGTCTTCCACACTGCNAAGTGCACCCCAG GNAACTGCTCCTCTCGNCTGCTGCTGNCTGCTGCTGCNTGCTGCTGCTGCTGCTGCAGAGCTTCC GGAGGAAGCAGCAGCTGCTGCCACCGAGGGTCATCTGCTTCTACCTACACCAAACACACCTTCAA CACTAAACCCTAGAAAAAAACCCAAACCACAAACCCTAGACTCAAACCCTAACCCTAAACCTTAG GGCCAGCCCTAAGGAAAATACACAGAGGGTCCCCAAGCGCCCAAA Found at i:1988 original size:7 final size:7 Alignment explanation

Indices: 1969--1994 Score: 31 Period size: 7 Copynumber: 3.7 Consensus size: 7 1959 CTGAGACTCT * 1969 GCTGAGG 1 GCTTAGG * 1976 GTTTAGG 1 GCTTAGG 1983 GCTTAGG 1 GCTTAGG * 1990 GTTTA 1 GCTTA 1995 AGGTTTGCAG Statistics Matches: 15, Mismatches: 4, Indels: 0 0.79 0.21 0.00 Matches are distributed among these distances: 7 15 1.00 ACGTcount: A:0.15, C:0.08, G:0.42, T:0.35 Consensus pattern (7 bp): GCTTAGG Left flanking sequence: Indices 1469 -- 1968 CAACGCTGCCTGCTGCTGTTGCTGCTGCTGCTGCTGCTCCTGCTGTTGCTGCTGTTGCTCCTGCT GTTGCTGCTGCTGCTGCTGCTGCTGCACCACCTGCTGCAGAATCAGCAGCATCTGATCCGAAGGG GACAATGCGGTTTCTGCCTTTGCCGGAGAGCCTGCAGAGTCTGCATGCAAAACAAACCCTAAACC CTAAACTCTAAACCCTAAACCCTCGCGNAAATAACGCAAGGGGGAGGNCGGGAAAGGGNCCAAAA NGAAGCAGNCAACAACAGCAGNCNAAAAGCAGCAAANAGGAGACATGCCTTGCTGCTGCTGCGTC AGGAGCTCAAGGGCCTCTTCAGTTTGCCCACAGTGCTGCAGAGACACAGCAGCACAACCACTCCG AAATAAGGGTTTAGGGTTTAGGGTTTGGGGCTCAGTCTTGCAGCTAGCGCTGGGCATTCGGGCGC GGACTGGCTTGGATACGCTGCAGCAGTTTTTGAGGCTGAGACTCT Right flanking sequence: Indices 1995 -- 2483 AGGTTTGCAGCAGACCTTAAACCCAAAACCCTAAGCTGAGGGTTTAGGGTTTAGGGTTTGAAGCA AACCTGCAACAACGCAGCTAGGGCATCTGTGCGGCCCAAATACAGCAAAAATAAACNGGCAGTCT TCCACACTGCNAAGTGCACCCCAGGNAACTGCTCCTCTCGNCTGCTGCTGNCTGCTGCTGCNTGC TGCTGCTGCTGCTGCAGAGCTTCCGGAGGAAGCAGCAGCTGCTGCCACCGAGGGTCATCTGCTTC TACCTACACCAAACACACCTTCAACACTAAACCCTAGAAAAAAACCCAAACCACAAACCCTAGAC TCAAACCCTAACCCTAAACCTTAGGGCCAGCCCTAAGGAAAATACACAGAGGGTCCCCAAGCGCC CAAATTGNNAGGGTNNTTAGGGTTTGAGGGTNTTAGGGTNTTGGGTTGAGGGCNTTAGAGGACTT ACGAGGAGCTTGAGAAGAATCGTGTCAATGGCCT Found at i:1999 original size:7 final size:7 Alignment explanation

Indices: 1973--2000 Score: 42 Period size: 7 Copynumber: 4.0 Consensus size: 7 1963 GACTCTGCTG 1973 AGGGTTT 1 AGGGTTT * 1980 AGGGCTT 1 AGGGTTT 1987 AGGGTTT 1 AGGGTTT * 1994 AAGGTTT 1 AGGGTTT 2001 GCAGCAGACC Statistics Matches: 18, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 7 18 1.00 ACGTcount: A:0.18, C:0.04, G:0.39, T:0.39 Consensus pattern (7 bp): AGGGTTT Left flanking sequence: Indices 1473 -- 1972 GCTGCCTGCTGCTGTTGCTGCTGCTGCTGCTGCTCCTGCTGTTGCTGCTGTTGCTCCTGCTGTTG CTGCTGCTGCTGCTGCTGCTGCACCACCTGCTGCAGAATCAGCAGCATCTGATCCGAAGGGGACA ATGCGGTTTCTGCCTTTGCCGGAGAGCCTGCAGAGTCTGCATGCAAAACAAACCCTAAACCCTAA ACTCTAAACCCTAAACCCTCGCGNAAATAACGCAAGGGGGAGGNCGGGAAAGGGNCCAAAANGAA GCAGNCAACAACAGCAGNCNAAAAGCAGCAAANAGGAGACATGCCTTGCTGCTGCTGCGTCAGGA GCTCAAGGGCCTCTTCAGTTTGCCCACAGTGCTGCAGAGACACAGCAGCACAACCACTCCGAAAT AAGGGTTTAGGGTTTAGGGTTTGGGGCTCAGTCTTGCAGCTAGCGCTGGGCATTCGGGCGCGGAC TGGCTTGGATACGCTGCAGCAGTTTTTGAGGCTGAGACTCTGCTG Right flanking sequence: Indices 2001 -- 2483 GCAGCAGACCTTAAACCCAAAACCCTAAGCTGAGGGTTTAGGGTTTAGGGTTTGAAGCAAACCTG CAACAACGCAGCTAGGGCATCTGTGCGGCCCAAATACAGCAAAAATAAACNGGCAGTCTTCCACA CTGCNAAGTGCACCCCAGGNAACTGCTCCTCTCGNCTGCTGCTGNCTGCTGCTGCNTGCTGCTGC TGCTGCTGCAGAGCTTCCGGAGGAAGCAGCAGCTGCTGCCACCGAGGGTCATCTGCTTCTACCTA CACCAAACACACCTTCAACACTAAACCCTAGAAAAAAACCCAAACCACAAACCCTAGACTCAAAC CCTAACCCTAAACCTTAGGGCCAGCCCTAAGGAAAATACACAGAGGGTCCCCAAGCGCCCAAATT GNNAGGGTNNTTAGGGTTTGAGGGTNTTAGGGTNTTGGGTTGAGGGCNTTAGAGGACTTACGAGG AGCTTGAGAAGAATCGTGTCAATGGCCT Found at i:2043 original size:7 final size:7 Alignment explanation

Indices: 2033--2053 Score: 42 Period size: 7 Copynumber: 3.0 Consensus size: 7 2023 CCCTAAGCTG 2033 AGGGTTT 1 AGGGTTT 2040 AGGGTTT 1 AGGGTTT 2047 AGGGTTT 1 AGGGTTT 2054 GAAGCAAACC Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 14 1.00 ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43 Consensus pattern (7 bp): AGGGTTT Left flanking sequence: Indices 1533 -- 2032 TGTTGCTGCTGCTGCTGCTGCTGCTGCACCACCTGCTGCAGAATCAGCAGCATCTGATCCGAAGG GGACAATGCGGTTTCTGCCTTTGCCGGAGAGCCTGCAGAGTCTGCATGCAAAACAAACCCTAAAC CCTAAACTCTAAACCCTAAACCCTCGCGNAAATAACGCAAGGGGGAGGNCGGGAAAGGGNCCAAA ANGAAGCAGNCAACAACAGCAGNCNAAAAGCAGCAAANAGGAGACATGCCTTGCTGCTGCTGCGT CAGGAGCTCAAGGGCCTCTTCAGTTTGCCCACAGTGCTGCAGAGACACAGCAGCACAACCACTCC GAAATAAGGGTTTAGGGTTTAGGGTTTGGGGCTCAGTCTTGCAGCTAGCGCTGGGCATTCGGGCG CGGACTGGCTTGGATACGCTGCAGCAGTTTTTGAGGCTGAGACTCTGCTGAGGGTTTAGGGCTTA GGGTTTAAGGTTTGCAGCAGACCTTAAACCCAAAACCCTAAGCTG Right flanking sequence: Indices 2054 -- 2483 GAAGCAAACCTGCAACAACGCAGCTAGGGCATCTGTGCGGCCCAAATACAGCAAAAATAAACNGG CAGTCTTCCACACTGCNAAGTGCACCCCAGGNAACTGCTCCTCTCGNCTGCTGCTGNCTGCTGCT GCNTGCTGCTGCTGCTGCTGCAGAGCTTCCGGAGGAAGCAGCAGCTGCTGCCACCGAGGGTCATC TGCTTCTACCTACACCAAACACACCTTCAACACTAAACCCTAGAAAAAAACCCAAACCACAAACC CTAGACTCAAACCCTAACCCTAAACCTTAGGGCCAGCCCTAAGGAAAATACACAGAGGGTCCCCA AGCGCCCAAATTGNNAGGGTNNTTAGGGTTTGAGGGTNTTAGGGTNTTGGGTTGAGGGCNTTAGA GGACTTACGAGGAGCTTGAGAAGAATCGTGTCAATGGCCT 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 i:2325 original size:26 final size:26 Alignment explanation

Indices: 2283--2343 Score: 73 Period size: 26 Copynumber: 2.3 Consensus size: 26 2273 CTTCAACACT 2283 AAACCCTAGAAAAAAACCCAAACCAC 1 AAACCCTAGAAAAAAACCCAAACCAC *** * ** 2309 AAACCCTAGACTCAAACCCTAACCCT 1 AAACCCTAGAAAAAAACCCAAACCAC * 2335 AAACCTTAG 1 AAACCCTAG 2344 GGCCAGCCCT Statistics Matches: 28, Mismatches: 7, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 26 28 1.00 ACGTcount: A:0.48, C:0.36, G:0.05, T:0.11 Consensus pattern (26 bp): AAACCCTAGAAAAAAACCCAAACCAC Left flanking sequence: Indices 1783 -- 2282 GCTGCTGCGTCAGGAGCTCAAGGGCCTCTTCAGTTTGCCCACAGTGCTGCAGAGACACAGCAGCA CAACCACTCCGAAATAAGGGTTTAGGGTTTAGGGTTTGGGGCTCAGTCTTGCAGCTAGCGCTGGG CATTCGGGCGCGGACTGGCTTGGATACGCTGCAGCAGTTTTTGAGGCTGAGACTCTGCTGAGGGT TTAGGGCTTAGGGTTTAAGGTTTGCAGCAGACCTTAAACCCAAAACCCTAAGCTGAGGGTTTAGG GTTTAGGGTTTGAAGCAAACCTGCAACAACGCAGCTAGGGCATCTGTGCGGCCCAAATACAGCAA AAATAAACNGGCAGTCTTCCACACTGCNAAGTGCACCCCAGGNAACTGCTCCTCTCGNCTGCTGC TGNCTGCTGCTGCNTGCTGCTGCTGCTGCTGCAGAGCTTCCGGAGGAAGCAGCAGCTGCTGCCAC CGAGGGTCATCTGCTTCTACCTACACCAAACACACCTTCAACACT Right flanking sequence: Indices 2344 -- 2483 GGCCAGCCCTAAGGAAAATACACAGAGGGTCCCCAAGCGCCCAAATTGNNAGGGTNNTTAGGGTT TGAGGGTNTTAGGGTNTTGGGTTGAGGGCNTTAGAGGACTTACGAGGAGCTTGAGAAGAATCGTG TCAATGGCCT Found at i:2338 original size:13 final size:12 Alignment explanation

Indices: 2296--2339 Score: 47 Period size: 13 Copynumber: 3.4 Consensus size: 12 2286 CCCTAGAAAA * 2296 AAACCCAAACCAC 1 AAACCCTAACC-C * 2309 AAACCCTAGACTC 1 AAACCCTA-ACCC 2322 AAACCCTAACCC 1 AAACCCTAACCC 2334 TAAACC 1 -AAACC 2340 TTAGGGCCAG Statistics Matches: 26, Mismatches: 3, Indels: 4 0.79 0.09 0.12 Matches are distributed among these distances: 12 3 0.12 13 21 0.81 14 2 0.08 ACGTcount: A:0.45, C:0.43, G:0.02, T:0.09 Consensus pattern (12 bp): AAACCCTAACCC 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 i:2422 original size:8 final size:7 Alignment explanation

Indices: 2401--2436 Score: 33 Period size: 7 Copynumber: 4.9 Consensus size: 7 2391 GNNAGGGTNN 2401 TTAGGGT 1 TTAGGGT 2408 TTGAGGGT 1 TT-AGGGT 2416 NTTAGGGT 1 -TTAGGGT * * 2424 NTTGGGT 1 TTAGGGT * 2431 TGAGGG 1 TTAGGG 2437 CNTTAGAGGA Statistics Matches: 22, Mismatches: 5, Indels: 4 0.71 0.16 0.13 Matches are distributed among these distances: 7 10 0.45 8 10 0.45 9 2 0.09 ACGTcount: A:0.11, C:0.00, G:0.47, T:0.36 Consensus pattern (7 bp): TTAGGGT Left flanking sequence: Indices 1901 -- 2400 GCTAGCGCTGGGCATTCGGGCGCGGACTGGCTTGGATACGCTGCAGCAGTTTTTGAGGCTGAGAC TCTGCTGAGGGTTTAGGGCTTAGGGTTTAAGGTTTGCAGCAGACCTTAAACCCAAAACCCTAAGC TGAGGGTTTAGGGTTTAGGGTTTGAAGCAAACCTGCAACAACGCAGCTAGGGCATCTGTGCGGCC CAAATACAGCAAAAATAAACNGGCAGTCTTCCACACTGCNAAGTGCACCCCAGGNAACTGCTCCT CTCGNCTGCTGCTGNCTGCTGCTGCNTGCTGCTGCTGCTGCTGCAGAGCTTCCGGAGGAAGCAGC AGCTGCTGCCACCGAGGGTCATCTGCTTCTACCTACACCAAACACACCTTCAACACTAAACCCTA GAAAAAAACCCAAACCACAAACCCTAGACTCAAACCCTAACCCTAAACCTTAGGGCCAGCCCTAA GGAAAATACACAGAGGGTCCCCAAGCGCCCAAATTGNNAGGGTNN Right flanking sequence: Indices 2437 -- 2483 CNTTAGAGGACTTACGAGGAGCTTGAGAAGAATCGTGTCAATGGCCT