Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: VEPZ01003234.1 Hibiscus syriacus cultivar Beakdansim tig00006806_pilon, whole genome shotgun sequence 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: 77029 ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33 Found at i:1592 original size:19 final size:19 Alignment explanation
Indices: 1529--1584 Score: 103 Period size: 19 Copynumber: 2.9 Consensus size: 19 1519 AATGTCGAGT * 1529 TAATTTTGTATAAGATTTA 1 TAATTTTGTATACGATTTA 1548 TAATTTTGTATACGATTTA 1 TAATTTTGTATACGATTTA 1567 TAATTTTGTATACGATTT 1 TAATTTTGTATACGATTT 1585 TATATTTTTT Statistics Matches: 36, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 19 36 1.00 ACGTcount: A:0.32, C:0.04, G:0.11, T:0.54 Consensus pattern (19 bp): TAATTTTGTATACGATTTA Found at i:2381 original size:194 final size:199 Alignment explanation
Indices: 1673--2811 Score: 1885 Period size: 194 Copynumber: 5.8 Consensus size: 199 1663 TTAAGGGTCA * *** * 1673 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGTGCATC 1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC * 1737 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAATTATAAT 66 AATAAAGTGTCGATCCA-ATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT 1802 GTAATATGTAA-TTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA 130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA 1866 TAATG 195 TAATG 1871 TGTCGACACT-ATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC 1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC * 1935 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT 66 AATAAAGTGTCGATCCA-ATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT 2000 GT--TATGTAATTTTTTAATCTAACCGGTACAATTATACCGG-TTTAT--GAGAATAAGTCTAAA 130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA 2060 TAATG 195 TAATG 2065 TGTCG--ACT-A-ATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC 1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC * 2126 CATAAAGTGTCGATCC-ATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT 66 AATAAAGTGTCGATCCAATATA-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT 2190 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA 130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA 2255 TAATG 195 TAATG *** * 2260 TGTCGACACTAATATAGTTTGTGTCGAT-TTTTTTT-CCAGAATGAATT-TTTACAAGGTGCATC 1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC 2322 AATAAAGTGTCGATCC-ATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG 66 AATAAAGTGTCGATCCAATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG * 2385 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT 131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT 2450 AATG 196 AATG 2454 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC 1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC * 2519 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT 66 AATAAAGTGTCGATCCA-ATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT 2584 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAG-ATAAGTCTAAA 130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA 2648 TAATG 195 TAATG * *** * 2653 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGTGCATC 1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC * 2717 AATAAAGTGTCGATCC-ATATATAAAAGTGTCGATCCCAAAATCATCGAACCC-AAAG--TAATG 66 AATAAAGTGTCGATCCAATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG * 2778 TAATATGTAATTTTTTAATCTAACCAGTACAATT 131 TAATATGTAATTTTTTAATCTAACCGGTACAATT 2812 TGCTTCTCGA Statistics Matches: 896, Mismatches: 27, Indels: 41 0.93 0.03 0.04 Matches are distributed among these distances: 189 5 0.01 190 44 0.05 191 68 0.08 192 42 0.05 193 43 0.05 194 164 0.18 195 36 0.04 196 89 0.10 197 108 0.12 198 120 0.13 199 83 0.09 200 94 0.10 ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33 Consensus pattern (199 bp): TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC AATAAAGTGTCGATCCAATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT AATG Found at i:2659 original size:393 final size:391 Alignment explanation
Indices: 1673--2811 Score: 1946 Period size: 393 Copynumber: 2.9 Consensus size: 391 1663 TTAAGGGTCA * *** * 1673 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGTGCATC 1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC * * 1737 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAATTATAAT 66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT 1802 GTAATATGTAA-TTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA 131 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA *** 1866 TAATGTGTCGACACT-ATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGT 196 TAATGTGTCGACACTAATATAGTTTGTGTCGAT-TTTTTTT-CCAGAATGAATT-TTTACAAGGT * * 1930 GCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT 258 GCATCAATAAAGTGTCGATCC--ATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT 1995 ATAATGT--TATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTATGAGAATAAGTCTA 320 ATAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTATGAGAATAAGTCTA 2058 AATAATG 385 AATAATG 2065 TGTCG--ACT-A-ATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC 1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC 2126 CATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT 66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT 2190 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA 131 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA 2255 TAATGTGTCGACACTAATATAGTTTGTGTCGATTTTTTTTCCAGAATGAATTTTTACAAGGTGCA 196 TAATGTGTCGACACTAATATAGTTTGTGTCGATTTTTTTTCCAGAATGAATTTTTACAAGGTGCA 2320 TCAATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG 261 TCAATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG * 2385 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT 326 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGG-TTTAT--GAGAATAAGTCTAAAT 2450 AATG 388 AATG 2454 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC 1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC 2519 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT 66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT 2584 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAG-ATAAGTCTAAA 131 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA 2648 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTG 196 TAATGTGTCGACACTAATATAGTTTGTGTCG--ATTTTTTTTCCAGAATGAATTTTTACAAGGTG 2713 CATCAATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAACCC-AAAG--TA 259 CATCAATAAAGTGTCGATCCATATA-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA * 2775 ATGTAATATGTAATTTTTTAATCTAACCAGTACAATT 323 ATGTAATATGTAATTTTTTAATCTAACCGGTACAATT 2812 TGCTTCTCGA Statistics Matches: 716, Mismatches: 15, Indels: 31 0.94 0.02 0.04 Matches are distributed among these distances: 384 44 0.06 385 4 0.01 386 37 0.05 387 31 0.04 388 99 0.14 389 133 0.19 390 20 0.03 391 3 0.00 392 6 0.01 393 153 0.21 394 95 0.13 395 61 0.09 396 30 0.04 ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33 Consensus pattern (391 bp): TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA TAATGTGTCGACACTAATATAGTTTGTGTCGATTTTTTTTCCAGAATGAATTTTTACAAGGTGCA TCAATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTATGAGAATAAGTCTAAATAAT G Found at i:5149 original size:23 final size:23 Alignment explanation
Indices: 5118--5180 Score: 90 Period size: 23 Copynumber: 2.7 Consensus size: 23 5108 ATAGGTAAAC * 5118 ATATGATGTAATAGGTAGCCCTT 1 ATATAATGTAATAGGTAGCCCTT * ** 5141 ATATAATGTAATAGGTATCGTTT 1 ATATAATGTAATAGGTAGCCCTT 5164 ATATAATGTAATAGGTA 1 ATATAATGTAATAGGTA 5181 ATGGTTATAT Statistics Matches: 36, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 23 36 1.00 ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38 Consensus pattern (23 bp): ATATAATGTAATAGGTAGCCCTT Found at i:5188 original size:23 final size:23 Alignment explanation
Indices: 5118--5190 Score: 85 Period size: 23 Copynumber: 3.2 Consensus size: 23 5108 ATAGGTAAAC * * ** 5118 ATATGATGTAATAGGTAGCCCTT 1 ATATAATGTAATAGGTATCGGTT * 5141 ATATAATGTAATAGGTATCGTTT 1 ATATAATGTAATAGGTATCGGTT 5164 ATATAATGTAATAGGTAAT-GGTT 1 ATATAATGTAATAGGT-ATCGGTT 5187 ATAT 1 ATAT 5191 TGTAAAGTGT Statistics Matches: 44, Mismatches: 5, Indels: 2 0.86 0.10 0.04 Matches are distributed among these distances: 23 42 0.95 24 2 0.05 ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40 Consensus pattern (23 bp): ATATAATGTAATAGGTATCGGTT Found at i:6184 original size:2 final size:2 Alignment explanation
Indices: 6179--6221 Score: 72 Period size: 2 Copynumber: 22.5 Consensus size: 2 6169 ACACACATAA 6179 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT -T 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 6219 AT A 1 AT A 6222 CTTTATAGAT Statistics Matches: 39, Mismatches: 0, Indels: 4 0.91 0.00 0.09 Matches are distributed among these distances: 1 2 0.05 2 37 0.95 ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49 Consensus pattern (2 bp): AT Found at i:14974 original size:15 final size:15 Alignment explanation
Indices: 14954--14985 Score: 55 Period size: 15 Copynumber: 2.1 Consensus size: 15 14944 GGAGGTCAAG * 14954 GAAGATGAAAAGGGA 1 GAAGATGAAAAGAGA 14969 GAAGATGAAAAGAGA 1 GAAGATGAAAAGAGA 14984 GA 1 GA 14986 TACCTGAGAA Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 16 1.00 ACGTcount: A:0.56, C:0.00, G:0.38, T:0.06 Consensus pattern (15 bp): GAAGATGAAAAGAGA Found at i:17582 original size:21 final size:22 Alignment explanation
Indices: 17541--17584 Score: 63 Period size: 22 Copynumber: 2.0 Consensus size: 22 17531 TTATATTGAT * 17541 TTTAAAAGAACAAATAATTTAA 1 TTTAAAAAAACAAATAATTTAA * 17563 TTTAAAAAAATAAA-AATTTAA 1 TTTAAAAAAACAAATAATTTAA 17584 T 1 T 17585 ATATTATTTT Statistics Matches: 20, Mismatches: 2, Indels: 1 0.87 0.09 0.04 Matches are distributed among these distances: 21 8 0.40 22 12 0.60 ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34 Consensus pattern (22 bp): TTTAAAAAAACAAATAATTTAA Found at i:18254 original size:92 final size:89 Alignment explanation
Indices: 18082--18265 Score: 305 Period size: 92 Copynumber: 2.0 Consensus size: 89 18072 CTTTACCAGG 18082 AAAAATAAAAAAGGTGAAGTAAAAAAGAAAATATTAGAAAAGGGAGCAGTACCGGAGGCAGAGGA 1 AAAAATAAAAAAGGTGAAGTAAAAAAGAAAATATTAGAAAAGGGAGCAGTACCGGAGGCAGAGGA * * 18147 TTGAGGGTGGAGTTCAGAAGCAGC 66 TGGAGGATGGAGTTCAGAAGCAGC * * 18171 AAAAATAAAAAAAGGGTGAAGTAAAAAAGAAAATATTAGAAAACGGGTGCAGTACCTGAGGCAGA 1 AAAAAT-AAAAAA-GGTGAAGTAAAAAAGAAAATATTAGAAAA-GGGAGCAGTACCGGAGGCAGA 18236 GGATGGAGGATGGAGTTCAGAAGCAGC 63 GGATGGAGGATGGAGTTCAGAAGCAGC 18263 AAA 1 AAA 18266 GGTTTGAGAG Statistics Matches: 88, Mismatches: 4, Indels: 3 0.93 0.04 0.03 Matches are distributed among these distances: 89 6 0.07 90 6 0.07 91 29 0.33 92 47 0.53 ACGTcount: A:0.48, C:0.08, G:0.30, T:0.14 Consensus pattern (89 bp): AAAAATAAAAAAGGTGAAGTAAAAAAGAAAATATTAGAAAAGGGAGCAGTACCGGAGGCAGAGGA TGGAGGATGGAGTTCAGAAGCAGC Found at i:25521 original size:19 final size:21 Alignment explanation
Indices: 25478--25522 Score: 58 Period size: 19 Copynumber: 2.2 Consensus size: 21 25468 TTAACTTTTT * 25478 TTTATAAATAAAATAATATAT 1 TTTATAAATAAAATAATATAA * 25499 TTTA-AAATAAAA-AATCTAA 1 TTTATAAATAAAATAATATAA 25518 TTTAT 1 TTTAT 25523 TGTTAAACCC Statistics Matches: 21, Mismatches: 2, Indels: 3 0.81 0.08 0.12 Matches are distributed among these distances: 19 9 0.43 20 8 0.38 21 4 0.19 ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42 Consensus pattern (21 bp): TTTATAAATAAAATAATATAA Found at i:26592 original size:21 final size:20 Alignment explanation
Indices: 26568--26685 Score: 109 Period size: 19 Copynumber: 5.9 Consensus size: 20 26558 TTGAAGTTCG * * 26568 CGTTGCGATTTATTACAAATT 1 CGTTGCGA-TTAGTCCAAATT * 26589 CGTTGCGA-TAGTCCAAGTT 1 CGTTGCGATTAGTCCAAATT * * 26608 CGTTGCGA-TAGTCGAAGTT 1 CGTTGCGATTAGTCCAAATT * 26627 CGCGTTGCGATTTATTCCAAATT 1 --CGTTGCGA-TTAGTCCAAATT * 26650 CGTTGCGA-TAGTCCAAGTT 1 CGTTGCGATTAGTCCAAATT 26669 CGTTGCGA-TAGTCCAAA 1 CGTTGCGATTAGTCCAAA 26686 ATCGCAACGA Statistics Matches: 83, Mismatches: 10, Indels: 10 0.81 0.10 0.10 Matches are distributed among these distances: 19 51 0.61 21 24 0.29 23 8 0.10 ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34 Consensus pattern (20 bp): CGTTGCGATTAGTCCAAATT Found at i:26611 original size:19 final size:19 Alignment explanation
Indices: 26587--26684 Score: 133 Period size: 19 Copynumber: 4.9 Consensus size: 19 26577 TTATTACAAA 26587 TTCGTTGCGATAGTCCAAG 1 TTCGTTGCGATAGTCCAAG * 26606 TTCGTTGCGATAGTCGAAG 1 TTCGTTGCGATAGTCCAAG * * 26625 TTCGCGTTGCGATTTATTCCAAA 1 TT--CGTTGCGA--TAGTCCAAG 26648 TTCGTTGCGATAGTCCAAG 1 TTCGTTGCGATAGTCCAAG 26667 TTCGTTGCGATAGTCCAA 1 TTCGTTGCGATAGTCCAA 26685 AATCGCAACG Statistics Matches: 69, Mismatches: 6, Indels: 8 0.83 0.07 0.10 Matches are distributed among these distances: 19 45 0.65 21 16 0.23 23 8 0.12 ACGTcount: A:0.21, C:0.20, G:0.24, T:0.34 Consensus pattern (19 bp): TTCGTTGCGATAGTCCAAG Found at i:26628 original size:61 final size:61 Alignment explanation
Indices: 26549--26681 Score: 248 Period size: 61 Copynumber: 2.2 Consensus size: 61 26539 GGAAACTGAT * 26549 TTGCGATAGTTGAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTCG 1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTCG * 26610 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCG 1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTCG 26671 TTGCGATAGTC 1 TTGCGATAGTC 26682 CAAAATCGCA Statistics Matches: 70, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 61 70 1.00 ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35 Consensus pattern (61 bp): TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTCG Found at i:26646 original size:42 final size:40 Alignment explanation
Indices: 26587--26677 Score: 123 Period size: 42 Copynumber: 2.3 Consensus size: 40 26577 TTATTACAAA * * * 26587 TTCGTTGCGA--TAGTCCAAGTTCGTTGCGATAGTCGAAG 1 TTCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAG 26625 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAG 1 TT--CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAG 26667 TTCGTTGCGAT 1 TTCGTTGCGAT 26678 AGTCCAAAAT Statistics Matches: 46, Mismatches: 3, Indels: 6 0.84 0.05 0.11 Matches are distributed among these distances: 38 2 0.04 40 17 0.37 42 27 0.59 ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35 Consensus pattern (40 bp): TTCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAG Found at i:29019 original size:26 final size:26 Alignment explanation
Indices: 28990--29039 Score: 64 Period size: 26 Copynumber: 1.9 Consensus size: 26 28980 TGTCAAGGTT * * 28990 GAATTTATAAATTTTTAAGAGAATAC 1 GAATTCATAAAGTTTTAAGAGAATAC * * 29016 GAATTCATAACGTTTTATGAGAAT 1 GAATTCATAAAGTTTTAAGAGAAT 29040 GAAAATATAA Statistics Matches: 20, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 26 20 1.00 ACGTcount: A:0.42, C:0.06, G:0.14, T:0.38 Consensus pattern (26 bp): GAATTCATAAAGTTTTAAGAGAATAC Found at i:37780 original size:19 final size:19 Alignment explanation
Indices: 37753--37789 Score: 65 Period size: 19 Copynumber: 1.9 Consensus size: 19 37743 TTAAAAATGT * 37753 AATATAATATTTTTATTTC 1 AATAGAATATTTTTATTTC 37772 AATAGAATATTTTTATTT 1 AATAGAATATTTTTATTT 37790 TAGTATTTTA Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 19 17 1.00 ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57 Consensus pattern (19 bp): AATAGAATATTTTTATTTC Found at i:41436 original size:17 final size:18 Alignment explanation
Indices: 41389--41441 Score: 56 Period size: 20 Copynumber: 2.9 Consensus size: 18 41379 AGTTTAATAT * 41389 TTATATATAATAGACTTAAA 1 TTATATATTATA-A-TTAAA * 41409 TTATTTATTATAATTAAA 1 TTATATATTATAATTAAA 41427 -TATATATTAT-ATTAA 1 TTATATATTATAATTAA 41442 GGCTAAAACA Statistics Matches: 30, Mismatches: 3, Indels: 4 0.81 0.08 0.11 Matches are distributed among these distances: 16 5 0.17 17 9 0.30 18 5 0.17 19 1 0.03 20 10 0.33 ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49 Consensus pattern (18 bp): TTATATATTATAATTAAA Found at i:42461 original size:32 final size:32 Alignment explanation
Indices: 42400--42463 Score: 83 Period size: 32 Copynumber: 2.0 Consensus size: 32 42390 ATTATCACAT * * * * 42400 CAATACTATTAATAATATTTCTTTAAAAAAAC 1 CAATACTACTAATAACATGTCGTTAAAAAAAC * 42432 CAATACTACTAATAACATGTCGTTGAAAAAAC 1 CAATACTACTAATAACATGTCGTTAAAAAAAC 42464 AACGAAAGGA Statistics Matches: 27, Mismatches: 5, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 32 27 1.00 ACGTcount: A:0.48, C:0.16, G:0.05, T:0.31 Consensus pattern (32 bp): CAATACTACTAATAACATGTCGTTAAAAAAAC Found at i:49049 original size:86 final size:86 Alignment explanation
Indices: 48899--49069 Score: 306 Period size: 86 Copynumber: 2.0 Consensus size: 86 48889 TAACATTATC * * 48899 GTTGGTTATAAAATGATCCTTCGATGTTAACCGCGGTTGATAGACATGACGAAAACACAACTAGA 1 GTTGATTATAAAATGATCATTCGATGTTAACCGCGGTTGATAGACATGACGAAAACACAACTAGA * 48964 TTGTATCTAATGAGTTAGATA 66 TTATATCTAATGAGTTAGATA * 48985 GTTGATTATAAAATGATCATTCGATGTTAACCGCGGTTGATAGACGTGACGAAAACACAACTAGA 1 GTTGATTATAAAATGATCATTCGATGTTAACCGCGGTTGATAGACATGACGAAAACACAACTAGA 49050 TTATATCTAATGAGTTAGAT 66 TTATATCTAATGAGTTAGAT 49070 CATTGACCGC Statistics Matches: 81, Mismatches: 4, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 86 81 1.00 ACGTcount: A:0.36, C:0.13, G:0.20, T:0.30 Consensus pattern (86 bp): GTTGATTATAAAATGATCATTCGATGTTAACCGCGGTTGATAGACATGACGAAAACACAACTAGA TTATATCTAATGAGTTAGATA Found at i:49823 original size:21 final size:21 Alignment explanation
Indices: 49797--49841 Score: 63 Period size: 21 Copynumber: 2.1 Consensus size: 21 49787 GATTTCTGGG * * 49797 CAAGGGGAATCGGTACCCATT 1 CAAGGGGAACCGATACCCATT * 49818 CAAGGGGAACCGATACCCCTT 1 CAAGGGGAACCGATACCCATT 49839 CAA 1 CAA 49842 ACGAACAACA Statistics Matches: 21, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 21 21 1.00 ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16 Consensus pattern (21 bp): CAAGGGGAACCGATACCCATT Found at i:50442 original size:18 final size:18 Alignment explanation
Indices: 50419--50453 Score: 54 Period size: 18 Copynumber: 1.9 Consensus size: 18 50409 CTAGGAGATT 50419 TGAACATA-AATGATAAGA 1 TGAACATATAA-GATAAGA 50437 TGAACATATAAGATAAG 1 TGAACATATAAGATAAG 50454 CTAGATGGGA Statistics Matches: 16, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 18 14 0.88 19 2 0.12 ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23 Consensus pattern (18 bp): TGAACATATAAGATAAGA Found at i:51515 original size:143 final size:143 Alignment explanation
Indices: 51347--51651 Score: 476 Period size: 145 Copynumber: 2.1 Consensus size: 143 51337 GAGTCGAGGG ** * 51347 TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTC-TG-GTGAGAC-A 1 TCTACGCGGTCCTTCGGG--ATATATATATTC--TGGAACATGTGTGAAGTCTTGAAAGACACAA 51409 -TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATA 62 CTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATA 51473 TGGCACTACGGTGCAAT 127 TGGCACTACGGTGCAAT 51490 TCTACGCGGTCCTTCGGGATATATATATTCTGGAACATGTGTGAAGTCTTGAAAGACACATACTT 1 TCTACGCGGTCCTTCGGGATATATATATTCTGGAACATGTGTGAAGTCTTGAAAGACACA-AC-T * 51555 GATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTATATG 64 GATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATG 51620 GCACTACGGTGCAAT 129 GCACTACGGTGCAAT 51635 TCTACGCGG-CACTTCGG 1 TCTACGCGGTC-CTTCGG 51652 TGCAATTATA Statistics Matches: 151, Mismatches: 4, Indels: 12 0.90 0.02 0.07 Matches are distributed among these distances: 139 18 0.12 140 2 0.01 141 16 0.11 143 19 0.13 144 1 0.01 145 95 0.63 ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34 Consensus pattern (143 bp): TCTACGCGGTCCTTCGGGATATATATATTCTGGAACATGTGTGAAGTCTTGAAAGACACAACTGA TCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGC ACTACGGTGCAAT Found at i:51652 original size:23 final size:23 Alignment explanation
Indices: 51619--51663 Score: 72 Period size: 23 Copynumber: 2.0 Consensus size: 23 51609 ATTATTATAT * 51619 GGCACTACGGTGCAATTCTACGC 1 GGCACTACGGTGCAATTATACGC * 51642 GGCACTTCGGTGCAATTATACG 1 GGCACTACGGTGCAATTATACG 51664 AGCTGTGGTG Statistics Matches: 20, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 23 20 1.00 ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24 Consensus pattern (23 bp): GGCACTACGGTGCAATTATACGC Found at i:53370 original size:16 final size:15 Alignment explanation
Indices: 53349--53399 Score: 50 Period size: 16 Copynumber: 3.2 Consensus size: 15 53339 AGTTATGGAG 53349 AAGAAAAGTGAAGAAA 1 AAGAAAAG-GAAGAAA * 53365 AAGAAAGAAGAAGAAA 1 AAGAAA-AGGAAGAAA 53381 AATGAAGAA-GAAGAAA 1 AA-GAA-AAGGAAGAAA 53397 AAG 1 AAG 53400 GTGGAATTGG Statistics Matches: 31, Mismatches: 1, Indels: 7 0.79 0.03 0.18 Matches are distributed among these distances: 15 1 0.03 16 24 0.77 17 5 0.16 18 1 0.03 ACGTcount: A:0.71, C:0.00, G:0.25, T:0.04 Consensus pattern (15 bp): AAGAAAAGGAAGAAA Found at i:53380 original size:26 final size:26 Alignment explanation
Indices: 53347--53396 Score: 82 Period size: 26 Copynumber: 1.9 Consensus size: 26 53337 GTAGTTATGG * 53347 AGAAGAAAAGTGAAGAAAAAGAAAGA 1 AGAAGAAAAATGAAGAAAAAGAAAGA * 53373 AGAAGAAAAATGAAGAAGAAGAAA 1 AGAAGAAAAATGAAGAAAAAGAAA 53397 AAGGTGGAAT Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 26 22 1.00 ACGTcount: A:0.70, C:0.00, G:0.26, T:0.04 Consensus pattern (26 bp): AGAAGAAAAATGAAGAAAAAGAAAGA Found at i:56863 original size:14 final size:14 Alignment explanation
Indices: 56822--56873 Score: 54 Period size: 14 Copynumber: 3.8 Consensus size: 14 56812 AACAGACATA * 56822 AGATTTTAAATAAAT 1 AGATTTT-AATATAT 56837 AGA-TTTAAT-TAT 1 AGATTTTAATATAT 56849 AGATTTTAATATAT 1 AGATTTTAATATAT * * 56863 ATATATTAATA 1 AGATTTTAATA 56874 ACATTATTTT Statistics Matches: 32, Mismatches: 3, Indels: 5 0.80 0.08 0.12 Matches are distributed among these distances: 12 5 0.16 13 9 0.28 14 15 0.47 15 3 0.09 ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46 Consensus pattern (14 bp): AGATTTTAATATAT Found at i:58172 original size:3 final size:3 Alignment explanation
Indices: 58164--58189 Score: 52 Period size: 3 Copynumber: 8.7 Consensus size: 3 58154 TTAAGCTCCT 58164 TTC TTC TTC TTC TTC TTC TTC TTC TT 1 TTC TTC TTC TTC TTC TTC TTC TTC TT 58190 TGTCGTCGTC Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 23 1.00 ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69 Consensus pattern (3 bp): TTC Found at i:65043 original size:3 final size:3 Alignment explanation
Indices: 65037--65097 Score: 70 Period size: 3 Copynumber: 20.0 Consensus size: 3 65027 AATAATTATT * ** 65037 TAA TAA TAA T-A TAA TAT TATA TATA TAA TAA TAA TAA TAA TAA TTT 1 TAA TAA TAA TAA TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA 65083 TAA TAA TAA TAA TAA 1 TAA TAA TAA TAA TAA 65098 AAATGAAAAA Statistics Matches: 50, Mismatches: 6, Indels: 4 0.83 0.10 0.07 Matches are distributed among these distances: 2 2 0.04 3 42 0.84 4 6 0.12 ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41 Consensus pattern (3 bp): TAA Found at i:74631 original size:18 final size:18 Alignment explanation
Indices: 74604--74639 Score: 56 Period size: 18 Copynumber: 2.0 Consensus size: 18 74594 AATACTCCAT 74604 AAATCTATTGA-AAAAGA 1 AAATCTATTGAGAAAAGA 74621 AAATACTATTGAGAAAAGA 1 AAAT-CTATTGAGAAAAGA 74640 GAAACAATAT Statistics Matches: 17, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 17 4 0.24 18 7 0.41 19 6 0.35 ACGTcount: A:0.58, C:0.06, G:0.14, T:0.22 Consensus pattern (18 bp): AAATCTATTGAGAAAAGA Found at i:76477 original size:21 final size:21 Alignment explanation
Indices: 76451--76491 Score: 82 Period size: 21 Copynumber: 2.0 Consensus size: 21 76441 CTAGCATAGC 76451 CCTTAACAATCTCCTAAGCTT 1 CCTTAACAATCTCCTAAGCTT 76472 CCTTAACAATCTCCTAAGCT 1 CCTTAACAATCTCCTAAGCT 76492 AAAAGCGTGT Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 20 1.00 ACGTcount: A:0.29, C:0.34, G:0.05, T:0.32 Consensus pattern (21 bp): CCTTAACAATCTCCTAAGCTT Done.