Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: VEPZ01000120.1 Hibiscus syriacus cultivar Beakdansim tig00000217_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: 78955 ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34 Found at i:877 original size:109 final size:109 Alignment explanation
Indices: 681--1051 Score: 383 Period size: 109 Copynumber: 3.4 Consensus size: 109 671 CCATATCCAT * * * * ** 681 GACAATAATAATTTCAAATGGCATAGAACTTTAACTATTCACATTCTTTTTTCCAGTAAAATGTC 1 GACAATAATAATTTCAAATGACAGAGAATTTTAACTATTCACATT-TTTTTT-CAGTGAAACATC * * * * ** 746 ACATCAGATTAAAACTTTAATTATAGTGAAAGGGAAATCATATTGAG 64 ACCTCAAATCAGAACTTTAATTATAGTGAAAGAAAAATCATATT-AG * *** 793 GATAATAATAATTT-AAATGACAGAGAATTTTAACTATTCGTGTTTTTTTTCTAGTGAAACATCA 1 GACAATAATAATTTCAAATGACAGAGAATTTTAACTATTCACATTTTTTTTC-AGTGAAACATCA * * 857 CCTCAAATCAGAAC-TTAATTATAGT-AGAAGAAAAATCATACTCAT 65 CCTCAAATCAGAACTTTAATTATAGTGA-AAGAAAAATCATA-TTAG * * ** ** 902 AACAATAATAATTTCAAAT-AAAGAGAATTTTAACTATTCACATCCTTTTTCAACGAAACATCAC 1 GACAATAATAATTTCAAATGACAGAGAATTTTAACTATTCACATTTTTTTTCAGTGAAACATCAC * * 966 CTCAAATCAGAACTTTCATTATAGTGAAAGAAAAATCAGATCTAG 66 CTCAAATCAGAACTTTAATTATAGTGAAAGAAAAATCATAT-TAG * * 1011 GACAATAATAATTTCAAATGAC-GTAAAATCTTAACTATTCA 1 GACAATAATAATTTCAAATGACAG-AGAATTTTAACTATTCA 1052 TGTCCTTGTT Statistics Matches: 214, Mismatches: 36, Indels: 20 0.79 0.13 0.07 Matches are distributed among these distances: 108 26 0.12 109 104 0.49 110 47 0.22 111 24 0.11 112 13 0.06 ACGTcount: A:0.43, C:0.15, G:0.10, T:0.33 Consensus pattern (109 bp): GACAATAATAATTTCAAATGACAGAGAATTTTAACTATTCACATTTTTTTTCAGTGAAACATCAC CTCAAATCAGAACTTTAATTATAGTGAAAGAAAAATCATATTAG Found at i:1345 original size:14 final size:13 Alignment explanation
Indices: 1298--1345 Score: 51 Period size: 14 Copynumber: 3.5 Consensus size: 13 1288 TATGTCATGT * 1298 TTTTTTAATTTTA 1 TTTTTTATTTTTA * 1311 TTTATTTATTATTA 1 TTT-TTTATTTTTA 1325 TTATTTTATTTTTAA 1 TT-TTTTATTTTT-A 1340 TTTTTT 1 TTTTTT 1346 GAAATGAGGT Statistics Matches: 29, Mismatches: 3, Indels: 5 0.78 0.08 0.14 Matches are distributed among these distances: 13 3 0.10 14 22 0.76 15 4 0.14 ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77 Consensus pattern (13 bp): TTTTTTATTTTTA Found at i:5231 original size:19 final size:19 Alignment explanation
Indices: 5206--5257 Score: 79 Period size: 19 Copynumber: 2.7 Consensus size: 19 5196 CACACAATAT 5206 CGGTACTATT-ATACAGTA 1 CGGTACTATTCATACAGTA 5224 CTGGTACTATTCATACAGTA 1 C-GGTACTATTCATACAGTA * 5244 CAGTACTATTCATA 1 CGGTACTATTCATA 5258 AAAACATTTT Statistics Matches: 31, Mismatches: 1, Indels: 3 0.89 0.03 0.09 Matches are distributed among these distances: 18 1 0.03 19 21 0.68 20 9 0.29 ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35 Consensus pattern (19 bp): CGGTACTATTCATACAGTA Found at i:5508 original size:20 final size:20 Alignment explanation
Indices: 5465--5508 Score: 63 Period size: 21 Copynumber: 2.2 Consensus size: 20 5455 ATATTTAATG 5465 AAAAGATATCAATTGTTAAC 1 AAAAGATATCAATTGTTAAC * 5485 AAAAGGATATGAATTGTTAA- 1 AAAA-GATATCAATTGTTAAC 5505 AAAA 1 AAAA 5509 TACAAATTGT Statistics Matches: 22, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 20 8 0.36 21 14 0.64 ACGTcount: A:0.55, C:0.05, G:0.14, T:0.27 Consensus pattern (20 bp): AAAAGATATCAATTGTTAAC Found at i:8934 original size:30 final size:30 Alignment explanation
Indices: 8900--8966 Score: 89 Period size: 30 Copynumber: 2.2 Consensus size: 30 8890 GGTATTAAAT * * 8900 GAACACGTTGAACAATAAATAAACGAAAAC 1 GAACACGTTCAAAAATAAATAAACGAAAAC * * * 8930 GAACACCTTCAAAAATAAATAAACTAACAC 1 GAACACGTTCAAAAATAAATAAACGAAAAC 8960 GAACACG 1 GAACACG 8967 AAATAAACAT Statistics Matches: 31, Mismatches: 6, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 30 31 1.00 ACGTcount: A:0.55, C:0.21, G:0.10, T:0.13 Consensus pattern (30 bp): GAACACGTTCAAAAATAAATAAACGAAAAC Found at i:12743 original size:25 final size:25 Alignment explanation
Indices: 12726--12776 Score: 93 Period size: 25 Copynumber: 2.0 Consensus size: 25 12716 TTATCTTGAT * 12726 TCGAGTTTTAATTTTTTATTTCGAG 1 TCGAGCTTTAATTTTTTATTTCGAG 12751 TCGAGCTTTAATTTTTTATTTCGAG 1 TCGAGCTTTAATTTTTTATTTCGAG 12776 T 1 T 12777 TTGAATCGAA Statistics Matches: 25, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 25 25 1.00 ACGTcount: A:0.20, C:0.10, G:0.16, T:0.55 Consensus pattern (25 bp): TCGAGCTTTAATTTTTTATTTCGAG Found at i:16335 original size:23 final size:22 Alignment explanation
Indices: 16288--16336 Score: 55 Period size: 22 Copynumber: 2.2 Consensus size: 22 16278 TTTCATATGT * * 16288 AATATATATTATTAAAAATAAA 1 AATATATATTATAAAAAAGAAA 16310 AATATA-ATTATAATAAAAGAAGA 1 AATATATATTATAA-AAAAGAA-A 16333 AATA 1 AATA 16337 GTGGGAGAAC Statistics Matches: 23, Mismatches: 2, Indels: 3 0.82 0.07 0.11 Matches are distributed among these distances: 21 6 0.26 22 12 0.52 23 5 0.22 ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31 Consensus pattern (22 bp): AATATATATTATAAAAAAGAAA Found at i:17071 original size:31 final size:31 Alignment explanation
Indices: 17002--17086 Score: 136 Period size: 30 Copynumber: 2.8 Consensus size: 31 16992 AATGATTTTG * * * 17002 AAAAATGAAAGTTTAGGTACTAAAACAGATC 1 AAAACTGATAGTTTAGGTACTAAAACAAATC 17033 -AAACTGATAGTTTAGGTACTAAAACAAATC 1 AAAACTGATAGTTTAGGTACTAAAACAAATC 17063 AAAACTGATAGTTTAGGTACTAAA 1 AAAACTGATAGTTTAGGTACTAAA 17087 TGCATATTTT Statistics Matches: 50, Mismatches: 3, Indels: 2 0.91 0.05 0.04 Matches are distributed among these distances: 30 27 0.54 31 23 0.46 ACGTcount: A:0.48, C:0.11, G:0.15, T:0.26 Consensus pattern (31 bp): AAAACTGATAGTTTAGGTACTAAAACAAATC Found at i:18331 original size:130 final size:130 Alignment explanation
Indices: 18190--18436 Score: 413 Period size: 130 Copynumber: 1.9 Consensus size: 130 18180 ATTTATATAA * 18190 TCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGT 1 TCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGT * * * 18255 TAGCACATGATCATGACACATGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCTT 66 TAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTT 18320 TCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGT 1 TCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGT * ** * * 18385 TAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA 66 TAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA 18437 GAAGAAAATT Statistics Matches: 108, Mismatches: 9, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 130 108 1.00 ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37 Consensus pattern (130 bp): TCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGT TAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTT Found at i:18467 original size:130 final size:129 Alignment explanation
Indices: 18203--18467 Score: 300 Period size: 130 Copynumber: 2.0 Consensus size: 129 18193 ATTTGGTCCT * * 18203 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA 1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA * * *** * * * **** * 18268 TGACACATGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCTTTCAATTTGGTCCT 66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTTACAAAGAAGT-CA 18333 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA 1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA * ** * * 18398 TGATATGTGTTATTGGTGACACATGTCACCTCCTAATTAGAAGAAAATTAAG-TTACAAAGAAGT 66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTTACAAAGAAGT 18462 -A 128 CA 18463 AAATT 1 AAATT 18468 TGGGTCTTGG Statistics Matches: 112, Mismatches: 20, Indels: 6 0.81 0.14 0.04 Matches are distributed among these distances: 130 99 0.88 132 10 0.09 133 3 0.03 ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35 Consensus pattern (129 bp): AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTTACAAAGAAGTCA Found at i:18794 original size:28 final size:27 Alignment explanation
Indices: 18763--18825 Score: 63 Period size: 28 Copynumber: 2.3 Consensus size: 27 18753 AGTTGATACA * 18763 ATATTTTAAAAGAATAAATTTAAGATTT 1 ATATTTTAAAA-AATAAATTTAAGAATT ** * * 18791 ATATATTTTTAAACTAAATTTAATAATT 1 ATAT-TTTAAAAAATAAATTTAAGAATT 18819 ATATTTT 1 ATATTTT 18826 TCATATTTAT Statistics Matches: 29, Mismatches: 5, Indels: 3 0.78 0.14 0.08 Matches are distributed among these distances: 27 3 0.10 28 21 0.72 29 5 0.17 ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49 Consensus pattern (27 bp): ATATTTTAAAAAATAAATTTAAGAATT Found at i:19085 original size:21 final size:21 Alignment explanation
Indices: 19061--19103 Score: 86 Period size: 21 Copynumber: 2.0 Consensus size: 21 19051 TATTACCTTA 19061 AATTGAAGTATTTTAGAATTT 1 AATTGAAGTATTTTAGAATTT 19082 AATTGAAGTATTTTAGAATTT 1 AATTGAAGTATTTTAGAATTT 19103 A 1 A 19104 GGGTTTAGAA Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 22 1.00 ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47 Consensus pattern (21 bp): AATTGAAGTATTTTAGAATTT Found at i:19121 original size:35 final size:35 Alignment explanation
Indices: 19072--19157 Score: 100 Period size: 35 Copynumber: 2.5 Consensus size: 35 19062 ATTGAAGTAT ** * * 19072 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG 1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG * * * 19107 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG 1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG * 19142 TTTAGAATGAAATTGA 1 TTTAGAATAAAATTGA 19158 TGACTGTTTT Statistics Matches: 43, Mismatches: 8, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 35 43 1.00 ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41 Consensus pattern (35 bp): TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG Found at i:19340 original size:29 final size:29 Alignment explanation
Indices: 19288--19345 Score: 82 Period size: 29 Copynumber: 2.0 Consensus size: 29 19278 GCAAACGGAA * * 19288 TAAATGTTGGGGGACTGTATTGCAAGTTT 1 TAAATGTTGGGGGACTGAAATGCAAGTTT 19317 TAAATGTTGGGGGACCT-AAATGCAAGTTT 1 TAAATGTTGGGGGA-CTGAAATGCAAGTTT 19346 CAGAAATGTT Statistics Matches: 26, Mismatches: 2, Indels: 2 0.87 0.07 0.07 Matches are distributed among these distances: 29 24 0.92 30 2 0.08 ACGTcount: A:0.28, C:0.09, G:0.29, T:0.34 Consensus pattern (29 bp): TAAATGTTGGGGGACTGAAATGCAAGTTT Found at i:23745 original size:148 final size:148 Alignment explanation
Indices: 23477--23774 Score: 587 Period size: 148 Copynumber: 2.0 Consensus size: 148 23467 TTCAAGCTGC 23477 AACGAAGACTTGGGTACGACATGATATGATTAAAGGTCAAGATTAGATGGCCAAATGTCCTCTGC 1 AACGAAGACTTGGGTACGACATGATATGATTAAAGGTCAAGATTAGATGGCCAAATGTCCTCTGC * 23542 TCATTTAGTAGTAATTAAACCAAAGACATTAAGTTAAAGAAATTGTCATGTTCTAAGAAAGATAC 66 TCATTTAGTAGTAATTAAACCAAAGACATTAAGTTAAAGAAATTGCCATGTTCTAAGAAAGATAC 23607 ACAAGCGAAGACATTTGT 131 ACAAGCGAAGACATTTGT 23625 AACGAAGACTTGGGTACGACATGATATGATTAAAGGTCAAGATTAGATGGCCAAATGTCCTCTGC 1 AACGAAGACTTGGGTACGACATGATATGATTAAAGGTCAAGATTAGATGGCCAAATGTCCTCTGC 23690 TCATTTAGTAGTAATTAAACCAAAGACATTAAGTTAAAGAAATTGCCATGTTCTAAGAAAGATAC 66 TCATTTAGTAGTAATTAAACCAAAGACATTAAGTTAAAGAAATTGCCATGTTCTAAGAAAGATAC 23755 ACAAGCGAAGACATTTGT 131 ACAAGCGAAGACATTTGT 23773 AA 1 AA 23775 AAAATCTGCT Statistics Matches: 149, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 148 149 1.00 ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27 Consensus pattern (148 bp): AACGAAGACTTGGGTACGACATGATATGATTAAAGGTCAAGATTAGATGGCCAAATGTCCTCTGC TCATTTAGTAGTAATTAAACCAAAGACATTAAGTTAAAGAAATTGCCATGTTCTAAGAAAGATAC ACAAGCGAAGACATTTGT Found at i:30957 original size:25 final size:25 Alignment explanation
Indices: 30929--31000 Score: 110 Period size: 25 Copynumber: 2.9 Consensus size: 25 30919 CCGGGTATCA * 30929 GGTAATCGGGTACCCGGATTTTGCG 1 GGTAATCGGATACCCGGATTTTGCG 30954 GGT-ATCCGGATACCCGGATTTTGCG 1 GGTAAT-CGGATACCCGGATTTTGCG * 30979 GGTATTCGGATACCCGGATTTT 1 GGTAATCGGATACCCGGATTTT 31001 TTTCTTCAAA Statistics Matches: 43, Mismatches: 2, Indels: 4 0.88 0.04 0.08 Matches are distributed among these distances: 24 2 0.05 25 40 0.93 26 1 0.02 ACGTcount: A:0.17, C:0.21, G:0.32, T:0.31 Consensus pattern (25 bp): GGTAATCGGATACCCGGATTTTGCG Found at i:32261 original size:64 final size:64 Alignment explanation
Indices: 32192--32412 Score: 243 Period size: 64 Copynumber: 3.5 Consensus size: 64 32182 TTGAAGGTGT * ** 32192 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAACATCGAATGCAATTCATG 1 ATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCAATTCATG 32255 C 64 C * * ** 32256 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGGTGC 1 ATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC ** * * ** * 32320 ATCGATGCATAAGG-AGTGCATCGATGCATCCCAGCAATAATAATACATCGAATACCTTTTATGC 1 ATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC * 32384 ACCGATGCATCA-GTAGTGCATCGATGCAT 1 ATCGATGCAT-AGGTAGTGCATCGATGCAT 32413 ACCTTCATTA Statistics Matches: 134, Mismatches: 19, Indels: 8 0.83 0.12 0.05 Matches are distributed among these distances: 63 1 0.01 64 127 0.95 65 6 0.04 ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27 Consensus pattern (64 bp): ATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC Found at i:32738 original size:12 final size:12 Alignment explanation
Indices: 32720--32755 Score: 63 Period size: 12 Copynumber: 3.0 Consensus size: 12 32710 TATATATGTT 32720 CATGTGATATGA 1 CATGTGATATGA * 32732 TATGTGATATGA 1 CATGTGATATGA 32744 CATGTGATATGA 1 CATGTGATATGA 32756 GAACATGATA Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 12 22 1.00 ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36 Consensus pattern (12 bp): CATGTGATATGA Found at i:32777 original size:23 final size:26 Alignment explanation
Indices: 32720--32788 Score: 85 Period size: 24 Copynumber: 2.8 Consensus size: 26 32710 TATATATGTT ** 32720 CATGTGATAT--GATATGTGATATGA 1 CATGTGATATGAGATACATGATATGA 32744 CATGTGATATGAGA-ACATGATATGA 1 CATGTGATATGAGATACATGATATGA 32769 -A-GTGATATGAGATACATGAT 1 CATGTGATATGAGATACATGAT 32789 CACAAGAGAA Statistics Matches: 40, Mismatches: 2, Indels: 6 0.83 0.04 0.12 Matches are distributed among these distances: 23 11 0.28 24 18 0.45 25 9 0.22 26 2 0.05 ACGTcount: A:0.38, C:0.06, G:0.25, T:0.32 Consensus pattern (26 bp): CATGTGATATGAGATACATGATATGA Found at i:35229 original size:17 final size:17 Alignment explanation
Indices: 35204--35244 Score: 64 Period size: 17 Copynumber: 2.4 Consensus size: 17 35194 TTTATGATTT * 35204 TTTTATTAAATTTAAGGA 1 TTTT-TTAAATTTAAAGA 35222 TTTTTTAAATTTAAAGA 1 TTTTTTAAATTTAAAGA 35239 TTTTTT 1 TTTTTT 35245 TTGGGTTCAA Statistics Matches: 22, Mismatches: 1, Indels: 1 0.92 0.04 0.04 Matches are distributed among these distances: 17 18 0.82 18 4 0.18 ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59 Consensus pattern (17 bp): TTTTTTAAATTTAAAGA Found at i:35794 original size:9 final size:9 Alignment explanation
Indices: 35780--35805 Score: 52 Period size: 9 Copynumber: 2.9 Consensus size: 9 35770 GAAATCGGTT 35780 AATTAACCG 1 AATTAACCG 35789 AATTAACCG 1 AATTAACCG 35798 AATTAACC 1 AATTAACC 35806 TTTAAATATA Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 9 17 1.00 ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23 Consensus pattern (9 bp): AATTAACCG Found at i:36256 original size:21 final size:20 Alignment explanation
Indices: 36222--36266 Score: 63 Period size: 21 Copynumber: 2.2 Consensus size: 20 36212 ACCTTATAAA ** 36222 TATATTTAAATTTATTTTTT 1 TATATTTAAATTTATAATTT 36242 TATATTTATAATTTATAATTT 1 TATATTTA-AATTTATAATTT 36263 TATA 1 TATA 36267 ATTTCTTTAA Statistics Matches: 22, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 20 8 0.36 21 14 0.64 ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64 Consensus pattern (20 bp): TATATTTAAATTTATAATTT Found at i:36277 original size:24 final size:24 Alignment explanation
Indices: 36250--36303 Score: 72 Period size: 24 Copynumber: 2.2 Consensus size: 24 36240 TTTATATTTA 36250 TAATTTATAATTTTATAATTTCTT 1 TAATTTATAATTTTATAATTTCTT ** * * 36274 TAATTGGTTATTTTATAATTTTTT 1 TAATTTATAATTTTATAATTTCTT 36298 TAATTT 1 TAATTT 36304 TACTTAAAAT Statistics Matches: 25, Mismatches: 5, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 24 25 1.00 ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65 Consensus pattern (24 bp): TAATTTATAATTTTATAATTTCTT Found at i:55535 original size:14 final size:13 Alignment explanation
Indices: 55510--55542 Score: 50 Period size: 13 Copynumber: 2.5 Consensus size: 13 55500 CAAGATTGAG 55510 TATTATAGAGTAA 1 TATTATAGAGTAA 55523 TATTATGAGAGTAA 1 TATTAT-AGAGTAA 55537 T-TTATA 1 TATTATA 55543 AGGTGGGATT Statistics Matches: 19, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 12 1 0.05 13 10 0.53 14 8 0.42 ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42 Consensus pattern (13 bp): TATTATAGAGTAA Found at i:59926 original size:36 final size:34 Alignment explanation
Indices: 59872--59940 Score: 111 Period size: 36 Copynumber: 2.0 Consensus size: 34 59862 TGACTAAAAC 59872 AATTTAAAATACCACACATCCACAATTTATTTGG 1 AATTTAAAATACCACACATCCACAATTTATTTGG * 59906 AATTTAACAGATATCACACATCCACAATTTATTTG 1 AATTTAA-A-ATACCACACATCCACAATTTATTTG 59941 AGAAGAAATT Statistics Matches: 32, Mismatches: 1, Indels: 2 0.91 0.03 0.06 Matches are distributed among these distances: 34 7 0.22 35 1 0.03 36 24 0.75 ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33 Consensus pattern (34 bp): AATTTAAAATACCACACATCCACAATTTATTTGG Found at i:63702 original size:12 final size:12 Alignment explanation
Indices: 63685--63716 Score: 64 Period size: 12 Copynumber: 2.7 Consensus size: 12 63675 CAATATCTAA 63685 GACATGAAGATT 1 GACATGAAGATT 63697 GACATGAAGATT 1 GACATGAAGATT 63709 GACATGAA 1 GACATGAA 63717 ACTTCTACAA Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 20 1.00 ACGTcount: A:0.44, C:0.09, G:0.25, T:0.22 Consensus pattern (12 bp): GACATGAAGATT Found at i:66303 original size:26 final size:26 Alignment explanation
Indices: 66263--66312 Score: 66 Period size: 26 Copynumber: 1.9 Consensus size: 26 66253 TGACAGGTGA * * 66263 ATTTGAGGGGTTTTTAGT-TGCCTAAC 1 ATTTGAGGAGCTTTT-GTCTGCCTAAC 66289 ATTTGAGGAGCTTTTGTCTGCCTA 1 ATTTGAGGAGCTTTTGTCTGCCTA 66313 GTATAGATAG Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 25 2 0.10 26 19 0.90 ACGTcount: A:0.18, C:0.14, G:0.26, T:0.42 Consensus pattern (26 bp): ATTTGAGGAGCTTTTGTCTGCCTAAC Found at i:67496 original size:20 final size:22 Alignment explanation
Indices: 67441--67504 Score: 55 Period size: 20 Copynumber: 3.0 Consensus size: 22 67431 ATTTCTTAAT * 67441 ATTAAAAATAA-ATAAATATTA 1 ATTAAAATTAATATAAATATTA * ** 67462 ATAAAAATTTCTATAAA-A-TA 1 ATTAAAATTAATATAAATATTA 67482 ATTAAAATTAATATATAAT-TTA 1 ATTAAAATTAATATA-AATATTA 67504 A 1 A 67505 GAATATGATA Statistics Matches: 32, Mismatches: 7, Indels: 7 0.70 0.15 0.15 Matches are distributed among these distances: 20 14 0.44 21 10 0.31 22 8 0.25 ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38 Consensus pattern (22 bp): ATTAAAATTAATATAAATATTA Found at i:67618 original size:2 final size:2 Alignment explanation
Indices: 67611--67650 Score: 73 Period size: 2 Copynumber: 20.5 Consensus size: 2 67601 ATTTAAACAA 67611 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 67651 AAATAATAAT Statistics Matches: 37, Mismatches: 0, Indels: 2 0.95 0.00 0.05 Matches are distributed among these distances: 1 1 0.03 2 36 0.97 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:69061 original size:3 final size:3 Alignment explanation
Indices: 69055--69127 Score: 101 Period size: 3 Copynumber: 24.3 Consensus size: 3 69045 TTTTTTTATT * * * * * 69055 TAA TAA TAA TAA TAA TAA TCA TCA TCA TCA TAA TCA TAA TAA TAA TAA 1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA 69103 TAA TAA TAA TAA TAA TAA TAA TAA T 1 TAA TAA TAA TAA TAA TAA TAA TAA T 69128 CCAAATGGAA Statistics Matches: 66, Mismatches: 4, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 3 66 1.00 ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34 Consensus pattern (3 bp): TAA Found at i:69510 original size:19 final size:17 Alignment explanation
Indices: 69471--69504 Score: 68 Period size: 17 Copynumber: 2.0 Consensus size: 17 69461 GTTGAACAAG 69471 TTCTTCTCATTATGAAC 1 TTCTTCTCATTATGAAC 69488 TTCTTCTCATTATGAAC 1 TTCTTCTCATTATGAAC 69505 ACTTCTGAAA Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 17 1.00 ACGTcount: A:0.24, C:0.24, G:0.06, T:0.47 Consensus pattern (17 bp): TTCTTCTCATTATGAAC Found at i:69682 original size:124 final size:121 Alignment explanation
Indices: 69488--69868 Score: 427 Period size: 124 Copynumber: 3.2 Consensus size: 121 69478 CATTATGAAC * 69488 TTCTTCTCATTATGAACAC-T-TCT-GAAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAC 1 TTCTTCTCATTATGAACTCTTCTCTGGAAAATG-T-ATGCTGATCTATCTCCTTC--TGATAGAC * 69550 TC-ATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAG 62 TCGA-GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAG * 69610 TTCTTCTCATTATGAACTCTTCTCTGGAAAAGTGTATGCTGATCTATCTCCTTCTACGATAGAGT 1 TTCTTCTCATTATGAACTCTTCTCTGGAAAA-TGTATGCTGATCTATCTCCTTCT--GATAGACT * * 69675 CGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTCTTCAGATAAG 63 CGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAG * ** * 69734 TTCTTCTCATTATGAA--CTTCTTTGGAGAAAT-TGATGC--ATC-A------AGTGAT-GAATT 1 TTCTTCTCATTATGAACTCTTCTCTGGA-AAATGT-ATGCTGATCTATCTCCTTCTGATAG-ACT * * * 69786 CGAGCCAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAG 63 CGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAG 69846 TTCTTCTCATTATGAACTCTTCT 1 TTCTTCTCATTATGAACTCTTCT 69869 GGAAATGTTG Statistics Matches: 232, Mismatches: 14, Indels: 34 0.83 0.05 0.12 Matches are distributed among these distances: 110 1 0.00 111 48 0.21 112 27 0.12 113 1 0.00 114 5 0.02 119 1 0.00 120 3 0.01 121 1 0.00 122 33 0.14 123 4 0.02 124 99 0.43 125 7 0.03 126 2 0.01 ACGTcount: A:0.26, C:0.21, G:0.15, T:0.39 Consensus pattern (121 bp): TTCTTCTCATTATGAACTCTTCTCTGGAAAATGTATGCTGATCTATCTCCTTCTGATAGACTCGA GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAG Found at i:72222 original size:18 final size:18 Alignment explanation
Indices: 72185--72222 Score: 67 Period size: 18 Copynumber: 2.1 Consensus size: 18 72175 TATGTGAAAG * 72185 AATAAATTGAATTTCGAA 1 AATAAATTGAATTTCAAA 72203 AATAAATTGAATTTCAAA 1 AATAAATTGAATTTCAAA 72221 AA 1 AA 72223 GATAATCTTG Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 18 19 1.00 ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32 Consensus pattern (18 bp): AATAAATTGAATTTCAAA Done.