Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: VEPZ01003450.1 Hibiscus syriacus cultivar Beakdansim tig00007287_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: 40468 ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34 Found at i:3607 original size:20 final size:22 Alignment explanation
Indices: 3569--3608 Score: 66 Period size: 20 Copynumber: 1.9 Consensus size: 22 3559 ATTTTGTAGA 3569 AAAATCATCCCCAAACGGCTTC 1 AAAATCATCCCCAAACGGCTTC 3591 AAAA-CATCCCC-AACGGCT 1 AAAATCATCCCCAAACGGCT 3609 AGATATGACT Statistics Matches: 18, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 20 7 0.39 21 7 0.39 22 4 0.22 ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15 Consensus pattern (22 bp): AAAATCATCCCCAAACGGCTTC Found at i:6446 original size:17 final size:17 Alignment explanation
Indices: 6424--6479 Score: 67 Period size: 17 Copynumber: 3.1 Consensus size: 17 6414 CAACAATTGG * 6424 TAACAATTGGTATCTTT 1 TAACAATTGATATCTTT 6441 TAACAATTGATATCATTTTGT 1 TAACAATTGATATC---TT-T 6462 TAACAATTGATATCTTT 1 TAACAATTGATATCTTT 6479 T 1 T 6480 TCATTAAACA Statistics Matches: 34, Mismatches: 1, Indels: 8 0.79 0.02 0.19 Matches are distributed among these distances: 17 15 0.44 18 2 0.06 20 2 0.06 21 15 0.44 ACGTcount: A:0.32, C:0.11, G:0.09, T:0.48 Consensus pattern (17 bp): TAACAATTGATATCTTT Found at i:6464 original size:21 final size:21 Alignment explanation
Indices: 6440--6480 Score: 73 Period size: 21 Copynumber: 2.0 Consensus size: 21 6430 TTGGTATCTT 6440 TTAACAATTGATATCATTTTG 1 TTAACAATTGATATCATTTTG * 6461 TTAACAATTGATATCTTTTT 1 TTAACAATTGATATCATTTT 6481 CATTAAACAT Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 21 19 1.00 ACGTcount: A:0.32, C:0.10, G:0.07, T:0.51 Consensus pattern (21 bp): TTAACAATTGATATCATTTTG Found at i:6895 original size:21 final size:21 Alignment explanation
Indices: 6869--6909 Score: 73 Period size: 21 Copynumber: 2.0 Consensus size: 21 6859 TTTGAATTTA 6869 ATGAAGGAGTACCGATACCCT 1 ATGAAGGAGTACCGATACCCT * 6890 ATGAAGGGGTACCGATACCC 1 ATGAAGGAGTACCGATACCC 6910 CCTGTTATGG Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 21 19 1.00 ACGTcount: A:0.32, C:0.24, G:0.27, T:0.17 Consensus pattern (21 bp): ATGAAGGAGTACCGATACCCT Found at i:7568 original size:45 final size:45 Alignment explanation
Indices: 7497--7666 Score: 252 Period size: 45 Copynumber: 3.8 Consensus size: 45 7487 AATCCGAACA ** * 7497 GCATCCTTTCATGATAATAATACACCCATATGCATTTCAATTATG 1 GCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATG * * * 7542 GCATCATTTAATGCCAATAATGCACCCATATGCATTTAAATTATG 1 GCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATG * 7587 ACATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATG 1 GCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATG * * 7632 GCATCCTTTCATGCC-TTAACGCACCCATATGCATT 1 GCATCCTTTCATGCCAATAATGCACCCATATGCATT 7667 ATTTTAATCA Statistics Matches: 112, Mismatches: 13, Indels: 1 0.89 0.10 0.01 Matches are distributed among these distances: 44 18 0.16 45 94 0.84 ACGTcount: A:0.31, C:0.25, G:0.10, T:0.34 Consensus pattern (45 bp): GCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATG Found at i:8123 original size:21 final size:20 Alignment explanation
Indices: 8080--8135 Score: 58 Period size: 21 Copynumber: 2.7 Consensus size: 20 8070 TGACTCAATA * 8080 GTATCGATACCCCTACCATG 1 GTATCGATACCCATACCATG * * 8100 GTATCGATACACTATACTATG 1 GTATCGATAC-CCATACCATG * 8121 GTACCGATACTCCAT 1 GTATCGATAC-CCAT 8136 CACAGTACCG Statistics Matches: 29, Mismatches: 6, Indels: 1 0.81 0.17 0.03 Matches are distributed among these distances: 20 10 0.34 21 19 0.66 ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29 Consensus pattern (20 bp): GTATCGATACCCATACCATG Found at i:10253 original size:28 final size:28 Alignment explanation
Indices: 10204--10284 Score: 126 Period size: 28 Copynumber: 2.9 Consensus size: 28 10194 AGAGTCGAGG * 10204 GTTCTACGTGGTCCTTTAGGACATATGT 1 GTTCTATGTGGTCCTTTAGGACATATGT * * 10232 GTTTTATGTGGTCCTTTGGGACATATGT 1 GTTCTATGTGGTCCTTTAGGACATATGT * 10260 GTTCTATGTGGTCCTTCAGGACATA 1 GTTCTATGTGGTCCTTTAGGACATA 10285 GTGGTCCTTC Statistics Matches: 47, Mismatches: 6, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 28 47 1.00 ACGTcount: A:0.17, C:0.16, G:0.26, T:0.41 Consensus pattern (28 bp): GTTCTATGTGGTCCTTTAGGACATATGT Found at i:10526 original size:15 final size:15 Alignment explanation
Indices: 10506--10535 Score: 51 Period size: 15 Copynumber: 2.0 Consensus size: 15 10496 ATAATCATAT 10506 GATAATAAGAATGAG 1 GATAATAAGAATGAG * 10521 GATAATATGAATGAG 1 GATAATAAGAATGAG 10536 TGTGTATGTG Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.50, C:0.00, G:0.27, T:0.23 Consensus pattern (15 bp): GATAATAAGAATGAG Found at i:14695 original size:28 final size:28 Alignment explanation
Indices: 14654--14734 Score: 126 Period size: 28 Copynumber: 2.9 Consensus size: 28 14644 AGAGTCGAGG * * * 14654 GTTCTACGTAGTCCTTCGGGACATATGT 1 GTTCTATGTGGTCCTTCGGGACATACGT * 14682 GTTCTATGTGGTCCTTTGGGACATACGT 1 GTTCTATGTGGTCCTTCGGGACATACGT 14710 GTTCTATGTGGTCCTTCGGGACATA 1 GTTCTATGTGGTCCTTCGGGACATA 14735 GTGGTCCTTT Statistics Matches: 48, Mismatches: 5, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 28 48 1.00 ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37 Consensus pattern (28 bp): GTTCTATGTGGTCCTTCGGGACATACGT Found at i:15261 original size:14 final size:15 Alignment explanation
Indices: 15242--15280 Score: 62 Period size: 14 Copynumber: 2.6 Consensus size: 15 15232 GTTACATGAG 15242 ATATATACAAATATAT 1 ATATATAC-AATATAT 15258 ATATATACAA-ATAT 1 ATATATACAATATAT 15272 ATATATACA 1 ATATATACA 15281 TGCATTTGTT Statistics Matches: 23, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 14 13 0.57 15 2 0.09 16 8 0.35 ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36 Consensus pattern (15 bp): ATATATACAATATAT Found at i:15263 original size:16 final size:16 Alignment explanation
Indices: 15242--15278 Score: 74 Period size: 16 Copynumber: 2.3 Consensus size: 16 15232 GTTACATGAG 15242 ATATATACAAATATAT 1 ATATATACAAATATAT 15258 ATATATACAAATATAT 1 ATATATACAAATATAT 15274 ATATA 1 ATATA 15279 CATGCATTTG Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 21 1.00 ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38 Consensus pattern (16 bp): ATATATACAAATATAT Found at i:16945 original size:24 final size:24 Alignment explanation
Indices: 16917--16963 Score: 69 Period size: 24 Copynumber: 2.0 Consensus size: 24 16907 TTTTAATTTA * 16917 AAATATACAAA-TATAGAAAAAATT 1 AAATATAAAAATTATA-AAAAAATT 16941 AAATATAAAAATTATAAAAAAAT 1 AAATATAAAAATTATAAAAAAAT 16964 AATTATTAAA Statistics Matches: 21, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 24 17 0.81 25 4 0.19 ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26 Consensus pattern (24 bp): AAATATAAAAATTATAAAAAAATT Found at i:16980 original size:2 final size:2 Alignment explanation
Indices: 16975--17005 Score: 62 Period size: 2 Copynumber: 15.5 Consensus size: 2 16965 ATTATTAAAT 16975 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 17006 CATAGTGATT Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 29 1.00 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (2 bp): TA Found at i:16980 original size:24 final size:26 Alignment explanation
Indices: 16927--16980 Score: 60 Period size: 23 Copynumber: 2.2 Consensus size: 26 16917 AAATATACAA 16927 ATATAGAAAAAATTAAATATAAAAAT 1 ATATAGAAAAAATTAAATATAAAAAT * * * 16953 -TATA-AAAAAA-TAATTATTAAATT 1 ATATAGAAAAAATTAAATATAAAAAT 16976 ATATA 1 ATATA 16981 TATATATATA Statistics Matches: 24, Mismatches: 3, Indels: 4 0.77 0.10 0.13 Matches are distributed among these distances: 23 10 0.42 24 10 0.42 25 4 0.17 ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33 Consensus pattern (26 bp): ATATAGAAAAAATTAAATATAAAAAT Found at i:17616 original size:22 final size:24 Alignment explanation
Indices: 17591--17635 Score: 76 Period size: 24 Copynumber: 2.0 Consensus size: 24 17581 TTAATTTTTA 17591 TTTTTG-AT-ATTTTATATTTAAC 1 TTTTTGAATAATTTTATATTTAAC 17613 TTTTTGAATAATTTTATATTTAA 1 TTTTTGAATAATTTTATATTTAA 17636 ATTAGAAATA Statistics Matches: 21, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 22 6 0.29 23 2 0.10 24 13 0.62 ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62 Consensus pattern (24 bp): TTTTTGAATAATTTTATATTTAAC Found at i:24611 original size:12 final size:12 Alignment explanation
Indices: 24594--24618 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 24584 CGAAAATTAG 24594 AAAATTTAAATT 1 AAAATTTAAATT 24606 AAAATTTAAATT 1 AAAATTTAAATT 24618 A 1 A 24619 CTCGATTCGA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 13 1.00 ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40 Consensus pattern (12 bp): AAAATTTAAATT Found at i:26117 original size:6 final size:6 Alignment explanation
Indices: 26106--26141 Score: 54 Period size: 6 Copynumber: 5.8 Consensus size: 6 26096 ATAAACGAAT * 26106 AATAAA AATAAA AATAAA AACAAA TAATAAA AATAA 1 AATAAA AATAAA AATAAA AATAAA -AATAAA AATAA 26142 TTATATATAT Statistics Matches: 27, Mismatches: 2, Indels: 2 0.87 0.06 0.06 Matches are distributed among these distances: 6 22 0.81 7 5 0.19 ACGTcount: A:0.81, C:0.03, G:0.00, T:0.17 Consensus pattern (6 bp): AATAAA Found at i:26131 original size:25 final size:27 Alignment explanation
Indices: 26085--26141 Score: 84 Period size: 25 Copynumber: 2.2 Consensus size: 27 26075 GAAAAAACAT * 26085 AAAT-AAAATAAATAAACGAATAATAA 1 AAATAAAAATAAATAAACAAATAATAA 26111 AAATAAAAAT-AA-AAACAAATAATAA 1 AAATAAAAATAAATAAACAAATAATAA 26136 AAATAA 1 AAATAA 26142 TTATATATAT Statistics Matches: 29, Mismatches: 1, Indels: 3 0.88 0.03 0.09 Matches are distributed among these distances: 25 18 0.62 26 6 0.21 27 5 0.17 ACGTcount: A:0.77, C:0.04, G:0.02, T:0.18 Consensus pattern (27 bp): AAATAAAAATAAATAAACAAATAATAA Found at i:27092 original size:27 final size:27 Alignment explanation
Indices: 27062--27114 Score: 72 Period size: 27 Copynumber: 2.0 Consensus size: 27 27052 AATGATTTAA * 27062 AAATAATATATTAAAT-TTATAAATATG 1 AAATAATA-AATAAATATTATAAATATG * 27089 AAATAATAAATAAATATTATATATAT 1 AAATAATAAATAAATATTATAAATAT 27115 ATATATATAT Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 26 6 0.26 27 17 0.74 ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40 Consensus pattern (27 bp): AAATAATAAATAAATATTATAAATATG Found at i:27105 original size:35 final size:36 Alignment explanation
Indices: 27028--27105 Score: 83 Period size: 35 Copynumber: 2.2 Consensus size: 36 27018 CTTAATATTG ** 27028 ATAAATATATTAAAATATGATTAAAATGATTTAAAA 1 ATAAATATATTAAAATATGATTAAAATGAAATAAAA * 27064 AT-AATATATT-AAAT-TTA-TAAATATGAAATAATAA 1 ATAAATATATTAAAATATGATTAAA-ATGAAATAA-AA 27098 ATAAATAT 1 ATAAATAT 27106 TATATATATA Statistics Matches: 36, Mismatches: 3, Indels: 7 0.78 0.07 0.15 Matches are distributed among these distances: 32 4 0.11 33 9 0.25 34 8 0.22 35 13 0.36 36 2 0.06 ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37 Consensus pattern (36 bp): ATAAATATATTAAAATATGATTAAAATGAAATAAAA Found at i:27461 original size:66 final size:65 Alignment explanation
Indices: 27386--27512 Score: 152 Period size: 66 Copynumber: 1.9 Consensus size: 65 27376 ATATTAATAT * * 27386 GGGACTAAAATAAATTTTAAT-AAAGTTATAAGGGATTAATTATA-ATA-TTTACCTAAATTATT 1 GGGACTAAAATAAATATTAATAAAAG-TATAA-GGACTAA--ATACATATTTTACCTAAATTATT 27448 AGTC 62 AGTC * * * 27452 GGGATTAAAATAAATATTATTAAAAGTGTAAGGACTAAATACATATTTTACCTAAATTATT 1 GGGACTAAAATAAATATTAATAAAAGTATAAGGACTAAATACATATTTTACCTAAATTATT 27513 TATATAAATA Statistics Matches: 53, Mismatches: 5, Indels: 7 0.82 0.08 0.11 Matches are distributed among these distances: 63 3 0.06 64 3 0.06 65 21 0.40 66 22 0.42 67 4 0.08 ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37 Consensus pattern (65 bp): GGGACTAAAATAAATATTAATAAAAGTATAAGGACTAAATACATATTTTACCTAAATTATTAGTC Found at i:29175 original size:114 final size:114 Alignment explanation
Indices: 28858--29418 Score: 827 Period size: 114 Copynumber: 5.0 Consensus size: 114 28848 TGATCAAGCT * * * 28858 AAGGTTGAACAAGTTATTCTCATTATGAACTTCTTC-TCATTCTTCAGATGAGTTCTTCTCATTA 1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA * * * * 28922 TGAACTCTAC-CTGGCAAT--GGTGATCCATCGAGTGATGAATTCAAGAAA 66 TGAACT-TCCTCTGG-AATCAGTTGATCCATCGAATGATGAATTCAAGCAA * 28970 AAGGTTTAAACAAGTTCTTCTCATTATG-ACTTCTTCTTCC-TCTCCAGATGAGTTCTTC-CTAT 1 AAGG-TTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC-AT 29032 TATGAACTTCCTCTGGAATCAGTTGATCCATCGAATGATGAATTCAAGCAA 64 TATGAACTTCCTCTGGAATCAGTTGATCCATCGAATGATGAATTCAAGCAA * 29083 AAGGTTAAACAAGTTTTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA 1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA * * 29148 TGAACTTCCTCTAGAATCAGTTGATCCATCGAATGATGAATTCACGCAA 66 TGAACTTCCTCTGGAATCAGTTGATCCATCGAATGATGAATTCAAGCAA * * * 29197 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAAATGAGTTGTTCTCATTA 1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA * * 29262 GGAACTTCCTCTGGAATCAGTTGATTCATCGAATGATGAATTCAAGCAA 66 TGAACTTCCTCTGGAATCAGTTGATCCATCGAATGATGAATTCAAGCAA * * 29311 AAGGTTAAACAAGTTCTTCTCATGATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCACATTA 1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA * * 29376 TGAAC-ACTTCTGGAA--ATGTTGATCCATCGAATGATGAATTCAA 66 TGAACTTCCTCTGGAATCA-GTTGATCCATCGAATGATGAATTCAA 29419 ATCTTTTCTA Statistics Matches: 410, Mismatches: 29, Indels: 20 0.89 0.06 0.04 Matches are distributed among these distances: 111 7 0.02 112 90 0.22 113 74 0.18 114 238 0.58 115 1 0.00 ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37 Consensus pattern (114 bp): AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA TGAACTTCCTCTGGAATCAGTTGATCCATCGAATGATGAATTCAAGCAA Found at i:30932 original size:16 final size:15 Alignment explanation
Indices: 30911--30945 Score: 52 Period size: 15 Copynumber: 2.3 Consensus size: 15 30901 ATATATATAT 30911 TTTTCATCATTTTTCA 1 TTTTCAT-ATTTTTCA * 30927 TTTTCATTTTTTTCA 1 TTTTCATATTTTTCA 30942 TTTT 1 TTTT 30946 TTTCTTCATT Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 15 11 0.61 16 7 0.39 ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71 Consensus pattern (15 bp): TTTTCATATTTTTCA Found at i:30946 original size:16 final size:17 Alignment explanation
Indices: 30909--30946 Score: 53 Period size: 16 Copynumber: 2.4 Consensus size: 17 30899 ATATATATAT 30909 ATTTTTCATCATTTTTC 1 ATTTTTCATCATTTTTC * 30926 A-TTTTCAT-TTTTTTC 1 ATTTTTCATCATTTTTC 30941 ATTTTT 1 ATTTTT 30947 TTCTTCATTT Statistics Matches: 19, Mismatches: 1, Indels: 3 0.83 0.04 0.13 Matches are distributed among these distances: 15 7 0.37 16 11 0.58 17 1 0.05 ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71 Consensus pattern (17 bp): ATTTTTCATCATTTTTC Found at i:30948 original size:12 final size:12 Alignment explanation
Indices: 30933--30966 Score: 50 Period size: 12 Copynumber: 2.8 Consensus size: 12 30923 TTCATTTTCA 30933 TTTTTTTCATTT 1 TTTTTTTCATTT * 30945 TTTTCTTCATTT 1 TTTTTTTCATTT 30957 TTTTTCTTCA 1 TTTTT-TTCA 30967 AGCATAATAT Statistics Matches: 19, Mismatches: 2, Indels: 1 0.86 0.09 0.05 Matches are distributed among these distances: 12 15 0.79 13 4 0.21 ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76 Consensus pattern (12 bp): TTTTTTTCATTT Found at i:30960 original size:13 final size:13 Alignment explanation
Indices: 30923--30966 Score: 54 Period size: 13 Copynumber: 3.3 Consensus size: 13 30913 TTCATCATTT * 30923 TTCATTTTCATTTTT 1 TTCATTTT--TTTTC 30938 TTCA-TTTTTTTC 1 TTCATTTTTTTTC 30950 TTCATTTTTTTTC 1 TTCATTTTTTTTC 30963 TTCA 1 TTCA 30967 AGCATAATAT Statistics Matches: 27, Mismatches: 1, Indels: 4 0.84 0.03 0.12 Matches are distributed among these distances: 12 8 0.30 13 12 0.44 14 3 0.11 15 4 0.15 ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73 Consensus pattern (13 bp): TTCATTTTTTTTC Done.