Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: VEPZ01006240.1 Hibiscus syriacus cultivar Beakdansim tig00014868_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: 79291 ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34 Found at i:1805 original size:20 final size:20 Alignment explanation
Indices: 1776--1822 Score: 60 Period size: 20 Copynumber: 2.4 Consensus size: 20 1766 ATCATCAAAC 1776 TTAAAATTATA-TATATATAT 1 TTAAAATTATAGTAT-TATAT * 1796 TTAAATTTATAGTATTATAT 1 TTAAAATTATAGTATTATAT * 1816 CTAAAAT 1 TTAAAAT 1823 ATTTTTATCT Statistics Matches: 23, Mismatches: 3, Indels: 2 0.82 0.11 0.07 Matches are distributed among these distances: 20 20 0.87 21 3 0.13 ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49 Consensus pattern (20 bp): TTAAAATTATAGTATTATAT Found at i:11107 original size:19 final size:19 Alignment explanation
Indices: 11083--11128 Score: 83 Period size: 19 Copynumber: 2.4 Consensus size: 19 11073 AAACCCCAAA 11083 TTCCTTTTCAATCTCGAAT 1 TTCCTTTTCAATCTCGAAT * 11102 TTCCTTTTCGATCTCGAAT 1 TTCCTTTTCAATCTCGAAT 11121 TTCCTTTT 1 TTCCTTTT 11129 TCGCTTCTCT Statistics Matches: 26, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 19 26 1.00 ACGTcount: A:0.15, C:0.26, G:0.07, T:0.52 Consensus pattern (19 bp): TTCCTTTTCAATCTCGAAT Found at i:16557 original size:32 final size:32 Alignment explanation
Indices: 16475--16596 Score: 108 Period size: 32 Copynumber: 3.8 Consensus size: 32 16465 TAAGGGAAAG * * * 16475 CCTTGGGGCCTTAGAGCCTACTCAAGGAATG-- 1 CCTTGGGGACTGAGAGCCTACCCAAGGAA-GCA * * 16506 CCTT-AGGACCTCAGAGCCTACCCAAGGAAGCA 1 CCTTGGGGA-CTGAGAGCCTACCCAAGGAAGCA * * 16538 CCTTGGGGACTGAGAGCCTACCCAATGAATCA 1 CCTTGGGGACTGAGAGCCTACCCAAGGAAGCA * * 16570 CAC-TGGGGCCTGAGAACCTACCCAAGG 1 C-CTTGGGGACTGAGAGCCTACCCAAGG 16597 GAACATCACG Statistics Matches: 75, Mismatches: 11, Indels: 9 0.79 0.12 0.09 Matches are distributed among these distances: 30 3 0.04 31 22 0.29 32 46 0.61 33 4 0.05 ACGTcount: A:0.27, C:0.30, G:0.26, T:0.16 Consensus pattern (32 bp): CCTTGGGGACTGAGAGCCTACCCAAGGAAGCA Found at i:23707 original size:29 final size:29 Alignment explanation
Indices: 23620--23708 Score: 81 Period size: 29 Copynumber: 3.0 Consensus size: 29 23610 TAAAATATAT 23620 AACTTTTAAAAATTACAATTTTAGGTC-CTA 1 AACTTTTAAAAATTAC-ATTTTA-GTCACTA ** * * * 23650 AACTTTTTAAAGTTTATACTTTAGCCACTA 1 AAC-TTTTAAAAATTACATTTTAGTCACTA * * 23680 AACTTTCAAAACTTACATTTTAGTCACTA 1 AACTTTTAAAAATTACATTTTAGTCACTA 23709 GTCAAAATTT Statistics Matches: 46, Mismatches: 11, Indels: 5 0.74 0.18 0.08 Matches are distributed among these distances: 29 22 0.48 30 14 0.30 31 10 0.22 ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40 Consensus pattern (29 bp): AACTTTTAAAAATTACATTTTAGTCACTA Found at i:25017 original size:15 final size:15 Alignment explanation
Indices: 24999--25028 Score: 60 Period size: 15 Copynumber: 2.0 Consensus size: 15 24989 AATGAGCTTT 24999 GGTAAGATGATCTTC 1 GGTAAGATGATCTTC 25014 GGTAAGATGATCTTC 1 GGTAAGATGATCTTC 25029 CTTCAGTTCT Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33 Consensus pattern (15 bp): GGTAAGATGATCTTC Found at i:30557 original size:65 final size:65 Alignment explanation
Indices: 30453--30759 Score: 373 Period size: 65 Copynumber: 4.7 Consensus size: 65 30443 TATTGGGCCC * * * ** 30453 TCACTCATATGACTCGTGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATAATGGACAGA 1 TCACTCATATGACTCATGTACCTTTGTGGTGCATAAGGTGGAGTGATAATTGAATACTACACAGA * * * * 30518 TCACTCATAAGACTCATGTACCTTTGTAGTGCATAAGGTGGAGTGATAATTAAATACTACACATA 1 TCACTCATATGACTCATGTACCTTTGTGGTGCATAAGGTGGAGTGATAATTGAATACTACACAGA ** * * * 30583 TCACTCATATGACTCATGTATTTTTGTAGTGCATGAGGTGGAGTGATAATTGAATACTGCACAGA 1 TCACTCATATGACTCATGTACCTTTGTGGTGCATAAGGTGGAGTGATAATTGAATACTACACAGA * ** * ** 30648 CCACTCATATGACTCATGTACCTTTGTGGTGCATTGGGTGGAGTGATAATTGAATACTATATTGA 1 TCACTCATATGACTCATGTACCTTTGTGGTGCATAAGGTGGAGTGATAATTGAATACTACACAGA * * ** 30713 TCACTTA-ATGAGACTTATGTACCTTTGTGGTATATAAGGTGGAGTGA 1 TCACTCATAT--GACTCATGTACCTTTGTGGTGCATAAGGTGGAGTGA 30760 CTATATGATA Statistics Matches: 207, Mismatches: 33, Indels: 3 0.85 0.14 0.01 Matches are distributed among these distances: 64 2 0.01 65 174 0.84 66 31 0.15 ACGTcount: A:0.29, C:0.14, G:0.23, T:0.33 Consensus pattern (65 bp): TCACTCATATGACTCATGTACCTTTGTGGTGCATAAGGTGGAGTGATAATTGAATACTACACAGA Found at i:31028 original size:16 final size:18 Alignment explanation
Indices: 30979--31057 Score: 101 Period size: 18 Copynumber: 4.5 Consensus size: 18 30969 TAAGATATAA 30979 AACAATATAAGAAAAAGG 1 AACAATATAAGAAAAAGG * 30997 AACAATATAAGAAAAATG 1 AACAATATAAGAAAAAGG * 31015 AACAATA-AAGAAAAGAGA 1 AACAATATAAGAAAA-AGG 31033 AACAATAT-A-AAAAAGG 1 AACAATATAAGAAAAAGG * 31049 AACATTATA 1 AACAATATA 31058 GGAAGAAATA Statistics Matches: 53, Mismatches: 5, Indels: 7 0.82 0.08 0.11 Matches are distributed among these distances: 16 9 0.17 17 11 0.21 18 33 0.62 ACGTcount: A:0.67, C:0.06, G:0.13, T:0.14 Consensus pattern (18 bp): AACAATATAAGAAAAAGG Found at i:36251 original size:2 final size:2 Alignment explanation
Indices: 36244--36271 Score: 56 Period size: 2 Copynumber: 14.0 Consensus size: 2 36234 TATTAAAGTC 36244 TA TA TA TA TA TA TA TA TA TA TA TA TA TA 1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA 36272 GCTATGAATT Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 26 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): TA Found at i:40900 original size:31 final size:31 Alignment explanation
Indices: 40858--40921 Score: 119 Period size: 31 Copynumber: 2.1 Consensus size: 31 40848 TTTTATTATT 40858 TCGGGTCGGGTGAAATCTTGTTTTGGTCGGG 1 TCGGGTCGGGTGAAATCTTGTTTTGGTCGGG * 40889 TCGGGTTGGGTGAAATCTTGTTTTGGTCGGG 1 TCGGGTCGGGTGAAATCTTGTTTTGGTCGGG 40920 TC 1 TC 40922 AGGTGGACCA Statistics Matches: 32, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 31 32 1.00 ACGTcount: A:0.09, C:0.12, G:0.41, T:0.38 Consensus pattern (31 bp): TCGGGTCGGGTGAAATCTTGTTTTGGTCGGG Found at i:61044 original size:32 final size:32 Alignment explanation
Indices: 61003--61079 Score: 91 Period size: 32 Copynumber: 2.4 Consensus size: 32 60993 AATTTGGTTT * 61003 GGGTTACTTTTGGATAGAGTTAAACTCAGTTC 1 GGGTTACTTTCGGATAGAGTTAAACTCAGTTC * * * * * 61035 GGGTTACTTTCGGTTTGAGTTATATTCTGTTC 1 GGGTTACTTTCGGATAGAGTTAAACTCAGTTC * 61067 GGGTTGCTTTCGG 1 GGGTTACTTTCGG 61080 CTCGGGCTAA Statistics Matches: 38, Mismatches: 7, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 32 38 1.00 ACGTcount: A:0.16, C:0.13, G:0.29, T:0.43 Consensus pattern (32 bp): GGGTTACTTTCGGATAGAGTTAAACTCAGTTC Found at i:63659 original size:20 final size:21 Alignment explanation
Indices: 63624--63674 Score: 86 Period size: 20 Copynumber: 2.5 Consensus size: 21 63614 TGACAGATAA 63624 ACTGTCACGTCAGTATCATGG 1 ACTGTCACGTCAGTATCATGG 63645 ACTGTCACG-CAGTATCATGG 1 ACTGTCACGTCAGTATCATGG * 63665 ACTGCCACGT 1 ACTGTCACGT 63675 TAGTGCCGTG Statistics Matches: 28, Mismatches: 1, Indels: 2 0.90 0.03 0.06 Matches are distributed among these distances: 20 19 0.68 21 9 0.32 ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25 Consensus pattern (21 bp): ACTGTCACGTCAGTATCATGG Found at i:64320 original size:43 final size:43 Alignment explanation
Indices: 64245--64479 Score: 135 Period size: 43 Copynumber: 5.4 Consensus size: 43 64235 TAATTTTAGT * ** * * * 64245 TTTTTATTTTTATAATTGATGTCCATAATTTTTGT-AATCCTAC 1 TTTTTATCTTTATAATTGA-AACCCTTATTTTTTTCAATCCTAC * 64288 TTTTTATCTTTATAATTGAAACCCTTATTTTTTTTTCAAACC--C 1 TTTTTATCTTTATAATTGAAACCCTTA--TTTTTTTCAATCCTAC * * ** 64331 GTTTTTTTACATTTATAATTGATAA-TCTTAAGTTTTTCAATCCTAC 1 -TTTTTAT-C-TTTATAATTGA-AACCCTTATTTTTTTCAATCCTAC * * * 64377 TTTGTACCTTTATAATTG-AACTCCTGATTTTTTTCAAT-CTCAC 1 TTTTTATCTTTATAATTGAAAC-CCTTATTTTTTTCAATCCT-AC * * * * * * 64420 TTTTTACCTTTATAATTGAAGCCCCTAATTTTTTCTAT-CTCC 1 TTTTTATCTTTATAATTGAAACCCTTATTTTTTTCAATCCTAC 64462 TTTTT-TACTTCTATAATT 1 TTTTTAT-CTT-TATAATT 64480 TAGGCCCCTA Statistics Matches: 150, Mismatches: 27, Indels: 30 0.72 0.13 0.14 Matches are distributed among these distances: 41 2 0.01 42 15 0.10 43 81 0.54 44 25 0.17 45 9 0.06 46 16 0.11 47 2 0.01 ACGTcount: A:0.25, C:0.17, G:0.05, T:0.53 Consensus pattern (43 bp): TTTTTATCTTTATAATTGAAACCCTTATTTTTTTCAATCCTAC Found at i:64346 original size:89 final size:89 Alignment explanation
Indices: 64244--64410 Score: 214 Period size: 89 Copynumber: 1.9 Consensus size: 89 64234 TTAATTTTAG ** * * * * 64244 TTTTTTATTTTTATAATTGAT-GTCCATAA-TTTTTGTAATCCTACTTTTTATCTTTATAATTGA 1 TTTTTTACATTTATAATTGATAAT-CATAAGTTTTT-CAATCCTACTTTGTACCTTTATAATTG- * 64307 AAC-CCTTATTTTTTTTTCAAACCCGT 63 AACTCCTGATTTTTTTTTCAAACCCGT * 64333 TTTTTTACATTTATAATTGATAATCTTAAGTTTTTCAATCCTACTTTGTACCTTTATAATTGAAC 1 TTTTTTACATTTATAATTGATAATCATAAGTTTTTCAATCCTACTTTGTACCTTTATAATTGAAC 64398 TCCTGATTTTTTT 66 TCCTGATTTTTTT 64411 CAATCTCACT Statistics Matches: 67, Mismatches: 8, Indels: 6 0.83 0.10 0.07 Matches are distributed among these distances: 88 3 0.04 89 58 0.87 90 6 0.09 ACGTcount: A:0.25, C:0.14, G:0.06, T:0.54 Consensus pattern (89 bp): TTTTTTACATTTATAATTGATAATCATAAGTTTTTCAATCCTACTTTGTACCTTTATAATTGAAC TCCTGATTTTTTTTTCAAACCCGT Found at i:64487 original size:43 final size:43 Alignment explanation
Indices: 64363--64537 Score: 173 Period size: 43 Copynumber: 4.1 Consensus size: 43 64353 TAATCTTAAG * * * * * 64363 TTTTTCAATCCTAC-TTTGTACCTTTATAATTGA-ACTCCTGATT 1 TTTTTCAAT-CTCCTTTTTTACCTTTATAATTGAGGCCCCT-AAT * 64406 TTTTTCAATCTCAC-TTTTTACCTTTATAATTGAAGCCCCTAAT 1 TTTTTCAATCTC-CTTTTTTACCTTTATAATTGAGGCCCCTAAT * * 64449 TTTTTCTATCTCCTTTTTTA-CTTCTATAATTTAGGCCCCTAA- 1 TTTTTCAATCTCCTTTTTTACCTT-TATAATTGAGGCCCCTAAT * * * 64491 -TTTTCAATCTCGTTTATTACCTTTAAAATTGAGGCCCCTAAT 1 TTTTTCAATCTCCTTTTTTACCTTTATAATTGAGGCCCCTAAT 64533 TTTTT 1 TTTTT 64538 TTAATCTAAC Statistics Matches: 112, Mismatches: 13, Indels: 14 0.81 0.09 0.10 Matches are distributed among these distances: 41 32 0.29 42 9 0.08 43 67 0.60 44 4 0.04 ACGTcount: A:0.23, C:0.22, G:0.06, T:0.49 Consensus pattern (43 bp): TTTTTCAATCTCCTTTTTTACCTTTATAATTGAGGCCCCTAAT Found at i:64526 original size:41 final size:40 Alignment explanation
Indices: 64407--64535 Score: 152 Period size: 41 Copynumber: 3.1 Consensus size: 40 64397 CTCCTGATTT * 64407 TTTTCAATCTCACTTTTTACCTTTATAATTGAAGCCCCTAA 1 TTTTCAATCTC-CTTTTTACCTTTATAATTGAGGCCCCTAA * * 64448 TTTTTTCTATCTCCTTTTTTA-CTTCTATAATTTAGGCCCCTAA 1 --TTTTCAATCTCC-TTTTTACCTT-TATAATTGAGGCCCCTAA * * 64491 TTTTCAATCTCGTTTATTACCTTTAAAATTGAGGCCCCTAA 1 TTTTCAATCTCCTTT-TTACCTTTATAATTGAGGCCCCTAA 64532 TTTT 1 TTTT 64536 TTTTAATCTA Statistics Matches: 75, Mismatches: 7, Indels: 10 0.82 0.08 0.11 Matches are distributed among these distances: 40 3 0.04 41 33 0.44 42 7 0.09 43 32 0.43 ACGTcount: A:0.23, C:0.22, G:0.06, T:0.48 Consensus pattern (40 bp): TTTTCAATCTCCTTTTTACCTTTATAATTGAGGCCCCTAA Found at i:64565 original size:44 final size:44 Alignment explanation
Indices: 64363--64622 Score: 148 Period size: 43 Copynumber: 6.0 Consensus size: 44 64353 TAATCTTAAG * * * * * 64363 TTTTTCAATCCTAC-TTTGTACCTTTATAATTGA-ACTCCTGATT 1 TTTTTTAAT-CTACGTTTATACCTTTATAATTGAGGCCCCTAATT * * * 64406 TTTTTCAATCTCAC-TTTTTACCTTTATAATTGAAGCCCCTAATT 1 TTTTTTAATCT-ACGTTTATACCTTTATAATTGAGGCCCCTAATT * * * * * 64450 TTTTCT-ATCTCCTTTTTTA-CTTCTATAATTTAGGCCCCTAA-- 1 TTTTTTAATCTACGTTTATACCTT-TATAATTGAGGCCCCTAATT * * 64491 -TTTTCAATCT-CGTTTATTACCTTTAAAATTGAGGCCCCTAATT 1 TTTTTTAATCTACGTTTA-TACCTTTATAATTGAGGCCCCTAATT * * * * 64534 TTTTTTAATCTAAC-TTGATACCTATATAATTGAGGTCTCT-ATT 1 TTTTTTAATCT-ACGTTTATACCTTTATAATTGAGGCCCCTAATT * * * * * * 64577 TTTTTTCAATCATACCTTT-GACTTTTATAGTTTAAGCCCCTAATT 1 TTTTTT-AATC-TACGTTTATACCTTTATAATTGAGGCCCCTAATT 64622 T 1 T 64623 AATCATTTTT Statistics Matches: 171, Mismatches: 30, Indels: 30 0.74 0.13 0.13 Matches are distributed among these distances: 40 7 0.04 41 22 0.13 42 9 0.05 43 64 0.37 44 58 0.34 45 10 0.06 46 1 0.01 ACGTcount: A:0.24, C:0.20, G:0.07, T:0.48 Consensus pattern (44 bp): TTTTTTAATCTACGTTTATACCTTTATAATTGAGGCCCCTAATT Found at i:64578 original size:84 final size:84 Alignment explanation
Indices: 64407--64568 Score: 193 Period size: 84 Copynumber: 1.9 Consensus size: 84 64397 CTCCTGATTT * * ** * 64407 TTTTCAATCTCACTTTTTACCTTTATAATTGAAGCCCCTAATTTTTTCTATCTCCTTTTTTACTT 1 TTTTCAATCTCACTTTTTACCTTTAAAATTGAAGCCCCTAATTTTTTCTATCTACTTTGATACCT * * 64472 CTATAATTTAGGCCCCTAA 66 ATATAATTGAGGCCCCTAA * * * 64491 TTTTCAATCTC-GTTTATTACCTTTAAAATTGAGGCCCCTAATTTTTTTTAATCTAAC-TTGATA 1 TTTTCAATCTCACTTT-TTACCTTTAAAATTGAAGCCCCTAATTTTTTCT-ATCT-ACTTTGATA 64554 CCTATATAATTGAGG 63 CCTATATAATTGAGG 64569 TCTCTATTTT Statistics Matches: 65, Mismatches: 10, Indels: 5 0.81 0.12 0.06 Matches are distributed among these distances: 83 3 0.05 84 41 0.63 85 20 0.31 86 1 0.02 ACGTcount: A:0.25, C:0.20, G:0.07, T:0.47 Consensus pattern (84 bp): TTTTCAATCTCACTTTTTACCTTTAAAATTGAAGCCCCTAATTTTTTCTATCTACTTTGATACCT ATATAATTGAGGCCCCTAA Found at i:75725 original size:13 final size:12 Alignment explanation
Indices: 75685--75739 Score: 58 Period size: 12 Copynumber: 4.6 Consensus size: 12 75675 ACCTTGACCG * 75685 AAAATAAAA-AT 1 AAAATAAAATAA * 75696 AAAATAAATTAA 1 AAAATAAAATAA * 75708 AAAATGAAATAA 1 AAAATAAAATAA 75720 AGAAATAAAATAA 1 A-AAATAAAATAA * 75733 ATAATAA 1 AAAATAA 75740 TATGTAATAA Statistics Matches: 36, Mismatches: 6, Indels: 3 0.80 0.13 0.07 Matches are distributed among these distances: 11 8 0.22 12 17 0.47 13 11 0.31 ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20 Consensus pattern (12 bp): AAAATAAAATAA Found at i:75736 original size:17 final size:18 Alignment explanation
Indices: 75686--75733 Score: 53 Period size: 17 Copynumber: 2.7 Consensus size: 18 75676 CCTTGACCGA * 75686 AAATAAAAATAAAATAAAT 1 AAAT-AAAATAAAATAAAG * * 75705 TAA-AAAATGAAATAAAG 1 AAATAAAATAAAATAAAG 75722 AAATAAAATAAA 1 AAATAAAATAAA 75734 TAATAATATG Statistics Matches: 23, Mismatches: 5, Indels: 3 0.74 0.16 0.10 Matches are distributed among these distances: 17 14 0.61 18 7 0.30 19 2 0.09 ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19 Consensus pattern (18 bp): AAATAAAATAAAATAAAG Found at i:76082 original size:35 final size:35 Alignment explanation
Indices: 75794--76081 Score: 307 Period size: 35 Copynumber: 8.3 Consensus size: 35 75784 ATTTTTTTAA ** * 75794 TATACGTTTTCAAAA-TCCTTTAAAAACCATATAT 1 TATACGTTTTCAAAACTATTTTAAAAACTATATAT * * * ** 75828 TACATGTTTTCAAAACCATTTCGAAAACTATAT-T 1 TATACGTTTTCAAAACTATTTTAAAAACTATATAT * * 75862 ATATATGTTTTCAAAACCATTTT-AAAACTATATAT 1 -TATACGTTTTCAAAACTATTTTAAAAACTATATAT * * * 75897 TATACATTTT-TAAACTATTTAAAAAACTATATAT 1 TATACGTTTTCAAAACTATTTTAAAAACTATATAT * 75931 TACACGTTTTCAAAACTATTTTAAAAACTATATAT 1 TATACGTTTTCAAAACTATTTTAAAAACTATATAT * * * * 75966 TATACATTTTCCAAACTATTTTGAAAAAATATATAC 1 TATACGTTTTCAAAACTATTTT-AAAAACTATATAT * * * 76002 TATATGTTATCAAAACCATTTT-AAAACTATATAT 1 TATACGTTTTCAAAACTATTTTAAAAACTATATAT * 76036 TATACGTTTTTTAAAACTATTTTAAAAACTATATAT 1 TATACG-TTTTCAAAACTATTTTAAAAACTATATAT * 76072 TATATGTTTT 1 TATACGTTTT 76082 TTAAAAATAA Statistics Matches: 210, Mismatches: 36, Indels: 15 0.80 0.14 0.06 Matches are distributed among these distances: 33 8 0.04 34 67 0.32 35 90 0.43 36 45 0.21 ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42 Consensus pattern (35 bp): TATACGTTTTCAAAACTATTTTAAAAACTATATAT Done.