Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: VEPZ01006102.1 Hibiscus syriacus cultivar Beakdansim tig00014461_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: 65298 ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33 Found at i:4642 original size:12 final size:12 Alignment explanation
Indices: 4627--4680 Score: 65 Period size: 12 Copynumber: 4.6 Consensus size: 12 4617 GTTATTTAAA 4627 CGGGTATTGGGC 1 CGGGTATTGGGC * 4639 CGGGTATT-GGT 1 CGGGTATTGGGC 4650 CGGGTATTGGGC 1 CGGGTATTGGGC * * * 4662 CGAGAATCGGGC 1 CGGGTATTGGGC 4674 CGGGTAT 1 CGGGTAT 4681 ATATATATTT Statistics Matches: 34, Mismatches: 7, Indels: 2 0.79 0.16 0.05 Matches are distributed among these distances: 11 10 0.29 12 24 0.71 ACGTcount: A:0.13, C:0.17, G:0.46, T:0.24 Consensus pattern (12 bp): CGGGTATTGGGC Found at i:4765 original size:42 final size:41 Alignment explanation
Indices: 4698--4781 Score: 98 Period size: 42 Copynumber: 2.0 Consensus size: 41 4688 TTTAAATTAA * * * 4698 ATATATAAATATATTTTTATTTAAATTAA-ATTTATTAATATT 1 ATATATAAATATATATATATATAAA-TAATATTT-TTAATATT * 4740 ATATATATATATATATATATATAAATAATTATTTTTAATATT 1 ATATATAAATATATATATATATAAATAA-TATTTTTAATATT 4782 TATCGGGTCG Statistics Matches: 36, Mismatches: 4, Indels: 4 0.82 0.09 0.09 Matches are distributed among these distances: 41 3 0.08 42 29 0.81 43 4 0.11 ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54 Consensus pattern (41 bp): ATATATAAATATATATATATATAAATAATATTTTTAATATT Found at i:4813 original size:13 final size:12 Alignment explanation
Indices: 4782--4817 Score: 54 Period size: 12 Copynumber: 2.9 Consensus size: 12 4772 TTTTAATATT * 4782 TATCGGGTCGGG 1 TATCGGGGCGGG 4794 TATCGGGGCGGG 1 TATCGGGGCGGG 4806 TAATCGGGGCGG 1 T-ATCGGGGCGG 4818 TGATTACCAA Statistics Matches: 22, Mismatches: 1, Indels: 1 0.92 0.04 0.04 Matches are distributed among these distances: 12 12 0.55 13 10 0.45 ACGTcount: A:0.11, C:0.17, G:0.53, T:0.19 Consensus pattern (12 bp): TATCGGGGCGGG Found at i:17671 original size:21 final size:20 Alignment explanation
Indices: 17639--17677 Score: 51 Period size: 21 Copynumber: 1.9 Consensus size: 20 17629 TAATTATAGA * * 17639 AAAAAATTATGTTTATTTTT 1 AAAAAATAATGTATATTTTT 17659 AAAAAATCAATGTATATTT 1 AAAAAAT-AATGTATATTT 17678 ATCTTTGAAA Statistics Matches: 16, Mismatches: 2, Indels: 1 0.84 0.11 0.05 Matches are distributed among these distances: 20 7 0.44 21 9 0.56 ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46 Consensus pattern (20 bp): AAAAAATAATGTATATTTTT Found at i:19014 original size:13 final size:13 Alignment explanation
Indices: 18996--19021 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 18986 TTTTCATATA 18996 ATTTATCTATTTT 1 ATTTATCTATTTT 19009 ATTTATCTATTTT 1 ATTTATCTATTTT 19022 TTATTGATGA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69 Consensus pattern (13 bp): ATTTATCTATTTT Found at i:27494 original size:3 final size:3 Alignment explanation
Indices: 27486--27570 Score: 136 Period size: 3 Copynumber: 28.7 Consensus size: 3 27476 TTAATATATT * 27486 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA 1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA * * 27534 TAA TGA TAA TGA TAA TAA TAA TAA TAA TAA TAA -AA TA 1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA 27571 TTAGTATCTT Statistics Matches: 75, Mismatches: 6, Indels: 2 0.90 0.07 0.02 Matches are distributed among these distances: 2 2 0.03 3 73 0.97 ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32 Consensus pattern (3 bp): TAA Found at i:28180 original size:114 final size:114 Alignment explanation
Indices: 27877--28402 Score: 948 Period size: 114 Copynumber: 4.6 Consensus size: 114 27867 AGAATTATGC * * 27877 AAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT 1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT * * * * * * 27942 TATGAACTTTCTCTGGAAAAGCTGATCCATCAA-ATGATGGATTCAAGT 66 TATGAACCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT 27990 -AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT 1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT * * 28054 TATGAACTTTCTCTGGAAAAGTTAATCCATCAATTTGATGAATTCAGGT 66 TATGAACCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT 28103 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT 1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT 28168 TATGAACCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT 66 TATGAACCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT 28217 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT 1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT 28282 TATGAACCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT 66 TATGAACCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT 28331 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT 1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT 28396 TATGAAC 66 TATGAAC 28403 TCTACCTGGC Statistics Matches: 402, Mismatches: 9, Indels: 3 0.97 0.02 0.01 Matches are distributed among these distances: 112 93 0.23 113 12 0.03 114 297 0.74 ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39 Consensus pattern (114 bp): AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT TATGAACCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT Found at i:29189 original size:83 final size:83 Alignment explanation
Indices: 29092--30055 Score: 1608 Period size: 83 Copynumber: 11.6 Consensus size: 83 29082 CCAAAACATA * * 29092 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATTCAATGAT 1 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGAT 29157 TGGTTCTGCTAAACCAGG 66 TGGTTCTGCTAAACCAGG * * * 29175 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCCAATTCAATGAT 1 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGAT 29240 TGGTTCTGCTAAACCAGG 66 TGGTTCTGCTAAACCAGG * * * 29258 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCCAATTCAATGAT 1 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGAT * 29323 TGGTTCTGCTAAACTAGG 66 TGGTTCTGCTAAACCAGG 29341 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGAT 1 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGAT 29406 TGGTTCTGCTAAACCAGG 66 TGGTTCTGCTAAACCAGG * * 29424 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTTATCTTCCAAATTCAATGAT 1 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGAT 29489 TGGTTCTGCTAAACCAGG 66 TGGTTCTGCTAAACCAGG * * 29507 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTTATCTTCCAAATTCAATGAT 1 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGAT 29572 TGGTTCTGCTAAACCAGG 66 TGGTTCTGCTAAACCAGG 29590 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGAT 1 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGAT 29655 TGGTTCTGCTAAACCAGG 66 TGGTTCTGCTAAACCAGG * * 29673 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTTATCTTCCAAATTCAATGAT 1 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGAT 29738 TGGTTCTGCTAAACCAGG 66 TGGTTCTGCTAAACCAGG * * 29756 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTTATCTTCCAAATTCAATGAT 1 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGAT 29821 TGGTTCTGCTAAACCAGG 66 TGGTTCTGCTAAACCAGG * * * 29839 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAACTCATCTTCTAAATTCAATGAT 1 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGAT ** * 29904 TGGTTCTG-TCCGACCAGA 66 TGGTTCTGCT-AAACCAGG * * * 29922 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAACTCATCTTCTAAATTCAATGAT 1 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGAT ** * 29987 TGGTTCTG-TCCGACCAGA 66 TGGTTCTGCT-AAACCAGG * * * 30005 TTAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAACTCATCTT 1 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTT 30056 TCAGTTAATG Statistics Matches: 855, Mismatches: 25, Indels: 2 0.97 0.03 0.00 Matches are distributed among these distances: 82 1 0.00 83 854 1.00 ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28 Consensus pattern (83 bp): TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGAT TGGTTCTGCTAAACCAGG Found at i:31111 original size:17 final size:17 Alignment explanation
Indices: 31091--31169 Score: 95 Period size: 17 Copynumber: 4.4 Consensus size: 17 31081 ACCTTAATCC 31091 TTTTTTCTTTTTTCTTT 1 TTTTTTCTTTTTTCTTT 31108 TTTTTTCTTTTTTCTTT 1 TTTTTTCTTTTTTCTTT * * 31125 TTTTTCTTTTCTTTTCTCCCT 1 TTTTT-TCTT-TTTTCT--TT 31146 TTTTTTCTTTTCTTCTTT 1 TTTTTTCTTTT-TTCTTT 31164 TTTTTT 1 TTTTTT 31170 TCTTCAAGCA Statistics Matches: 53, Mismatches: 4, Indels: 9 0.80 0.06 0.14 Matches are distributed among these distances: 17 22 0.42 18 10 0.19 19 8 0.15 20 7 0.13 21 6 0.11 ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84 Consensus pattern (17 bp): TTTTTTCTTTTTTCTTT Found at i:31149 original size:38 final size:39 Alignment explanation
Indices: 31093--31168 Score: 118 Period size: 38 Copynumber: 2.0 Consensus size: 39 31083 CTTAATCCTT * ** 31093 TTTTCTTTTTTCTTTTTTTTTCTTTT-TTCTTTTTTTTC 1 TTTTCTTTTCTCCCTTTTTTTCTTTTCTTCTTTTTTTTC 31131 TTTTCTTTTCTCCCTTTTTTTCTTTTCTTCTTTTTTTT 1 TTTTCTTTTCTCCCTTTTTTTCTTTTCTTCTTTTTTTT 31169 TTCTTCAAGC Statistics Matches: 34, Mismatches: 3, Indels: 1 0.89 0.08 0.03 Matches are distributed among these distances: 38 23 0.68 39 11 0.32 ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83 Consensus pattern (39 bp): TTTTCTTTTCTCCCTTTTTTTCTTTTCTTCTTTTTTTTC Found at i:31171 original size:14 final size:14 Alignment explanation
Indices: 31090--31174 Score: 72 Period size: 14 Copynumber: 6.1 Consensus size: 14 31080 CACCTTAATC 31090 CTTTTTTCTTTT-TT 1 CTTTTTT-TTTTCTT 31104 C-TTTTTTTTTCTT 1 CTTTTTTTTTTCTT 31117 -TTTTCTTTTTT-TT 1 CTTTT-TTTTTTCTT * 31130 CTTTTCTTTTCTCCCTT 1 CTTTT-TTTT-T-TCTT * 31147 -TTTTTCTTTTCTT 1 CTTTTTTTTTTCTT 31160 CTTTTTTTTTTCTT 1 CTTTTTTTTTTCTT 31174 C 1 C 31175 AAGCATAATA Statistics Matches: 59, Mismatches: 4, Indels: 16 0.75 0.05 0.20 Matches are distributed among these distances: 12 4 0.07 13 15 0.25 14 30 0.51 15 4 0.07 16 4 0.07 17 2 0.03 ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81 Consensus pattern (14 bp): CTTTTTTTTTTCTT Found at i:31172 original size:31 final size:26 Alignment explanation
Indices: 31091--31169 Score: 97 Period size: 26 Copynumber: 2.9 Consensus size: 26 31081 ACCTTAATCC 31091 TTTTTTCTTTTTTCTTTTTTTTTCTT 1 TTTTTTCTTTTTTCTTTTTTTTTCTT * 31117 TTTTCTT-TTTTTTCTTTTCTTTTCTCCCT 1 TTTT-TTCTTTTTTCTTTT-TTTT-T-CTT 31146 TTTTTTCTTTTCTTCTTTTTTTTT 1 TTTTTTCTTTT-TTCTTTTTTTTT 31170 TCTTCAAGCA Statistics Matches: 46, Mismatches: 1, Indels: 10 0.81 0.02 0.18 Matches are distributed among these distances: 26 15 0.33 27 6 0.13 28 4 0.09 29 14 0.30 30 7 0.15 ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84 Consensus pattern (26 bp): TTTTTTCTTTTTTCTTTTTTTTTCTT Found at i:43869 original size:3 final size:3 Alignment explanation
Indices: 43861--43941 Score: 135 Period size: 3 Copynumber: 27.0 Consensus size: 3 43851 TTAATATATT * 43861 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA 1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA * * 43909 TAA TGA TAA TGA TAA TAA TAA TAA TAA TAA TAA 1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA 43942 AAAAAATATT Statistics Matches: 72, Mismatches: 6, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 3 72 1.00 ACGTcount: A:0.64, C:0.01, G:0.02, T:0.32 Consensus pattern (3 bp): TAA Found at i:44219 original size:19 final size:20 Alignment explanation
Indices: 44182--44220 Score: 62 Period size: 19 Copynumber: 2.0 Consensus size: 20 44172 AATATCATTG * 44182 AATTTTAAGATTTTATATTC 1 AATTTTAAGATTATATATTC 44202 AATTTTAA-ATTATATATTC 1 AATTTTAAGATTATATATTC 44221 GATTAAATTA Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 19 10 0.56 20 8 0.44 ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54 Consensus pattern (20 bp): AATTTTAAGATTATATATTC Found at i:47025 original size:40 final size:41 Alignment explanation
Indices: 46970--47063 Score: 156 Period size: 40 Copynumber: 2.3 Consensus size: 41 46960 CTTGATAGTG 46970 GATGCTTAAGACATATGACCAAAGATAAGAGTCGGTTTAT- 1 GATGCTTAAGACATATGACCAAAGATAAGAGTCGGTTTATA * 47010 GATGCTTAAGACATATGACCGAAGATAAGAGTCGGTTTATA 1 GATGCTTAAGACATATGACCAAAGATAAGAGTCGGTTTATA 47051 GA-GCTTAACGACA 1 GATGCTTAA-GACA 47064 AAAATGGAGG Statistics Matches: 51, Mismatches: 1, Indels: 3 0.93 0.02 0.05 Matches are distributed among these distances: 40 45 0.88 41 6 0.12 ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26 Consensus pattern (41 bp): GATGCTTAAGACATATGACCAAAGATAAGAGTCGGTTTATA Found at i:57423 original size:18 final size:17 Alignment explanation
Indices: 57386--57419 Score: 68 Period size: 17 Copynumber: 2.0 Consensus size: 17 57376 AAATGAGAGA 57386 AGTGTTAAAGTAAGGGG 1 AGTGTTAAAGTAAGGGG 57403 AGTGTTAAAGTAAGGGG 1 AGTGTTAAAGTAAGGGG 57420 GAGTAATTTC 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:0.35, C:0.00, G:0.41, T:0.24 Consensus pattern (17 bp): AGTGTTAAAGTAAGGGG Found at i:61539 original size:22 final size:22 Alignment explanation
Indices: 61514--61557 Score: 70 Period size: 22 Copynumber: 2.0 Consensus size: 22 61504 ACATTTGAAT * 61514 GTTTTGGATTTGTGTGTTTTGG 1 GTTTTGGATATGTGTGTTTTGG * 61536 GTTTTGGATATGTTTGTTTTGG 1 GTTTTGGATATGTGTGTTTTGG 61558 ATTTGAATGG Statistics Matches: 20, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 22 20 1.00 ACGTcount: A:0.07, C:0.00, G:0.34, T:0.59 Consensus pattern (22 bp): GTTTTGGATATGTGTGTTTTGG Found at i:61573 original size:9 final size:9 Alignment explanation
Indices: 61559--61601 Score: 86 Period size: 9 Copynumber: 4.8 Consensus size: 9 61549 TTGTTTTGGA 61559 TTTGAATGG 1 TTTGAATGG 61568 TTTGAATGG 1 TTTGAATGG 61577 TTTGAATGG 1 TTTGAATGG 61586 TTTGAATGG 1 TTTGAATGG 61595 TTTGAAT 1 TTTGAAT 61602 ATTTAATTTG Statistics Matches: 34, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 9 34 1.00 ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47 Consensus pattern (9 bp): TTTGAATGG Found at i:61894 original size:13 final size:13 Alignment explanation
Indices: 61865--61898 Score: 52 Period size: 12 Copynumber: 2.7 Consensus size: 13 61855 GGGGAATAAT * 61865 TTTTCAAAATTGA 1 TTTTCAAAAATGA 61878 -TTTCAAAAATGA 1 TTTTCAAAAATGA 61890 TTTTCAAAA 1 TTTTCAAAA 61899 CCAAAATCTT Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 12 11 0.58 13 8 0.42 ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41 Consensus pattern (13 bp): TTTTCAAAAATGA Found at i:62034 original size:19 final size:20 Alignment explanation
Indices: 61992--62035 Score: 63 Period size: 20 Copynumber: 2.2 Consensus size: 20 61982 AATAAAGTAT * * 61992 TATTGAATTTTAAGATTTTA 1 TATTCAATTTTAAGATTATA 62012 TATTCAATTTTAA-ATTATA 1 TATTCAATTTTAAGATTATA 62031 TATTC 1 TATTC 62036 GATTAAATTA Statistics Matches: 22, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 19 10 0.45 20 12 0.55 ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55 Consensus pattern (20 bp): TATTCAATTTTAAGATTATA Done.