Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: VEPZ01009455.1 Hibiscus syriacus cultivar Beakdansim tig00113702_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: 65774 ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32 Found at i:9231 original size:4 final size:4 Alignment explanation
Indices: 9214--9243 Score: 51 Period size: 4 Copynumber: 7.5 Consensus size: 4 9204 TACTCTAACA * 9214 ATAC ATAT ATAC ATAC ATAC ATAC ATAC AT 1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT 9244 GTCATTATTC Statistics Matches: 24, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 4 24 1.00 ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30 Consensus pattern (4 bp): ATAC Found at i:9631 original size:18 final size:18 Alignment explanation
Indices: 9608--9642 Score: 70 Period size: 18 Copynumber: 1.9 Consensus size: 18 9598 ACTGAATATT 9608 TGTCCCGAAGGACCACTA 1 TGTCCCGAAGGACCACTA 9626 TGTCCCGAAGGACCACT 1 TGTCCCGAAGGACCACT 9643 GTTTGTCCTG Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 17 1.00 ACGTcount: A:0.26, C:0.34, G:0.23, T:0.17 Consensus pattern (18 bp): TGTCCCGAAGGACCACTA Found at i:9657 original size:20 final size:20 Alignment explanation
Indices: 9606--9680 Score: 100 Period size: 20 Copynumber: 3.9 Consensus size: 20 9596 GCACTGAATA * 9606 TTTGTCCCGAAGGACCAC-- 1 TTTGTCCCGGAGGACCACTG * * 9624 TATGTCCCGAAGGACCACTG 1 TTTGTCCCGGAGGACCACTG * 9644 TTTGTCCTGGAGGACCACTG 1 TTTGTCCCGGAGGACCACTG 9664 TTTGTCCCGGAGGACCA 1 TTTGTCCCGGAGGACCA 9681 TTGATAATCC Statistics Matches: 50, Mismatches: 5, Indels: 2 0.88 0.09 0.04 Matches are distributed among these distances: 18 17 0.34 20 33 0.66 ACGTcount: A:0.20, C:0.29, G:0.27, T:0.24 Consensus pattern (20 bp): TTTGTCCCGGAGGACCACTG Found at i:11828 original size:64 final size:63 Alignment explanation
Indices: 11740--11860 Score: 170 Period size: 64 Copynumber: 1.9 Consensus size: 63 11730 ATTGTTCAAG * * * * * 11740 GTGTATTGATGTACATGAAGTGCATCGATGCACTCCTTTAAAATAAAAACATCGAATGTCATTA 1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCATT-AAATAAAAACATCGAATGTCATTA * * 11804 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCATTAAATATAAACATCGAATG 1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCATTAAATAAAAACATCGAATG 11861 GGATTTATGC Statistics Matches: 50, Mismatches: 7, Indels: 1 0.86 0.12 0.02 Matches are distributed among these distances: 63 17 0.34 64 33 0.66 ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28 Consensus pattern (63 bp): GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCATTAAATAAAAACATCGAATGTCATTA Found at i:11877 original size:63 final size:64 Alignment explanation
Indices: 11758--11901 Score: 168 Period size: 63 Copynumber: 2.3 Consensus size: 64 11748 ATGTACATGA * * * * * 11758 AGTGCATCGATGCACTCCTTTAAAATAAAAACATCGAATGTCATTAGTGTATCGATGCACAAG-T 1 AGTGCATCGATGCACCCCATTAAAATAAAAACATCGAATGGCATTAGTGCACCGATGCA-AAGAT * * * * 11822 AGTGCATCGATGCACCCCATT-AAATATAAACATCGAATGGGATTTA-TGCACCGATGTATAGAT 1 AGTGCATCGATGCACCCCATTAAAATAAAAACATCGAATGGCA-TTAGTGCACCGATGCAAAGAT 11885 AGTGCATCGATGCACCC 1 AGTGCATCGATGCACCC 11902 GTCAAGGGAT Statistics Matches: 69, Mismatches: 9, Indels: 5 0.83 0.11 0.06 Matches are distributed among these distances: 62 2 0.03 63 45 0.65 64 22 0.32 ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26 Consensus pattern (64 bp): AGTGCATCGATGCACCCCATTAAAATAAAAACATCGAATGGCATTAGTGCACCGATGCAAAGAT Found at i:12593 original size:23 final size:23 Alignment explanation
Indices: 12540--12598 Score: 73 Period size: 23 Copynumber: 2.6 Consensus size: 23 12530 CAATCTTATA * * * 12540 TGGCACTACAGTGCAATTCTATG 1 TGGCACTTCGGTGCAATTCTACG * 12563 CGGCACTTCGGTGCAATTCTACG 1 TGGCACTTCGGTGCAATTCTACG * 12586 TGGCACTTTGGTG 1 TGGCACTTCGGTG 12599 TATTTATACG Statistics Matches: 30, Mismatches: 6, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 23 30 1.00 ACGTcount: A:0.19, C:0.24, G:0.27, T:0.31 Consensus pattern (23 bp): TGGCACTTCGGTGCAATTCTACG Found at i:12608 original size:23 final size:23 Alignment explanation
Indices: 12540--12608 Score: 57 Period size: 23 Copynumber: 3.0 Consensus size: 23 12530 CAATCTTATA * * * * 12540 TGGCACTACAGTGCAATTCTATG 1 TGGCACTTCGGTGCAATTATACG * * 12563 CGGCACTTCGGTGCAATTCTACG 1 TGGCACTTCGGTGCAATTATACG * * * 12586 TGGCACTTTGGTGTATTTATACG 1 TGGCACTTCGGTGCAATTATACG 12609 AGCTGTGGTG Statistics Matches: 37, Mismatches: 9, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 23 37 1.00 ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33 Consensus pattern (23 bp): TGGCACTTCGGTGCAATTATACG Found at i:18166 original size:64 final size:63 Alignment explanation
Indices: 18092--18212 Score: 172 Period size: 64 Copynumber: 1.9 Consensus size: 63 18082 ATCGTTCAAG * * * * 18092 GTGTATCGATGCACATGAAGTGCATTGATGCACTCCTTTAAAATTA-AAACATCGAATGTCATTA 1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCATT-AAA-TACAAACATCGAATGTCATTA * 18156 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCATTAAATACAAACATCGAATG 1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCATTAAATACAAACATCGAATG 18213 AGATTTATGA Statistics Matches: 51, Mismatches: 5, Indels: 3 0.86 0.08 0.05 Matches are distributed among these distances: 62 2 0.04 63 15 0.29 64 34 0.67 ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27 Consensus pattern (63 bp): GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCATTAAATACAAACATCGAATGTCATTA Found at i:18948 original size:23 final size:23 Alignment explanation
Indices: 18904--18955 Score: 68 Period size: 23 Copynumber: 2.3 Consensus size: 23 18894 TTGGCACTAA * 18904 AGTGCAATTCTACGCGGTACTTC 1 AGTGCAATTCTACGCGGCACTTC * * * 18927 GGTGCAATTCTATGTGGCACTTC 1 AGTGCAATTCTACGCGGCACTTC 18950 AGTGCA 1 AGTGCA 18956 TTTATACGAG Statistics Matches: 24, Mismatches: 5, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 23 24 1.00 ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31 Consensus pattern (23 bp): AGTGCAATTCTACGCGGCACTTC Found at i:26060 original size:31 final size:31 Alignment explanation
Indices: 26025--26105 Score: 119 Period size: 31 Copynumber: 2.6 Consensus size: 31 26015 AAACTATAAG * 26025 TTTAGTACTTAAACTATTAATTTTGGTCAAT 1 TTTAGTACCTAAACTATTAATTTTGGTCAAT * * * 26056 TTTAGTACCTAAATTATCAATTTTGGTCCAT 1 TTTAGTACCTAAACTATTAATTTTGGTCAAT 26087 TTTAGTACCTAAACT-TTAA 1 TTTAGTACCTAAACTATTAA 26106 AAAAAAATCA Statistics Matches: 44, Mismatches: 6, Indels: 1 0.86 0.12 0.02 Matches are distributed among these distances: 30 3 0.07 31 41 0.93 ACGTcount: A:0.32, C:0.14, G:0.09, T:0.46 Consensus pattern (31 bp): TTTAGTACCTAAACTATTAATTTTGGTCAAT Found at i:28885 original size:29 final size:29 Alignment explanation
Indices: 28850--28935 Score: 145 Period size: 29 Copynumber: 2.9 Consensus size: 29 28840 AAACTAAATT * 28850 GATGTCATTACTTACATCATTTAATTAAA 1 GATGTCATTGCTTACATCATTTAATTAAA * 28879 GATGTCATTGCTTACATCATTTAATTAAT 1 GATGTCATTGCTTACATCATTTAATTAAA 28908 GATGTCATTGCTTACATCAATTTAATTA 1 GATGTCATTGCTTACATC-ATTTAATTA 28936 GGTGAGAGTT Statistics Matches: 54, Mismatches: 2, Indels: 1 0.95 0.04 0.02 Matches are distributed among these distances: 29 45 0.83 30 9 0.17 ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43 Consensus pattern (29 bp): GATGTCATTGCTTACATCATTTAATTAAA Found at i:33651 original size:29 final size:29 Alignment explanation
Indices: 33616--33701 Score: 145 Period size: 29 Copynumber: 2.9 Consensus size: 29 33606 AAACTAAATT * 33616 GATGTCATTACTTACATCATTTAATTAAA 1 GATGTCATTGCTTACATCATTTAATTAAA * 33645 GATGTCATTGCTTACATCATTTAATTAAT 1 GATGTCATTGCTTACATCATTTAATTAAA 33674 GATGTCATTGCTTACATCAATTTAATTA 1 GATGTCATTGCTTACATC-ATTTAATTA 33702 GGTGAGAGTT Statistics Matches: 54, Mismatches: 2, Indels: 1 0.95 0.04 0.02 Matches are distributed among these distances: 29 45 0.83 30 9 0.17 ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43 Consensus pattern (29 bp): GATGTCATTGCTTACATCATTTAATTAAA Found at i:37138 original size:3 final size:3 Alignment explanation
Indices: 37125--37172 Score: 71 Period size: 3 Copynumber: 16.0 Consensus size: 3 37115 ATAATGTAAG * 37125 TAA TAA TTAA TAA TAA TAA TAA -AG TAA TAA TAA TAA TAA TAA TAA 1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA 37170 TAA 1 TAA 37173 GACCTATACA Statistics Matches: 41, Mismatches: 2, Indels: 4 0.87 0.04 0.09 Matches are distributed among these distances: 2 1 0.02 3 37 0.90 4 3 0.07 ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33 Consensus pattern (3 bp): TAA Found at i:37593 original size:138 final size:138 Alignment explanation
Indices: 37371--37768 Score: 575 Period size: 137 Copynumber: 2.9 Consensus size: 138 37361 GATAACATAA * * * 37371 TTCCTACGTGATGAGGAAGTCTGTTTATCTAAGGGTGACACTG-CTCCTACGTGATGAGGAGATC 1 TTCCTACGTGATGAGGAAGGCTGATTATCTAAGGGTGACGC-GACTCCTACGTGATGAGGAGATC * 37435 TGGTCGGTGGATGACACAGTTCCTACGTGATGAGGACGATTGGCCATCTTTAGGGATAAATATAG 65 TGGTCGGTGGATGACACAGTTCCTACGTGATGAGGACGGTTGGCCATCTTTAGGGATAAATATAG 37500 ATAACACGG 130 ATAACACGG * * * * 37509 TTCTTACGTGATGAGGACGGCTGGTTATCTAAGGGTGACGCGACTCCTACGTGATGAGGAGATAT 1 TTCCTACGTGATGAGGAAGGCTGATTATCTAAGGGTGACGCGACTCCTACGTGATGAGGAGATCT * * ** * 37574 GGTCGGTGGATGACACAGTTCCTACGTGATAAGGACGGTTGGTCATCTTTATTGAT-AATGTAGA 66 GGTCGGTGGATGACACAGTTCCTACGTGATGAGGACGGTTGGCCATCTTTAGGGATAAATATAGA * 37638 TAACATGG 131 TAACACGG * * 37646 TTCCTACGTGATGAGGATGGTTGATTATCTAAGGGTGACGCGACTCCTACGTGATGAGGAGATCT 1 TTCCTACGTGATGAGGAAGGCTGATTATCTAAGGGTGACGCGACTCCTACGTGATGAGGAGATCT * * * * * * 37711 GGTCGATGGATGACACGGTTCTTACGTGATGAGGATGGCTGACCATCTTTAGGGATAA 66 GGTCGGTGGATGACACAGTTCCTACGTGATGAGGACGGTTGGCCATCTTTAGGGATAA 37769 TTTTTCAAGG Statistics Matches: 230, Mismatches: 28, Indels: 4 0.88 0.11 0.02 Matches are distributed among these distances: 137 121 0.53 138 109 0.47 ACGTcount: A:0.25, C:0.16, G:0.30, T:0.28 Consensus pattern (138 bp): TTCCTACGTGATGAGGAAGGCTGATTATCTAAGGGTGACGCGACTCCTACGTGATGAGGAGATCT GGTCGGTGGATGACACAGTTCCTACGTGATGAGGACGGTTGGCCATCTTTAGGGATAAATATAGA TAACACGG Found at i:37826 original size:36 final size:36 Alignment explanation
Indices: 37786--37899 Score: 165 Period size: 36 Copynumber: 3.2 Consensus size: 36 37776 AGGGAAGTTC * ** * 37786 TCTCAAGAGAGACAAAACATGTTTCAAGGGACTCTA 1 TCTCAAGAGAGACAAAATATGTTTCAAGGGAAACAA * * 37822 TCTCAAGAGATACAAAATATATTTCAAGGGAAACAA 1 TCTCAAGAGAGACAAAATATGTTTCAAGGGAAACAA * 37858 TCTCAAGAGAGACAAAATATGTTTGAAGGGAAACAA 1 TCTCAAGAGAGACAAAATATGTTTCAAGGGAAACAA 37894 TCTCAA 1 TCTCAA 37900 TGATTATGTT Statistics Matches: 69, Mismatches: 9, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 36 69 1.00 ACGTcount: A:0.45, C:0.16, G:0.18, T:0.22 Consensus pattern (36 bp): TCTCAAGAGAGACAAAATATGTTTCAAGGGAAACAA Found at i:37927 original size:65 final size:66 Alignment explanation
Indices: 37843--38023 Score: 204 Period size: 65 Copynumber: 2.7 Consensus size: 66 37833 ACAAAATATA * ** * * * 37843 TTTCAAGGGAAACAATCTCAAGAGAGACAAAA-TATGTTTGAAGGGAAACAATCTC-AATGATTA 1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACT-TGTTTCAAGAGAAACAATCTCAAAGGATTA 37906 TG 65 TG * * * * 37908 TTTCAAGAGAAACTGTCTCAAGAGAGATAAAACTTGTTTCAACAGAAACAATCTCAAAGGTTTTT 1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGAGAAACAATCTCAAAGGATTAT 37973 G 66 G * * * * 37974 TTTCAAGAAAAAATGTCTCAAGAGATACAAAACTTTGTTTTAAGAGAAAC 1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC-TTGTTTCAAGAGAAAC 38024 TGTCTCAAGC Statistics Matches: 97, Mismatches: 16, Indels: 4 0.83 0.14 0.03 Matches are distributed among these distances: 65 46 0.47 66 37 0.38 67 14 0.14 ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27 Consensus pattern (66 bp): TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGAGAAACAATCTCAAAGGATTAT G Found at i:37955 original size:36 final size:36 Alignment explanation
Indices: 37906--38132 Score: 187 Period size: 36 Copynumber: 6.4 Consensus size: 36 37896 TCAATGATTA * 37906 TGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAACT 1 TGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAATT * ** * 37942 TGTTTCAACAGAAACAATCTCAA-AG-G-T---TTT 1 TGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAATT * * * * 37972 TGTTTCAAGAAAAAATGTCTCAAGAGATACAAAACTT 1 TGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAA-TT * * * 38009 TGTTTTAAGAGAAACTGTCTCAAGCGAGAAAAAATT 1 TGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAATT ** * * * * * * 38045 TGTTTTTAGGGAAAATAATCTCAAGCGAGATCAATTT 1 TGTTTCAAGAGAAACT-GTCTCAAGAGAGATAAAATT * * * 38082 TGTTTCAAGTGAGACTGTCTAAAGAGAGATAAAATT 1 TGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAATT 38118 TGTTTCAAGAGAAAC 1 TGTTTCAAGAGAAAC 38133 AATCTCAAAG Statistics Matches: 145, Mismatches: 38, Indels: 16 0.73 0.19 0.08 Matches are distributed among these distances: 30 19 0.13 31 2 0.01 33 1 0.01 34 1 0.01 35 2 0.01 36 63 0.43 37 57 0.39 ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30 Consensus pattern (36 bp): TGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAATT Found at i:38006 original size:66 final size:65 Alignment explanation
Indices: 37858--38032 Score: 199 Period size: 66 Copynumber: 2.7 Consensus size: 65 37848 AGGGAAACAA * * * * * 37858 TCTCAAGAGAGACAAAA-TATGTTTGAAGGGAAACAATCTCAATGATTATGTTTCAAGAGAAACT 1 TCTCAAGAGAGACAAAACT-TGTTTCAAGAGAAACAATCTCAAGGATTATGTTTCAAGAAAAAAT 37922 G 65 G * * * * 37923 TCTCAAGAGAGATAAAACTTGTTTCAACAGAAACAATCTCAAAGGTTTTTGTTTCAAGAAAAAAT 1 TCTCAAGAGAGACAAAACTTGTTTCAAGAGAAACAATCTC-AAGGATTATGTTTCAAGAAAAAAT 37988 G 65 G * * ** 37989 TCTCAAGAGATACAAAACTTTGTTTTAAGAGAAACTGTCTCAAG 1 TCTCAAGAGAGACAAAAC-TTGTTTCAAGAGAAACAATCTCAAG 38033 CGAGAAAAAA Statistics Matches: 92, Mismatches: 15, Indels: 5 0.82 0.13 0.04 Matches are distributed among these distances: 65 34 0.37 66 40 0.43 67 18 0.20 ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28 Consensus pattern (65 bp): TCTCAAGAGAGACAAAACTTGTTTCAAGAGAAACAATCTCAAGGATTATGTTTCAAGAAAAAATG Found at i:38429 original size:35 final size:37 Alignment explanation
Indices: 38360--38431 Score: 103 Period size: 37 Copynumber: 2.0 Consensus size: 37 38350 TAAGGAAGAC * * 38360 TGTCTCAAGTGAGACGAAATTTATTTTTAAGAGAAAA 1 TGTCTCAAGCGAGACAAAATTTATTTTTAAGAGAAAA * 38397 TGTCTTAAGCGAGACAAAATTT-TTTTT-AGAGAAAA 1 TGTCTCAAGCGAGACAAAATTTATTTTTAAGAGAAAA 38432 CAATCTCAAA Statistics Matches: 32, Mismatches: 3, Indels: 2 0.86 0.08 0.05 Matches are distributed among these distances: 35 8 0.25 36 5 0.16 37 19 0.59 ACGTcount: A:0.40, C:0.08, G:0.18, T:0.33 Consensus pattern (37 bp): TGTCTCAAGCGAGACAAAATTTATTTTTAAGAGAAAA Found at i:39897 original size:2 final size:2 Alignment explanation
Indices: 39885--39935 Score: 93 Period size: 2 Copynumber: 25.5 Consensus size: 2 39875 AACTTTATTG * 39885 TA TA CA TA TA TA TA 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 TA TA TA TA TA TA TA 39927 TA TA TA TA T 1 TA TA TA TA T 39936 TATGGGTATA Statistics Matches: 47, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 2 47 1.00 ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49 Consensus pattern (2 bp): TA Found at i:54746 original size:80 final size:78 Alignment explanation
Indices: 54606--54751 Score: 197 Period size: 80 Copynumber: 1.8 Consensus size: 78 54596 TAAATAAAAT * 54606 ATTATTTAATTAATTCAAATTAAATATACATTAAAGACTTATAATCTAAATTACAATC-TTTAAT 1 ATTATTTAATTAATTCAAATTAAATATACATTAAAGAATTATAATCTAAATTACAATCTTTTAAT 54670 TTTTATTTAGAAA 66 TTTTATTTAGAAA * * * * 54683 ATTATTTAATT-ATTCTTAATTATATATATCAATTAAAAGAATTGTAATCTAAATTACATTCTTT 1 ATTATTTAATTAATTC-AAATTAAATATA-C-ATT-AAAGAATTATAATCTAAATTACAATCTTT 54747 TAATT 62 TAATT 54752 CTTACTTAAT Statistics Matches: 59, Mismatches: 5, Indels: 6 0.84 0.07 0.09 Matches are distributed among these distances: 76 4 0.07 77 21 0.36 78 1 0.02 79 3 0.05 80 23 0.39 81 7 0.12 ACGTcount: A:0.43, C:0.08, G:0.03, T:0.47 Consensus pattern (78 bp): ATTATTTAATTAATTCAAATTAAATATACATTAAAGAATTATAATCTAAATTACAATCTTTTAAT TTTTATTTAGAAA Done.