Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: VEPZ01000579.1 Hibiscus syriacus cultivar Beakdansim tig00001131_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: 105151 ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32 Found at i:9917 original size:39 final size:39 Alignment explanation
Indices: 9874--9951 Score: 138 Period size: 39 Copynumber: 2.0 Consensus size: 39 9864 AGTTTTGGGG 9874 ATAAAGGCGTTTAAGCACCAAATTAAACCTTAAAACTAA 1 ATAAAGGCGTTTAAGCACCAAATTAAACCTTAAAACTAA * * 9913 ATAAAGGTGTTTAAGTACCAAATTAAACCTTAAAACTAA 1 ATAAAGGCGTTTAAGCACCAAATTAAACCTTAAAACTAA 9952 GTTTAGATAC Statistics Matches: 37, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 39 37 1.00 ACGTcount: A:0.49, C:0.15, G:0.10, T:0.26 Consensus pattern (39 bp): ATAAAGGCGTTTAAGCACCAAATTAAACCTTAAAACTAA Found at i:17235 original size:5 final size:5 Alignment explanation
Indices: 17227--17254 Score: 56 Period size: 5 Copynumber: 5.6 Consensus size: 5 17217 AGGGAAGGAA 17227 AAAGG AAAGG AAAGG AAAGG AAAGG AAA 1 AAAGG AAAGG AAAGG AAAGG AAAGG AAA 17255 AAGCAGAAAC Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 23 1.00 ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00 Consensus pattern (5 bp): AAAGG Found at i:17257 original size:12 final size:12 Alignment explanation
Indices: 17209--17257 Score: 62 Period size: 12 Copynumber: 3.8 Consensus size: 12 17199 AGCTGTGAAG * 17209 AAGGAAAAAGGG 1 AAGGAAAAAGGA 17221 AAGGAAAAAGGA 1 AAGGAAAAAGGA 17233 AAGGAAAGGAAAGGA 1 AAGG-AA--AAAGGA 17248 AAGGAAAAAG 1 AAGGAAAAAG 17258 CAGAAACACT Statistics Matches: 33, Mismatches: 1, Indels: 6 0.82 0.03 0.15 Matches are distributed among these distances: 12 19 0.58 13 2 0.06 14 2 0.06 15 10 0.30 ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00 Consensus pattern (12 bp): AAGGAAAAAGGA Found at i:19078 original size:2 final size:2 Alignment explanation
Indices: 19071--19108 Score: 76 Period size: 2 Copynumber: 19.0 Consensus size: 2 19061 ACCGACTTAA 19071 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 19109 GATCTATCAT Statistics Matches: 36, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 36 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:35868 original size:30 final size:31 Alignment explanation
Indices: 35818--35877 Score: 72 Period size: 30 Copynumber: 2.0 Consensus size: 31 35808 ATACCGGGTT * 35818 AGTGACCAAAGTGTGAAAATTTA-AAATTTC 1 AGTGACCAAAGTGTGAAAATTGAGAAATTTC 35848 AGTGACCAAA-T-TAGATAAATTGAGAAATTT 1 AGTGACCAAAGTGT-GA-AAATTGAGAAATTT 35878 AAGGATTTAA Statistics Matches: 26, Mismatches: 1, Indels: 5 0.81 0.03 0.16 Matches are distributed among these distances: 28 1 0.04 29 3 0.12 30 16 0.62 31 6 0.23 ACGTcount: A:0.45, C:0.08, G:0.17, T:0.30 Consensus pattern (31 bp): AGTGACCAAAGTGTGAAAATTGAGAAATTTC Found at i:37235 original size:22 final size:22 Alignment explanation
Indices: 37207--37267 Score: 95 Period size: 22 Copynumber: 2.8 Consensus size: 22 37197 GGGTTTACGC * 37207 GGTCCTTCGGGACATATACAGA 1 GGTCCTTCGGGACAAATACAGA * * 37229 GGTCCTTCGAGACAAATACATA 1 GGTCCTTCGGGACAAATACAGA 37251 GGTCCTTCGGGACAAAT 1 GGTCCTTCGGGACAAAT 37268 TTCACATGCC Statistics Matches: 35, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 22 35 1.00 ACGTcount: A:0.30, C:0.23, G:0.25, T:0.23 Consensus pattern (22 bp): GGTCCTTCGGGACAAATACAGA Found at i:42741 original size:17 final size:18 Alignment explanation
Indices: 42712--42764 Score: 58 Period size: 17 Copynumber: 3.1 Consensus size: 18 42702 AATATTTAGA * * 42712 TAAAA-ATTTAAAATTGT 1 TAAAATATTAAAAATTAT * 42729 TAAAGT-TTAAAAA-TAT 1 TAAAATATTAAAAATTAT 42745 TAAAATATTAAAAATTAT 1 TAAAATATTAAAAATTAT 42763 TA 1 TA 42765 TAAAATATAT Statistics Matches: 29, Mismatches: 4, Indels: 5 0.76 0.11 0.13 Matches are distributed among these distances: 16 7 0.24 17 17 0.59 18 5 0.17 ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40 Consensus pattern (18 bp): TAAAATATTAAAAATTAT Found at i:52594 original size:32 final size:31 Alignment explanation
Indices: 52548--52626 Score: 108 Period size: 32 Copynumber: 2.6 Consensus size: 31 52538 CAGGGGTGAG * * 52548 ATTGGTCGCTATGCAGTCGGGGCGAAGCAGGT 1 ATTGGTCGCCATGCAGTCGGGGCGAAG-AAGT * 52580 ATTGGTCACCATGCAGTCGGGGCGAAGAAGT 1 ATTGGTCGCCATGCAGTCGGGGCGAAGAAGT 52611 A--GGTCGCCATGCAGTC 1 ATTGGTCGCCATGCAGTC 52627 TGTTGAAGGT Statistics Matches: 43, Mismatches: 4, Indels: 3 0.86 0.08 0.06 Matches are distributed among these distances: 29 14 0.33 31 4 0.09 32 25 0.58 ACGTcount: A:0.22, C:0.22, G:0.37, T:0.20 Consensus pattern (31 bp): ATTGGTCGCCATGCAGTCGGGGCGAAGAAGT Found at i:52878 original size:27 final size:29 Alignment explanation
Indices: 52822--52891 Score: 117 Period size: 27 Copynumber: 2.4 Consensus size: 29 52812 ATTTTAACCC 52822 ATTATATTAAAGTTGTGTGGTTGTAAGAGT 1 ATTATATTAAAG-TGTGTGGTTGTAAGAGT 52852 ATTATATTAAAGTG-G-GGTTGTAAGAGT 1 ATTATATTAAAGTGTGTGGTTGTAAGAGT 52879 ATTATATTAAAGT 1 ATTATATTAAAGT 52892 ATATAAATAT Statistics Matches: 40, Mismatches: 0, Indels: 3 0.93 0.00 0.07 Matches are distributed among these distances: 27 25 0.62 28 1 0.03 29 2 0.05 30 12 0.30 ACGTcount: A:0.34, C:0.00, G:0.24, T:0.41 Consensus pattern (29 bp): ATTATATTAAAGTGTGTGGTTGTAAGAGT Found at i:53166 original size:13 final size:14 Alignment explanation
Indices: 53148--53179 Score: 50 Period size: 13 Copynumber: 2.4 Consensus size: 14 53138 TATTTATAAA 53148 AAAATAATATT-TT 1 AAAATAATATTATT 53161 AAAAT-ATATTATT 1 AAAATAATATTATT 53174 AAAATA 1 AAAATA 53180 CAATATACAA Statistics Matches: 17, Mismatches: 0, Indels: 3 0.85 0.00 0.15 Matches are distributed among these distances: 12 5 0.29 13 12 0.71 ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41 Consensus pattern (14 bp): AAAATAATATTATT Found at i:53732 original size:274 final size:279 Alignment explanation
Indices: 53210--53817 Score: 913 Period size: 274 Copynumber: 2.2 Consensus size: 279 53200 AAGTAACTAT * * * * * 53210 TGATTTTACGAACCCTAAACCCTAAAATATTTTGGTTGTTCCTGAAAACCTTTATAAATTCATGG 1 TGATATTATGAACCTTAAACCCTAAAATATTTTGGTTATTCCTGAAAACCTATATAAATTCATGG * 53275 TATGTTGAGGGAAATGAAAGTGGTAGAGGATGGTGATATCTACCATGATGGTGGTTACAAATTTG 66 TATGTTGAGGGAAATGAAAGGGGTAGAGGATGGTGATATCTACCATGATGGTGGTTACAAATTTG * * 53340 TTTTTTATAAGAAGAAATTGTTTGGATGGAGAATTGTTAGGGTTCAGGGTTTAAAGTCCAGAGTT 131 TTTTTTATAAGAAGAAATTGATTGGAGGGAGAA---TTA-GGTTCAGGGTTTAAAGTCCAGAGTT * 53405 TAGAGTTTTTAGCAACAACCAAAATATTTTAGGGTTTAGGGTTTAGGGTTCACAAAATCAATAGT 192 TAGAGTTTTTAGCAACAACCAAAATATTTTAGGGTTTAGGGTTTAGAGTTCACAAAATCAATAGT * 53470 TACTTATATTATTTGTTGTATAT 257 TACTTATATTATTTGTTGTATAC * * * 53493 TGATATTGTGAACCTTAAACCCTAAAATATTTTGGTTATTGCTGAGAACCTATATAAATTCATGG 1 TGATATTATGAACCTTAAACCCTAAAATATTTTGGTTATTCCTGAAAACCTATATAAATTCATGG * 53558 TATGTTGA-GGCAATGAAAGGGGTAGAGGATGGTGATATCTACCATGATGGTGGTTACAAATTTG 66 TATGTTGAGGGAAATGAAAGGGGTAGAGGATGGTGATATCTACCATGATGGTGGTTACAAATTTG ** * * 53622 -TTTTTATAAGAAGAAATTGATTGGAGGGAGAA-T-GGTT-AGGGTTTAAAGTTTAGGGTTTAGG 131 TTTTTTATAAGAAGAAATTGATTGGAGGGAGAATTAGGTTCAGGGTTTAAAGTCCAGAGTTTAGA * 53683 GTTTTTAGCAACAACCAAAATATTTTAGGGTTTAGGGTTTATAGTTCACAAAATCAATAGTTACT 196 GTTTTTAGCAACAACCAAAATATTTTAGGGTTTAGGGTTTAGAGTTCACAAAATCAATAGTTACT * 53748 TATATTATTTGTTGTGTAC 261 TATATTATTTGTTGTATAC * * * * 53767 TGATTTTATGAACCTTAAACCCT-AAATATTTTTGGTTGTTACTAAAAACCT 1 TGATATTATGAACCTTAAACCCTAAAATA-TTTTGGTTATTCCTGAAAACCT 53818 TTATCTACCA Statistics Matches: 298, Mismatches: 26, Indels: 11 0.89 0.08 0.03 Matches are distributed among these distances: 273 5 0.02 274 139 0.47 275 4 0.01 277 1 0.00 281 30 0.10 282 54 0.18 283 65 0.22 ACGTcount: A:0.32, C:0.10, G:0.22, T:0.37 Consensus pattern (279 bp): TGATATTATGAACCTTAAACCCTAAAATATTTTGGTTATTCCTGAAAACCTATATAAATTCATGG TATGTTGAGGGAAATGAAAGGGGTAGAGGATGGTGATATCTACCATGATGGTGGTTACAAATTTG TTTTTTATAAGAAGAAATTGATTGGAGGGAGAATTAGGTTCAGGGTTTAAAGTCCAGAGTTTAGA GTTTTTAGCAACAACCAAAATATTTTAGGGTTTAGGGTTTAGAGTTCACAAAATCAATAGTTACT TATATTATTTGTTGTATAC Found at i:53906 original size:56 final size:56 Alignment explanation
Indices: 53840--53953 Score: 201 Period size: 56 Copynumber: 2.0 Consensus size: 56 53830 CAATTTCTTC * * 53840 TTGTAAAAACAAATATGTAACCACCATCATGGTAGATATCACCCTCCTCTACCTCT 1 TTGTAAAAACAAATATGTAACCACCATCATGGTAGATATCACCATCCTCTACCCCT * 53896 TTGTAAAAACAAATTTGTAACCACCATCATGGTAGATATCACCATCCTCTACCCCT 1 TTGTAAAAACAAATATGTAACCACCATCATGGTAGATATCACCATCCTCTACCCCT 53952 TT 1 TT 53954 CATTGCCCTC Statistics Matches: 55, Mismatches: 3, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 56 55 1.00 ACGTcount: A:0.33, C:0.28, G:0.09, T:0.30 Consensus pattern (56 bp): TTGTAAAAACAAATATGTAACCACCATCATGGTAGATATCACCATCCTCTACCCCT Found at i:54700 original size:30 final size:27 Alignment explanation
Indices: 54637--54706 Score: 88 Period size: 27 Copynumber: 2.5 Consensus size: 27 54627 ATATTTATAT * 54637 ACTTTAATATAATACTCTTACAATCCC 1 ACTTTAATATAATACTCTTACAAACCC 54664 ACTTTAATATAATACTCTTA-AAACCAC 1 ACTTTAATATAATACTCTTACAAACC-C 54691 ATAACTTTAATATAAT 1 ---ACTTTAATATAAT 54707 GGGTTAAAAT Statistics Matches: 38, Mismatches: 1, Indels: 5 0.86 0.02 0.11 Matches are distributed among these distances: 26 4 0.11 27 21 0.55 30 13 0.34 ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37 Consensus pattern (27 bp): ACTTTAATATAATACTCTTACAAACCC Found at i:54963 original size:32 final size:31 Alignment explanation
Indices: 54902--54980 Score: 117 Period size: 32 Copynumber: 2.6 Consensus size: 31 54892 ACCTTCAACA * 54902 GACTGCATGGCGACC--TACTTCTTCGCCCC 1 GACTGCATGGCGACCAATACTGCTTCGCCCC * 54931 GACTGCATGACGACCAATACCTGCTTCGCCCC 1 GACTGCATGGCGACCAATA-CTGCTTCGCCCC 54963 GACTGCATGGCGACCAAT 1 GACTGCATGGCGACCAAT 54981 CTCACCCCTG Statistics Matches: 44, Mismatches: 3, Indels: 3 0.88 0.06 0.06 Matches are distributed among these distances: 29 14 0.32 31 2 0.05 32 28 0.64 ACGTcount: A:0.20, C:0.38, G:0.22, T:0.20 Consensus pattern (31 bp): GACTGCATGGCGACCAATACTGCTTCGCCCC Found at i:57287 original size:29 final size:30 Alignment explanation
Indices: 57237--57307 Score: 76 Period size: 29 Copynumber: 2.4 Consensus size: 30 57227 ATATCGGTGT * 57237 TATTTGATTCATTTTACTAGTGCGTAGATTA 1 TATTTGATTCATTTTA-TAGTGCATAGATTA * 57268 TATTTGATTC-TTTGT-TAGTGTATAGATTA 1 TATTTGATTCATTT-TATAGTGCATAGATTA * 57297 -AATTGATTCAT 1 TATTTGATTCAT 57308 CTATAGTAGA Statistics Matches: 35, Mismatches: 3, Indels: 6 0.80 0.07 0.14 Matches are distributed among these distances: 28 8 0.23 29 13 0.37 30 3 0.09 31 11 0.31 ACGTcount: A:0.27, C:0.07, G:0.15, T:0.51 Consensus pattern (30 bp): TATTTGATTCATTTTATAGTGCATAGATTA Found at i:59906 original size:22 final size:22 Alignment explanation
Indices: 59880--59923 Score: 61 Period size: 22 Copynumber: 2.0 Consensus size: 22 59870 TTTTTCCTCT * 59880 TTTAAGTTCTTCTGTTTTGGAA 1 TTTAAGTTCTTCTATTTTGGAA * * 59902 TTTAATTTTTTCTATTTTGGAA 1 TTTAAGTTCTTCTATTTTGGAA 59924 GTTGAACTTG Statistics Matches: 19, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 22 19 1.00 ACGTcount: A:0.20, C:0.07, G:0.14, T:0.59 Consensus pattern (22 bp): TTTAAGTTCTTCTATTTTGGAA Found at i:61069 original size:184 final size:184 Alignment explanation
Indices: 60760--61122 Score: 690 Period size: 184 Copynumber: 2.0 Consensus size: 184 60750 AGCTTCAAGT 60760 AGCAACTTTTCATGTGAATTTTGCTTCAGGGAATCATTCGTTGAGTTGAAGTTTTCATTGCTTTT 1 AGCAACTTTTCATGTGAATTTTGCTTCAGGGAATCATTCGTTGAGTTGAAGTTTTCATTGCTTTT 60825 TTGAGTTCTGATATATTTTATTAGCATTACATGTGTGGTGACCTACGTGAACATGCTATTTCAGA 66 TTGAGTTCTGATATATTTTATTAGCATTACATGTGTGGTGACCTACGTGAACATGCTATTTCAGA 60890 TGATAAAAGAACTCAAACTTGCACGGATGTCAGTGAGGCAACCCGGCATCTTGA 131 TGATAAAAGAACTCAAACTTGCACGGATGTCAGTGAGGCAACCCGGCATCTTGA * 60944 AGCAACTTTTCATGTGAATTTTGCTTCAGGGCATCATTCGTTGAGTTGAAGTTTTCATTGCTTTT 1 AGCAACTTTTCATGTGAATTTTGCTTCAGGGAATCATTCGTTGAGTTGAAGTTTTCATTGCTTTT * 61009 TTGAGTTCTGATATATTTTATTAGCATTACATGTGTGTTGACCTACGTGAACATGCTATTTCAGA 66 TTGAGTTCTGATATATTTTATTAGCATTACATGTGTGGTGACCTACGTGAACATGCTATTTCAGA * * 61074 TGATAAAAGTACTCAACCTTGCACGGATGTCAGTGAGGCAACCCGGCAT 131 TGATAAAAGAACTCAAACTTGCACGGATGTCAGTGAGGCAACCCGGCAT 61123 GGTTTAGAAT Statistics Matches: 175, Mismatches: 4, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 184 175 1.00 ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36 Consensus pattern (184 bp): AGCAACTTTTCATGTGAATTTTGCTTCAGGGAATCATTCGTTGAGTTGAAGTTTTCATTGCTTTT TTGAGTTCTGATATATTTTATTAGCATTACATGTGTGGTGACCTACGTGAACATGCTATTTCAGA TGATAAAAGAACTCAAACTTGCACGGATGTCAGTGAGGCAACCCGGCATCTTGA Found at i:62419 original size:58 final size:58 Alignment explanation
Indices: 62313--62423 Score: 136 Period size: 58 Copynumber: 1.9 Consensus size: 58 62303 TATAATATTG * * * ** 62313 ATTCTAAATTGATCCTTAAATTTTTTAATATTTCAATTTTATCCCTAAATTATGACTC 1 ATTCTAAATTGATCCTTAAACTTTTGAAGATTTCAATTCCATCCCTAAATTATGACTC * 62371 ATTCTAAATT-AGTCCTTAAACTTTTGAAGA-TTCTAATTCCATCTCTAAATTAT 1 ATTCTAAATTGA-TCCTTAAACTTTTGAAGATTTC-AATTCCATCCCTAAATTAT 62424 AACACCCTTT Statistics Matches: 45, Mismatches: 6, Indels: 4 0.82 0.11 0.07 Matches are distributed among these distances: 57 4 0.09 58 41 0.91 ACGTcount: A:0.33, C:0.16, G:0.05, T:0.46 Consensus pattern (58 bp): ATTCTAAATTGATCCTTAAACTTTTGAAGATTTCAATTCCATCCCTAAATTATGACTC Found at i:63081 original size:97 final size:97 Alignment explanation
Indices: 62970--63163 Score: 300 Period size: 97 Copynumber: 2.0 Consensus size: 97 62960 TCAGATATAA ** * 62970 ATTTGATTTAAAAAATTGACTGGTCCTATATAAACCTAATTTAATTATGTTCAAATCAACAATGA 1 ATTTGATTTAAAAAATTGACTAATCCGATATAAACCTAATTTAATTATGTTCAAATCAACAATGA * 63035 ACCAATTTAATGCTCGATTCAACCTGACTTAT 66 ACCAATTTAATACTCGATTCAACCTGACTTAT * * * 63067 ATTTGAATTT-AAAAATTGACTAATCCGATATAGACCTAGTTTAATTATGTTCAAATCGACAATG 1 ATTTG-ATTTAAAAAATTGACTAATCCGATATAAACCTAATTTAATTATGTTCAAATCAACAATG * 63131 AACCAATTTAATACTTGATTCAACCTGACTTAT 65 AACCAATTTAATACTCGATTCAACCTGACTTAT 63164 CATAGATTTG Statistics Matches: 88, Mismatches: 8, Indels: 2 0.90 0.08 0.02 Matches are distributed among these distances: 97 84 0.95 98 4 0.05 ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36 Consensus pattern (97 bp): ATTTGATTTAAAAAATTGACTAATCCGATATAAACCTAATTTAATTATGTTCAAATCAACAATGA ACCAATTTAATACTCGATTCAACCTGACTTAT Found at i:73542 original size:19 final size:19 Alignment explanation
Indices: 73518--73556 Score: 78 Period size: 19 Copynumber: 2.1 Consensus size: 19 73508 CTGGCATCAC 73518 ACTAACTTTCCTTTCAGCT 1 ACTAACTTTCCTTTCAGCT 73537 ACTAACTTTCCTTTCAGCT 1 ACTAACTTTCCTTTCAGCT 73556 A 1 A 73557 TTGAGAAAGT Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 20 1.00 ACGTcount: A:0.23, C:0.31, G:0.05, T:0.41 Consensus pattern (19 bp): ACTAACTTTCCTTTCAGCT Found at i:83995 original size:27 final size:27 Alignment explanation
Indices: 83956--84018 Score: 76 Period size: 27 Copynumber: 2.4 Consensus size: 27 83946 CAAAACAGAA * 83956 ATAGCATAATAATATAATCTTT-TATAT 1 ATAGAATAATAATATAAT-TTTCTATAT * * 83983 ATAGAATAGTAATATAATTTTCTATCT 1 ATAGAATAATAATATAATTTTCTATAT 84010 ATA-AATAAT 1 ATAGAATAAT 84019 TCTCACCTTA Statistics Matches: 31, Mismatches: 4, Indels: 3 0.82 0.11 0.08 Matches are distributed among these distances: 26 8 0.26 27 23 0.74 ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43 Consensus pattern (27 bp): ATAGAATAATAATATAATTTTCTATAT Done.