Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: VEPZ01002293.1 Hibiscus syriacus cultivar Beakdansim tig00004663_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: 74541 ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33 Found at i:1067 original size:15 final size:16 Alignment explanation
Indices: 1044--1077 Score: 52 Period size: 15 Copynumber: 2.2 Consensus size: 16 1034 TAGAAATTAT * 1044 TTTTATTGTTATTTTA 1 TTTTATTGTTAATTTA 1060 TTTT-TTGTTAATTTA 1 TTTTATTGTTAATTTA 1075 TTT 1 TTT 1078 GATGTTCATA Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 15 13 0.76 16 4 0.24 ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76 Consensus pattern (16 bp): TTTTATTGTTAATTTA Found at i:4949 original size:2 final size:2 Alignment explanation
Indices: 4942--4988 Score: 94 Period size: 2 Copynumber: 23.5 Consensus size: 2 4932 CCCATCATTC 4942 TA TA TA 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 4984 TA TA T 1 TA TA T 4989 GGGTAAATTA Statistics Matches: 45, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 45 1.00 ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51 Consensus pattern (2 bp): TA Found at i:7801 original size:2 final size:2 Alignment explanation
Indices: 7759--7790 Score: 57 Period size: 2 Copynumber: 16.5 Consensus size: 2 7749 TTTTATAATA 7759 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 7791 CAATTATATA Statistics Matches: 29, Mismatches: 0, Indels: 2 0.94 0.00 0.06 Matches are distributed among these distances: 1 1 0.03 2 28 0.97 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:8680 original size:2 final size:2 Alignment explanation
Indices: 8673--8710 Score: 76 Period size: 2 Copynumber: 19.0 Consensus size: 2 8663 TTCAGGAAAT 8673 TA 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 8711 AATTTGTTAA 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): TA Found at i:17797 original size:31 final size:32 Alignment explanation
Indices: 17755--17848 Score: 106 Period size: 31 Copynumber: 3.1 Consensus size: 32 17745 GTTTTTATCT * * * 17755 AATT-TATCAAATTGTTATAAAATGATCATTA 1 AATTCTATCAAATTATTATAAAATAAACATTA 17786 AA-TCTATCAAATTATTATAAAATAAACATTA 1 AATTCTATCAAATTATTATAAAATAAACATTA * * * 17817 AATTTTATCAAA--ATTATAAAACAATCATTA 1 AATTCTATCAAATTATTATAAAATAAACATTA 17847 AA 1 AA 17849 GTTATGAAAG Statistics Matches: 55, Mismatches: 6, Indels: 5 0.83 0.09 0.08 Matches are distributed among these distances: 30 19 0.35 31 28 0.51 32 8 0.15 ACGTcount: A:0.52, C:0.09, G:0.02, T:0.37 Consensus pattern (32 bp): AATTCTATCAAATTATTATAAAATAAACATTA Found at i:19390 original size:12 final size:12 Alignment explanation
Indices: 19373--19397 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 19363 CTCAAACAGA 19373 GAGAATGAACGT 1 GAGAATGAACGT 19385 GAGAATGAACGT 1 GAGAATGAACGT 19397 G 1 G 19398 TTGCATGGCA 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:0.40, C:0.08, G:0.36, T:0.16 Consensus pattern (12 bp): GAGAATGAACGT Found at i:19526 original size:33 final size:33 Alignment explanation
Indices: 19485--19569 Score: 100 Period size: 33 Copynumber: 2.6 Consensus size: 33 19475 GCGACCTACC * 19485 CTCGCTCGGCTT-CCCTCGGATTCCATCGCATAG 1 CTCGCTCGG-TTGCCCTCGGATGCCATCGCATAG * * 19518 CTCGCTCGGTTGCCCTCGGATGCCCTCGTATAG 1 CTCGCTCGGTTGCCCTCGGATGCCATCGCATAG * * * 19551 CTCGTTCGGATGGCCTCGG 1 CTCGCTCGGTTGCCCTCGG 19570 TCGGATGGCC Statistics Matches: 45, Mismatches: 6, Indels: 2 0.85 0.11 0.04 Matches are distributed among these distances: 32 2 0.04 33 43 0.96 ACGTcount: A:0.09, C:0.36, G:0.27, T:0.27 Consensus pattern (33 bp): CTCGCTCGGTTGCCCTCGGATGCCATCGCATAG Found at i:19573 original size:14 final size:14 Alignment explanation
Indices: 19551--19597 Score: 85 Period size: 14 Copynumber: 3.4 Consensus size: 14 19541 CCTCGTATAG * 19551 CTCGTTCGGATGGC 1 CTCGGTCGGATGGC 19565 CTCGGTCGGATGGC 1 CTCGGTCGGATGGC 19579 CTCGGTCGGATGGC 1 CTCGGTCGGATGGC 19593 CTCGG 1 CTCGG 19598 ATGGCCAATG Statistics Matches: 32, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 14 32 1.00 ACGTcount: A:0.06, C:0.30, G:0.40, T:0.23 Consensus pattern (14 bp): CTCGGTCGGATGGC Found at i:25980 original size:20 final size:19 Alignment explanation
Indices: 25955--26006 Score: 68 Period size: 19 Copynumber: 2.7 Consensus size: 19 25945 GCTGCTGGAA * * 25955 AACCGGTTTGACCAGTTTTG 1 AACCGGTTTGACC-GGTCTG 25975 AACCGGTTTGACCGGTCTG 1 AACCGGTTTGACCGGTCTG * 25994 AACCGGGTTGACC 1 AACCGGTTTGACC 26007 CGACCCGACT Statistics Matches: 29, Mismatches: 3, Indels: 1 0.88 0.09 0.03 Matches are distributed among these distances: 19 16 0.55 20 13 0.45 ACGTcount: A:0.19, C:0.25, G:0.29, T:0.27 Consensus pattern (19 bp): AACCGGTTTGACCGGTCTG Found at i:25984 original size:10 final size:10 Alignment explanation
Indices: 25955--26004 Score: 50 Period size: 10 Copynumber: 5.1 Consensus size: 10 25945 GCTGCTGGAA 25955 AACCGGTTTG 1 AACCGGTTTG * 25965 -ACCAGTTTTG 1 AACC-GGTTTG 25975 AACCGGTTTG 1 AACCGGTTTG * 25985 -ACCGGTCTG 1 AACCGGTTTG * 25994 AACCGGGTTG 1 AACCGGTTTG 26004 A 1 A 26005 CCCGACCCGA Statistics Matches: 32, Mismatches: 5, Indels: 6 0.74 0.12 0.14 Matches are distributed among these distances: 9 11 0.34 10 18 0.56 11 3 0.09 ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28 Consensus pattern (10 bp): AACCGGTTTG Found at i:26021 original size:14 final size:14 Alignment explanation
Indices: 26002--26029 Score: 56 Period size: 14 Copynumber: 2.0 Consensus size: 14 25992 TGAACCGGGT 26002 TGACCCGACCCGAC 1 TGACCCGACCCGAC 26016 TGACCCGACCCGAC 1 TGACCCGACCCGAC 26030 CCGACTGTTG Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 14 1.00 ACGTcount: A:0.21, C:0.50, G:0.21, T:0.07 Consensus pattern (14 bp): TGACCCGACCCGAC Found at i:26044 original size:17 final size:17 Alignment explanation
Indices: 26000--26059 Score: 66 Period size: 17 Copynumber: 3.4 Consensus size: 17 25990 TCTGAACCGG 26000 GTTGACCCGACCCGACT 1 GTTGACCCGACCCGACT ** 26017 GACCCGACCCGACCCGACT 1 G--TTGACCCGACCCGACT * * 26036 GTTGACCCGACCCAACC 1 GTTGACCCGACCCGACT 26053 GTTGACC 1 GTTGACC 26060 GTTGACCGTT Statistics Matches: 35, Mismatches: 6, Indels: 4 0.78 0.13 0.09 Matches are distributed among these distances: 17 20 0.57 19 15 0.43 ACGTcount: A:0.20, C:0.45, G:0.22, T:0.13 Consensus pattern (17 bp): GTTGACCCGACCCGACT Found at i:27024 original size:63 final size:63 Alignment explanation
Indices: 26941--27064 Score: 148 Period size: 63 Copynumber: 2.0 Consensus size: 63 26931 CTAATGTGAC * * * 26941 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGC-CCTGC-GGCCCTAAGATGTG 1 TCTTAGGTAGGCTCTACGGCCCCGAAATCTA-TCTCGGGTAGGCTCC--CAGGCCCTAAGATGTG 27003 T 63 T * 27004 TCTTAGGTAGGC-CTCACGGCCCCGAAATCTATCTTGGGTAGGCTCCCAGGCCCTAAGATGT 1 TCTTAGGTAGGCTCT-ACGGCCCCGAAATCTATCTCGGGTAGGCTCCCAGGCCCTAAGATGT 27065 TCCCTTAGGG Statistics Matches: 53, Mismatches: 4, Indels: 8 0.82 0.06 0.12 Matches are distributed among these distances: 62 3 0.06 63 47 0.89 64 3 0.06 ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26 Consensus pattern (63 bp): TCTTAGGTAGGCTCTACGGCCCCGAAATCTATCTCGGGTAGGCTCCCAGGCCCTAAGATGTGT Found at i:33328 original size:14 final size:15 Alignment explanation
Indices: 33308--33353 Score: 67 Period size: 14 Copynumber: 3.0 Consensus size: 15 33298 CTGAACCGGG 33308 TTGACCCGACCCGAC 1 TTGACCCGACCCGAC 33323 -TGACCCGACCCGAC 1 TTGACCCGACCCGAC 33337 TGTTGACCCGACCCGAC 1 --TTGACCCGACCCGAC 33354 CGTTGACCGT Statistics Matches: 28, Mismatches: 0, Indels: 4 0.88 0.00 0.12 Matches are distributed among these distances: 14 14 0.50 17 14 0.50 ACGTcount: A:0.20, C:0.46, G:0.22, T:0.13 Consensus pattern (15 bp): TTGACCCGACCCGAC Found at i:33345 original size:17 final size:16 Alignment explanation
Indices: 33307--33361 Score: 78 Period size: 17 Copynumber: 3.4 Consensus size: 16 33297 TCTGAACCGG 33307 GTTGACCCGACCCGAC 1 GTTGACCCGACCCGAC 33323 --TGACCCGACCCGAC 1 GTTGACCCGACCCGAC 33337 TGTTGACCCGACCCGACC 1 -GTTGACCCGACCCGA-C 33355 GTTGACC 1 GTTGACC 33362 GTTGACTTCC Statistics Matches: 35, Mismatches: 0, Indels: 7 0.83 0.00 0.17 Matches are distributed among these distances: 14 14 0.40 17 20 0.57 18 1 0.03 ACGTcount: A:0.18, C:0.44, G:0.24, T:0.15 Consensus pattern (16 bp): GTTGACCCGACCCGAC Found at i:34320 original size:63 final size:63 Alignment explanation
Indices: 34237--34360 Score: 148 Period size: 63 Copynumber: 2.0 Consensus size: 63 34227 CTAATGTGAC * * * 34237 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGC-CCTGC-GGCCCTAAGATGTG 1 TCTTAGGTAGGCTCTACGGCCCCGAAATCTA-TCTCGGGTAGGCTCC--CAGGCCCTAAGATGTG 34299 T 63 T * 34300 TCTTAGGTAGGC-CTCACGGCCCCGAAATCTATCTTGGGTAGGCTCCCAGGCCCTAAGATGT 1 TCTTAGGTAGGCTCT-ACGGCCCCGAAATCTATCTCGGGTAGGCTCCCAGGCCCTAAGATGT 34361 TCCCTTAGGG Statistics Matches: 53, Mismatches: 4, Indels: 8 0.82 0.06 0.12 Matches are distributed among these distances: 62 3 0.06 63 47 0.89 64 3 0.06 ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26 Consensus pattern (63 bp): TCTTAGGTAGGCTCTACGGCCCCGAAATCTATCTCGGGTAGGCTCCCAGGCCCTAAGATGTGT Found at i:37900 original size:9 final size:9 Alignment explanation
Indices: 37886--37926 Score: 50 Period size: 9 Copynumber: 4.7 Consensus size: 9 37876 AAGTTATGTC * 37886 AATTAAGAT 1 AATTAAGCT 37895 AATTAA-CT 1 AATTAAGCT 37903 AATTTAAGCT 1 AA-TTAAGCT 37913 AATT-AGCT 1 AATTAAGCT 37921 AATTAA 1 AATTAA 37927 CACGCACATC Statistics Matches: 28, Mismatches: 1, Indels: 6 0.80 0.03 0.17 Matches are distributed among these distances: 8 11 0.39 9 13 0.46 10 4 0.14 ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37 Consensus pattern (9 bp): AATTAAGCT Found at i:37915 original size:18 final size:18 Alignment explanation
Indices: 37888--37924 Score: 56 Period size: 18 Copynumber: 2.1 Consensus size: 18 37878 GTTATGTCAA 37888 TTAAGATAATTAACTAAT 1 TTAAGATAATTAACTAAT * * 37906 TTAAGCTAATTAGCTAAT 1 TTAAGATAATTAACTAAT 37924 T 1 T 37925 AACACGCACA Statistics Matches: 17, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 18 17 1.00 ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41 Consensus pattern (18 bp): TTAAGATAATTAACTAAT Found at i:46371 original size:18 final size:18 Alignment explanation
Indices: 46350--46384 Score: 52 Period size: 18 Copynumber: 1.9 Consensus size: 18 46340 TGATTGTGAT 46350 CGTGACCATGATAGAGAG 1 CGTGACCATGATAGAGAG * * 46368 CGTGATCGTGATAGAGA 1 CGTGACCATGATAGAGA 46385 CCACGAGCGC Statistics Matches: 15, Mismatches: 2, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 18 15 1.00 ACGTcount: A:0.31, C:0.14, G:0.34, T:0.20 Consensus pattern (18 bp): CGTGACCATGATAGAGAG Found at i:46399 original size:30 final size:30 Alignment explanation
Indices: 46329--46400 Score: 72 Period size: 30 Copynumber: 2.4 Consensus size: 30 46319 TAGTGACTTT * * * * * 46329 GAGCGTGAGCGTGATTGTGATCGTGACCAT 1 GAGCGAGAGCGTGATCGTGATAGAGACCAC ** 46359 GATAGAGAGCGTGATCGTGATAGAGACCAC 1 GAGCGAGAGCGTGATCGTGATAGAGACCAC * 46389 GAGCGCGAGCGT 1 GAGCGAGAGCGT 46401 TACAGGGACC Statistics Matches: 32, Mismatches: 10, Indels: 0 0.76 0.24 0.00 Matches are distributed among these distances: 30 32 1.00 ACGTcount: A:0.25, C:0.18, G:0.38, T:0.19 Consensus pattern (30 bp): GAGCGAGAGCGTGATCGTGATAGAGACCAC Found at i:46488 original size:30 final size:30 Alignment explanation
Indices: 46452--46550 Score: 189 Period size: 30 Copynumber: 3.3 Consensus size: 30 46442 TGATCTTGAT 46452 CGTGATCATTATCAAGAACATGACCGCAAC 1 CGTGATCATTATCAAGAACATGACCGCAAC 46482 CGTGATCATTATCAAGAACATGACCGCAAC 1 CGTGATCATTATCAAGAACATGACCGCAAC * 46512 CGTGATCATTATCAAGAACATGACTGCAAC 1 CGTGATCATTATCAAGAACATGACCGCAAC 46542 CGTGATCAT 1 CGTGATCAT 46551 GACCATGACC Statistics Matches: 68, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 30 68 1.00 ACGTcount: A:0.35, C:0.25, G:0.17, T:0.22 Consensus pattern (30 bp): CGTGATCATTATCAAGAACATGACCGCAAC Found at i:55023 original size:24 final size:24 Alignment explanation
Indices: 54991--55065 Score: 114 Period size: 24 Copynumber: 3.1 Consensus size: 24 54981 TAGTGACTTT * 54991 GAGTATGATCGTGACCATGATAGA 1 GAGTGTGATCGTGACCATGATAGA 55015 GAGTGTGATCGTGACCATGATAGA 1 GAGTGTGATCGTGACCATGATAGA * * * 55039 GACTGTGATCGTGAGCATTATAGA 1 GAGTGTGATCGTGACCATGATAGA 55063 GAG 1 GAG 55066 CGAGACATGG Statistics Matches: 46, Mismatches: 5, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 24 46 1.00 ACGTcount: A:0.31, C:0.12, G:0.32, T:0.25 Consensus pattern (24 bp): GAGTGTGATCGTGACCATGATAGA Found at i:58969 original size:2 final size:2 Alignment explanation
Indices: 58962--59001 Score: 80 Period size: 2 Copynumber: 20.0 Consensus size: 2 58952 CTATCTAATA 58962 AT 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 AT 59002 GAATGTCTCA Statistics Matches: 38, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 38 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:61164 original size:17 final size:17 Alignment explanation
Indices: 61142--61187 Score: 83 Period size: 17 Copynumber: 2.7 Consensus size: 17 61132 GAAATTTTTG * 61142 GTTTTGAATGATTGAAA 1 GTTTTGAATGAATGAAA 61159 GTTTTGAATGAATGAAA 1 GTTTTGAATGAATGAAA 61176 GTTTTGAATGAA 1 GTTTTGAATGAA 61188 GGAAGGAATA Statistics Matches: 28, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 17 28 1.00 ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39 Consensus pattern (17 bp): GTTTTGAATGAATGAAA Found at i:61923 original size:47 final size:47 Alignment explanation
Indices: 61869--61962 Score: 152 Period size: 47 Copynumber: 2.0 Consensus size: 47 61859 TTAATAATTG ** * 61869 TTATAAAATAGTATAAAGTATAAACCCTTAAATATTTTTAAAGTATA 1 TTATAAAATAGTATAAAGTATAAACCCCAAAATAATTTTAAAGTATA * 61916 TTATAAAATAGTATAAAGTATAAACCCCAAAATAATTTTGAAGTATA 1 TTATAAAATAGTATAAAGTATAAACCCCAAAATAATTTTAAAGTATA 61963 CGCAATCTCT Statistics Matches: 43, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 47 43 1.00 ACGTcount: A:0.50, C:0.07, G:0.07, T:0.35 Consensus pattern (47 bp): TTATAAAATAGTATAAAGTATAAACCCCAAAATAATTTTAAAGTATA Found at i:65209 original size:19 final size:19 Alignment explanation
Indices: 65185--65247 Score: 72 Period size: 23 Copynumber: 3.1 Consensus size: 19 65175 TCGGGCTGGG * 65185 TATATACATTTAAATTAAA 1 TATATAAATTTAAATTAAA 65204 TATATAAATATTAAATATATATA 1 TATATAAAT-TTAAAT-TA-A-A 65227 TATATATAATTTAAATTAAA 1 TATATA-AATTTAAATTAAA 65247 T 1 T 65248 TTATTAATAT Statistics Matches: 38, Mismatches: 1, Indels: 9 0.79 0.02 0.19 Matches are distributed among these distances: 19 8 0.21 20 8 0.21 21 3 0.08 22 3 0.08 23 13 0.34 24 3 0.08 ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44 Consensus pattern (19 bp): TATATAAATTTAAATTAAA Found at i:65283 original size:43 final size:43 Alignment explanation
Indices: 65185--65279 Score: 140 Period size: 43 Copynumber: 2.2 Consensus size: 43 65175 TCGGGCTGGG 65185 TATATACATTTAAATTAAATATATAAATATTAAATATATATATA 1 TATATA-ATTTAAATTAAATATATAAATATTAAATATATATATA * * * 65229 TATATAATTTAAATTAAATTTATTAATATTATATATATATA-A 1 TATATAATTTAAATTAAATATATAAATATTAAATATATATATA 65271 TA-ATAATTT 1 TATATAATTT 65280 TTAATATTTA Statistics Matches: 48, Mismatches: 3, Indels: 3 0.89 0.06 0.06 Matches are distributed among these distances: 41 7 0.15 42 3 0.06 43 32 0.67 44 6 0.12 ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47 Consensus pattern (43 bp): TATATAATTTAAATTAAATATATAAATATTAAATATATATATA Found at i:72760 original size:7 final size:7 Alignment explanation
Indices: 72748--72772 Score: 50 Period size: 7 Copynumber: 3.6 Consensus size: 7 72738 CATGACAATG 72748 AATATGA 1 AATATGA 72755 AATATGA 1 AATATGA 72762 AATATGA 1 AATATGA 72769 AATA 1 AATA 72773 AAACAAAACA Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 18 1.00 ACGTcount: A:0.60, C:0.00, G:0.12, T:0.28 Consensus pattern (7 bp): AATATGA Done.