Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01004913.1 Hibiscus syriacus cultivar Beakdansim tig00011062_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: 58962
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:1565 original size:22 final size:21

Alignment explanation

Indices: 1523--1562 Score: 62 Period size: 21 Copynumber: 1.9 Consensus size: 21 1513 AAGACTATTT 1523 TCATTTTTCAATTTTGAAATA 1 TCATTTTTCAATTTTGAAATA ** 1544 TCATTTTTGTATTTTGAAA 1 TCATTTTTCAATTTTGAAA 1563 ATAGAGTCTT Statistics Matches: 17, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 21 17 1.00 ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55 Consensus pattern (21 bp): TCATTTTTCAATTTTGAAATA Found at i:6212 original size:13 final size:13 Alignment explanation

Indices: 6193--6230 Score: 51 Period size: 13 Copynumber: 2.8 Consensus size: 13 6183 TAATTTAATG 6193 ATTATAAATAA-A 1 ATTATAAATAAGA 6205 ATTTATAATATAAGA 1 A-TTATAA-ATAAGA 6220 ATTATAAATAA 1 ATTATAAATAA 6231 TATAAAGAAT Statistics Matches: 23, Mismatches: 0, Indels: 5 0.82 0.00 0.18 Matches are distributed among these distances: 12 1 0.04 13 10 0.43 14 10 0.43 15 2 0.09 ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37 Consensus pattern (13 bp): ATTATAAATAAGA Found at i:6240 original size:19 final size:19 Alignment explanation

Indices: 6209--6255 Score: 62 Period size: 19 Copynumber: 2.5 Consensus size: 19 6199 AATAAAATTT 6209 ATAATAT-AAGAATT-ATAA 1 ATAATATAAAGAATTGA-AA 6227 ATAATATAAAGAATTGAAA 1 ATAATATAAAGAATTGAAA * 6246 TTAATATAAA 1 ATAATATAAA 6256 AATCAAATTT Statistics Matches: 26, Mismatches: 1, Indels: 3 0.87 0.03 0.10 Matches are distributed among these distances: 18 7 0.27 19 18 0.69 20 1 0.04 ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32 Consensus pattern (19 bp): ATAATATAAAGAATTGAAA Found at i:9266 original size:29 final size:28 Alignment explanation

Indices: 9200--9266 Score: 66 Period size: 29 Copynumber: 2.3 Consensus size: 28 9190 TAAAATTATG 9200 TAAAAATATATTTTAAAAATCTTCTAATT 1 TAAAAATATATTTTAAAAA-CTTCTAATT * * 9229 GAAATATATATTTTATAAAA-TT-TAATTTT 1 TAAAAATATATTTTA-AAAACTTCTAA--TT 9258 TAAAAATAT 1 TAAAAATAT 9267 TCAAAATAAT Statistics Matches: 31, Mismatches: 4, Indels: 6 0.76 0.10 0.15 Matches are distributed among these distances: 27 3 0.10 28 2 0.06 29 22 0.71 30 4 0.13 ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46 Consensus pattern (28 bp): TAAAAATATATTTTAAAAACTTCTAATT Found at i:9599 original size:3 final size:3 Alignment explanation

Indices: 9593--9639 Score: 85 Period size: 3 Copynumber: 15.7 Consensus size: 3 9583 TTTTTATCCA * 9593 TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA 1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA 9640 AATATATATT Statistics Matches: 42, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 3 42 1.00 ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64 Consensus pattern (3 bp): TAT Found at i:9666 original size:14 final size:15 Alignment explanation

Indices: 9638--9672 Score: 63 Period size: 14 Copynumber: 2.4 Consensus size: 15 9628 TTATTATTAT 9638 TAAATATATATTAAA 1 TAAATATATATTAAA 9653 TAAATATATA-TAAA 1 TAAATATATATTAAA 9667 TAAATA 1 TAAATA 9673 ATTACAGACC Statistics Matches: 20, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 14 10 0.50 15 10 0.50 ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37 Consensus pattern (15 bp): TAAATATATATTAAA Found at i:22455 original size:12 final size:12 Alignment explanation

Indices: 22438--22465 Score: 56 Period size: 12 Copynumber: 2.3 Consensus size: 12 22428 TATTATGCTT 22438 AAAAAAAAGAGA 1 AAAAAAAAGAGA 22450 AAAAAAAAGAGA 1 AAAAAAAAGAGA 22462 AAAA 1 AAAA 22466 GGAGGGTCAA Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 16 1.00 ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00 Consensus pattern (12 bp): AAAAAAAAGAGA Found at i:23819 original size:84 final size:82 Alignment explanation

Indices: 23580--24069 Score: 842 Period size: 82 Copynumber: 5.9 Consensus size: 82 23570 TATGATATCC 23580 CAGAACAATCATTGAATTTAGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT 1 CAGAACAATCATTGAATTTAGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT 23645 TATCTGATCTGGTTGGA 66 TATCTGATCTGGTTGGA 23662 CAGAACAATCATTGAATTTAGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT 1 CAGAACAATCATTGAATTTAGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT 23727 TATCTGATCTGGTTGGA 66 TATCTGATCTGGTTGGA * 23744 CAGAACAATCATTGTGAGTTTAGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTG 1 CAGAACAATCA-T-TGAATTTAGAAGATGAATTTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTG 23808 AGTTATCTGATCTGGTTGGA 63 AGTTATCTGATCTGGTTGGA * * 23828 CAGAACAATCATTGTGAGTTTAGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTTTTCTTTG 1 CAGAACAATCA-T-TGAATTTAGAAGATGAATTTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTG 23892 AGTTATCTGATCTGGTTGGA 63 AGTTATCTGATCTGGTTGGA * 23912 CAGAACCAATCATTGAATTTAAAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAG 1 CAGAA-CAATCATTGAATTTAGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAG 23977 TTATCTGATCTGGTTGGA 65 TTATCTGATCTGGTTGGA * 23995 CAGAACAATCATTGAGTTTAGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAG 1 CAGAACAATCATTGAATTTAGAAGATGAATTTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAG 24059 TTATCTGATCT 65 TTATCTGATCT 24070 AGTTTGGTAG Statistics Matches: 395, Mismatches: 7, Indels: 12 0.95 0.02 0.03 Matches are distributed among these distances: 81 1 0.00 82 159 0.40 83 72 0.18 84 157 0.40 85 6 0.02 ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36 Consensus pattern (82 bp): CAGAACAATCATTGAATTTAGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGT TATCTGATCTGGTTGGA Found at i:24913 original size:41 final size:40 Alignment explanation

Indices: 24833--24936 Score: 190 Period size: 41 Copynumber: 2.6 Consensus size: 40 24823 GCTTTTCCAG * 24833 AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA 1 AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGA 24873 AGAAGTTCATAATGAGAAGAACATCATCTGAAGAAAGAAGA 1 AGAAGTTCATAATGAGAAGAAC-TCATCTGAAGAAAGAAGA 24914 AGAAGTTCATAATGAGAAGAACT 1 AGAAGTTCATAATGAGAAGAACT 24937 TGTTCAACTT Statistics Matches: 62, Mismatches: 1, Indels: 2 0.95 0.02 0.03 Matches are distributed among these distances: 40 23 0.37 41 39 0.63 ACGTcount: A:0.49, C:0.10, G:0.23, T:0.18 Consensus pattern (40 bp): AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGA Found at i:25029 original size:113 final size:113 Alignment explanation

Indices: 24875--25400 Score: 955 Period size: 113 Copynumber: 4.7 Consensus size: 113 24865 AAGGAAGAAG * * 24875 AAGTTCATAATGAGAAGAACATCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGT 1 AAGTTCATAATGAGAAGAAC-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT * 24940 TCAACTTTTTACCTGAATTCATCACTTGATGGATCATCTTTTCCAGAGA 65 TCAACCTTTTACCTGAATTCATCACTTGATGGATCATCTTTTCCAGAGA 24989 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT 1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT 25054 CAACCTTTTACCTGAATTCATCACTTGATGGATCATCTTTTCCAGAGA 66 CAACCTTTTACCTGAATTCATCACTTGATGGATCATCTTTTCCAGAGA 25102 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT 1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT * 25167 CAACCTTTTACCTGAATTCATCATTTGATGGATCATCTTTTCCAGAGA 66 CAACCTTTTACCTGAATTCATCACTTGATGGATCATCTTTTCCAGAGA 25215 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT 1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT * * 25280 CAACCTTTTACCTGAATTCATCAATTGATGGATTATCTTTTCCAGAG- 66 CAACCTTTTACCTGAATTCATCACTTGATGGATCATCTTTTCCAGAGA * * * 25327 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAATTTATT 1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT 25392 CAACCTTTT 66 CAACCTTTT 25401 GAATGACTCT Statistics Matches: 403, Mismatches: 9, Indels: 2 0.97 0.02 0.00 Matches are distributed among these distances: 112 71 0.18 113 312 0.77 114 20 0.05 ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29 Consensus pattern (113 bp): AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT CAACCTTTTACCTGAATTCATCACTTGATGGATCATCTTTTCCAGAGA Found at i:25726 original size:3 final size:3 Alignment explanation

Indices: 25718--25779 Score: 115 Period size: 3 Copynumber: 20.7 Consensus size: 3 25708 TTTTTATCCA * 25718 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT 1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT 25766 TAT TAT TAT TAT TA 1 TAT TAT TAT TAT TA 25780 AATATATATT Statistics Matches: 57, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 3 57 1.00 ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65 Consensus pattern (3 bp): TAT Found at i:25806 original size:14 final size:15 Alignment explanation

Indices: 25778--25812 Score: 63 Period size: 14 Copynumber: 2.4 Consensus size: 15 25768 TTATTATTAT 25778 TAAATATATATTAAA 1 TAAATATATATTAAA 25793 TAAATATATA-TAAA 1 TAAATATATATTAAA 25807 TAAATA 1 TAAATA 25813 ATTACAGACC Statistics Matches: 20, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 14 10 0.50 15 10 0.50 ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37 Consensus pattern (15 bp): TAAATATATATTAAA Found at i:35382 original size:82 final size:83 Alignment explanation

Indices: 35244--35401 Score: 239 Period size: 82 Copynumber: 1.9 Consensus size: 83 35234 TCAAATCTTA * * * * 35244 TAAGATTGTTTTTTTAATTTGGATTCATATTTAGGATGGAAATTTTTTACTTGAGATAATAATAT 1 TAAGATTGTTTTTTTAATTCGGATTCAGATTTAGGATGGAAATTTTTAACTCGAGATAATAATAT 35309 AATTATTCTTTATATATT 66 AATTATTCTTTATATATT * * 35327 TAAGATTTTTTTTTTAATTCGGATT-AGGTTTAGGAT-GAAACTTTTTAACTCGAGATAATAATA 1 TAAGATTGTTTTTTTAATTCGGATTCAGATTTAGGATGGAAA-TTTTTAACTCGAGATAATAATA 35390 TAATTATTCTTT 65 TAATTATTCTTT 35402 TGTATATTCA Statistics Matches: 68, Mismatches: 6, Indels: 3 0.88 0.08 0.04 Matches are distributed among these distances: 81 4 0.06 82 41 0.60 83 23 0.34 ACGTcount: A:0.32, C:0.05, G:0.13, T:0.50 Consensus pattern (83 bp): TAAGATTGTTTTTTTAATTCGGATTCAGATTTAGGATGGAAATTTTTAACTCGAGATAATAATAT AATTATTCTTTATATATT Found at i:36717 original size:41 final size:41 Alignment explanation

Indices: 36667--36757 Score: 130 Period size: 41 Copynumber: 2.2 Consensus size: 41 36657 CAACGAATTT * 36667 TCGCAACGAATTTGGAAA-ATCGCAACGACAACTGTAGACTA 1 TCGCAACGAATTTGGAAACATCGCAACGAAAACT-TAGACTA * * 36708 TCGCAACGAATTTGGAAACTATCGCAATGAAAACTTGGACTA 1 TCGCAACGAATTTGGAAAC-ATCGCAACGAAAACTTAGACTA 36750 TCGCAACG 1 TCGCAACG 36758 CGAAATGAAA Statistics Matches: 45, Mismatches: 3, Indels: 3 0.88 0.06 0.06 Matches are distributed among these distances: 41 18 0.40 42 14 0.31 43 13 0.29 ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21 Consensus pattern (41 bp): TCGCAACGAATTTGGAAACATCGCAACGAAAACTTAGACTA Found at i:36730 original size:21 final size:21 Alignment explanation

Indices: 36667--36734 Score: 77 Period size: 21 Copynumber: 3.3 Consensus size: 21 36657 CAACGAATTT 36667 TCGCAACGAATTTGGAAA--A 1 TCGCAACGAATTTGGAAACTA ** * * 36686 TCGCAACGACAACTGTAGACTA 1 TCGCAACGA-ATTTGGAAACTA 36708 TCGCAACGAATTTGGAAACTA 1 TCGCAACGAATTTGGAAACTA 36729 TCGCAA 1 TCGCAA 36735 TGAAAACTTG Statistics Matches: 38, Mismatches: 8, Indels: 4 0.76 0.16 0.08 Matches are distributed among these distances: 19 9 0.24 20 5 0.13 21 14 0.37 22 10 0.26 ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21 Consensus pattern (21 bp): TCGCAACGAATTTGGAAACTA Found at i:36809 original size:21 final size:21 Alignment explanation

Indices: 36746--36809 Score: 60 Period size: 21 Copynumber: 3.1 Consensus size: 21 36736 GAAAACTTGG 36746 ACTATCGCAACGCGAAATGA-A 1 ACTATCGCAACGCGAAAT-ACA * ** * 36767 A-AATCGCAACGCGATTTTCA 1 ACTATCGCAACGCGAAATACA * 36787 ACTATCGTAACGCGAAATACA 1 ACTATCGCAACGCGAAATACA 36808 AC 1 AC 36810 GCGAATTTGC Statistics Matches: 32, Mismatches: 9, Indels: 4 0.71 0.20 0.09 Matches are distributed among these distances: 20 15 0.47 21 17 0.53 ACGTcount: A:0.41, C:0.25, G:0.16, T:0.19 Consensus pattern (21 bp): ACTATCGCAACGCGAAATACA Found at i:41246 original size:29 final size:29 Alignment explanation

Indices: 41121--41237 Score: 216 Period size: 29 Copynumber: 4.0 Consensus size: 29 41111 TGATTGATAA * 41121 TTCAGCTCATCAAAGGGAGACTGAAACCT 1 TTCAGCTCATCAAAAGGAGACTGAAACCT 41150 TTCAGCTCATCAAAAGGAGACTGAAACCT 1 TTCAGCTCATCAAAAGGAGACTGAAACCT 41179 TTCAGCTCATCAAAAGGAGACTGAAACCT 1 TTCAGCTCATCAAAAGGAGACTGAAACCT * 41208 TTCAGCTCATCAAAAGGAGATTGAAACCT 1 TTCAGCTCATCAAAAGGAGACTGAAACCT 41237 T 1 T 41238 AGGATTCATT Statistics Matches: 86, Mismatches: 2, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 29 86 1.00 ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22 Consensus pattern (29 bp): TTCAGCTCATCAAAAGGAGACTGAAACCT Found at i:44638 original size:2 final size:2 Alignment explanation

Indices: 44631--44659 Score: 58 Period size: 2 Copynumber: 14.5 Consensus size: 2 44621 ATCAAGGGTT 44631 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T 44660 ACCCTTGACT Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 27 1.00 ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52 Consensus pattern (2 bp): TC Found at i:57836 original size:18 final size:17 Alignment explanation

Indices: 57807--57903 Score: 62 Period size: 18 Copynumber: 5.6 Consensus size: 17 57797 CTCCCATCAT 57807 ATATTT-AA-TTATCTAA 1 ATATTTAAATTTAT-TAA * 57823 ATATTTAAATTTATTAT 1 ATATTTAAATTTATTAA 57840 ATATTTGATAATTATATT-- 1 ATATTT-A-AATT-TATTAA * 57858 ATTTTTATAA-TTATATAA 1 ATATTTA-AATTTAT-TAA 57876 ATATTTAATATTT-TATAA 1 ATATTTAA-ATTTAT-TAA 57894 ATATTTAAAT 1 ATATTTAAAT 57904 ATTTAACTAG Statistics Matches: 68, Mismatches: 3, Indels: 19 0.76 0.03 0.21 Matches are distributed among these distances: 15 3 0.04 16 8 0.12 17 17 0.25 18 30 0.44 19 6 0.09 20 4 0.06 ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55 Consensus pattern (17 bp): ATATTTAAATTTATTAA Found at i:57837 original size:26 final size:26 Alignment explanation

Indices: 57812--57909 Score: 87 Period size: 26 Copynumber: 3.7 Consensus size: 26 57802 ATCATATATT * 57812 TAATTATCTAAATATTTAAATTTATTA 1 TAATTATATAAATATTTAAATTT-TTA * 57839 TATATT-TGATAATTATATT--ATTTTTA 1 TA-ATTAT-ATAAATAT-TTAAATTTTTA 57865 TAATTATATAAATATTT-AATATTTTA 1 TAATTATATAAATATTTAAAT-TTTTA * * 57891 TAAATATTTAAATATTTAA 1 TAATTATATAAATATTTAA 57910 CTAGCATAGA Statistics Matches: 59, Mismatches: 5, Indels: 14 0.76 0.06 0.18 Matches are distributed among these distances: 24 2 0.03 25 12 0.20 26 26 0.44 27 8 0.14 28 9 0.15 29 2 0.03 ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54 Consensus pattern (26 bp): TAATTATATAAATATTTAAATTTTTA Found at i:57853 original size:15 final size:16 Alignment explanation

Indices: 57835--57874 Score: 55 Period size: 17 Copynumber: 2.5 Consensus size: 16 57825 ATTTAAATTT 57835 ATTATATA-TTTGATA 1 ATTATATATTTTGATA * 57850 ATTATATTATTTTTATA 1 ATTATA-TATTTTGATA 57867 ATTATATA 1 ATTATATA 57875 AATATTTAAT Statistics Matches: 22, Mismatches: 1, Indels: 3 0.85 0.04 0.12 Matches are distributed among these distances: 15 6 0.27 16 4 0.18 17 12 0.55 ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57 Consensus pattern (16 bp): ATTATATATTTTGATA Found at i:57908 original size:18 final size:18 Alignment explanation

Indices: 57871--57907 Score: 65 Period size: 18 Copynumber: 2.0 Consensus size: 18 57861 TTTATAATTA 57871 TATAAATATTTAATATTT 1 TATAAATATTTAATATTT 57889 TATAAATATTTAAATATTT 1 TATAAATATTT-AATATTT 57908 AACTAGCATA Statistics Matches: 18, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 18 11 0.61 19 7 0.39 ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54 Consensus pattern (18 bp): TATAAATATTTAATATTT Done.