Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01000185.1 Hibiscus syriacus cultivar Beakdansim tig00000327_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: 76142
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:1654 original size:26 final size:25

Alignment explanation

Indices: 1614--1694 Score: 83 Period size: 27 Copynumber: 3.0 Consensus size: 25 1604 ATAAAATAGT 1614 AAGAAAAATAAATATAAAATAAAGAAA 1 AAGAAAAA-AAATATAAAATAAA-AAA 1641 AAGAAAAAAAATATATAAATAAAACAA 1 AAGAAAAAAAATATA-AAATAAAA-AA * 1668 ATA-AAAAAATAATAAAAAAGTAAAAAA 1 A-AGAAAAAA-AATATAAAA-TAAAAAA 1695 TATATATAAT Statistics Matches: 48, Mismatches: 1, Indels: 10 0.81 0.02 0.17 Matches are distributed among these distances: 26 8 0.17 27 29 0.60 28 11 0.23 ACGTcount: A:0.79, C:0.01, G:0.05, T:0.15 Consensus pattern (25 bp): AAGAAAAAAAATATAAAATAAAAAA Found at i:1664 original size:17 final size:17 Alignment explanation

Indices: 1617--1715 Score: 67 Period size: 17 Copynumber: 5.6 Consensus size: 17 1607 AAATAGTAAG 1617 AAAAATAAATATAAAATAAA 1 AAAAATAAA-A-AAAAT-AA * * 1637 GAAAAAGAAAAAAAATAT 1 -AAAAATAAAAAAAATAA * * 1655 ATAAATAAAACAAATAA 1 AAAAATAAAAAAAATAA 1672 AAAAATAATAAAAAAGT-A 1 AAAAATAA-AAAAAA-TAA * * * 1690 AAAAATATATATAAT-A 1 AAAAATAAAAAAAATAA 1706 AAAAATAAAA 1 AAAAATAAAA 1716 TAGTAAATAT Statistics Matches: 63, Mismatches: 13, Indels: 9 0.74 0.15 0.11 Matches are distributed among these distances: 16 10 0.16 17 24 0.38 18 14 0.22 19 6 0.10 20 1 0.02 21 8 0.13 ACGTcount: A:0.78, C:0.01, G:0.03, T:0.18 Consensus pattern (17 bp): AAAAATAAAAAAAATAA Found at i:1670 original size:43 final size:44 Alignment explanation

Indices: 1629--1715 Score: 119 Period size: 44 Copynumber: 2.0 Consensus size: 44 1619 AAATAAATAT 1629 AAAATAA-AGAAAAAGAAAAAAA-ATATATAAATAAAACAAATAAA 1 AAAATAATA-AAAAAGAAAAAAATATATAT-AATAAAACAAATAAA * 1673 AAAATAATAAAAAAGTAAAAAATATATATAAT-AAA-AAATAAA 1 AAAATAATAAAAAAGAAAAAAATATATATAATAAAACAAATAAA 1715 A 1 A 1716 TAGTAAATAT Statistics Matches: 40, Mismatches: 1, Indels: 6 0.85 0.02 0.13 Matches are distributed among these distances: 42 8 0.20 43 3 0.08 44 22 0.55 45 7 0.17 ACGTcount: A:0.78, C:0.01, G:0.03, T:0.17 Consensus pattern (44 bp): AAAATAATAAAAAAGAAAAAAATATATATAATAAAACAAATAAA Found at i:1683 original size:20 final size:20 Alignment explanation

Indices: 1618--1715 Score: 74 Period size: 23 Copynumber: 4.6 Consensus size: 20 1608 AATAGTAAGA * * 1618 AAAATAAATATAAAATA-AAG 1 AAAA-AAATAAAAAATATAAT * 1638 AAAAAGAAAAAAAATATATAAAT 1 AAAAA-AATAAAAA-ATAT-AAT 1661 AAAACAAATAAAAAA-ATAAT 1 AAAA-AAATAAAAAATATAAT * 1681 AAAAAAGTAAAAAATATATAT 1 AAAAAAATAAAAAATATA-AT 1702 AATAAAAAATAAAA 1 -A-AAAAAATAAAA 1716 TAGTAAATAT Statistics Matches: 63, Mismatches: 6, Indels: 15 0.75 0.07 0.18 Matches are distributed among these distances: 19 10 0.16 20 20 0.32 21 7 0.11 22 2 0.03 23 23 0.37 24 1 0.02 ACGTcount: A:0.78, C:0.01, G:0.03, T:0.18 Consensus pattern (20 bp): AAAAAAATAAAAAATATAAT Found at i:1703 original size:24 final size:23 Alignment explanation

Indices: 1646--1715 Score: 78 Period size: 23 Copynumber: 3.2 Consensus size: 23 1636 AGAAAAAGAA 1646 AAAAAATATATA-AATAAAACAAAT 1 AAAAAATATATATAAT-AAA-AAAT * 1670 AAAAAA-ATA-AT-A-AAAAAGT 1 AAAAAATATATATAATAAAAAAT 1689 AAAAAATATATATAATAAAAAAT 1 AAAAAATATATATAATAAAAAAT 1712 AAAA 1 AAAA 1716 TAGTAAATAT Statistics Matches: 39, Mismatches: 2, Indels: 11 0.75 0.04 0.21 Matches are distributed among these distances: 19 9 0.23 20 6 0.15 21 2 0.05 22 3 0.08 23 13 0.33 24 6 0.15 ACGTcount: A:0.77, C:0.01, G:0.01, T:0.20 Consensus pattern (23 bp): AAAAAATATATATAATAAAAAAT Found at i:1717 original size:47 final size:44 Alignment explanation

Indices: 1617--1714 Score: 119 Period size: 45 Copynumber: 2.2 Consensus size: 44 1607 AAATAGTAAG * 1617 AAAAATAAAT-ATAAAATAAAGAAAAAGAAAAAAAATATATAAA 1 AAAAATAAATAAAAAAATAAAGAAAAAGAAAAAAAATATATAAA * * * 1660 TAAAACAAATAAAAAAATAATA-AAAAAGTAAAAAATATATATAATA 1 AAAAATAAATAAAAAAATAA-AGAAAAAG-AAAAAAAATATATAA-A 1706 AAAAATAAA 1 AAAAATAAA 1715 ATAGTAAATA Statistics Matches: 45, Mismatches: 6, Indels: 5 0.80 0.11 0.09 Matches are distributed among these distances: 43 8 0.18 44 14 0.31 45 15 0.33 46 8 0.18 ACGTcount: A:0.78, C:0.01, G:0.03, T:0.18 Consensus pattern (44 bp): AAAAATAAATAAAAAAATAAAGAAAAAGAAAAAAAATATATAAA Found at i:1725 original size:24 final size:24 Alignment explanation

Indices: 1617--1726 Score: 75 Period size: 24 Copynumber: 4.5 Consensus size: 24 1607 AAATAGTAAG * * 1617 AAAAATAAATATAA-AATAAAGAA 1 AAAAATAAATATAATAAAAAAGTA * * ** 1640 AAAGAAAAAAAATATATAAATAAAACA 1 AAA-AATAAATATA-ATAAA-AAAGTA 1667 AATAAA-AAA-ATAATAAAAAAGTA 1 AA-AAATAAATATAATAAAAAAGTA * 1690 AAAAATATATATAATAAAAAA-TA 1 AAAAATAAATATAATAAAAAAGTA * 1713 AAATAGTAAATATA 1 AAA-AATAAATATA 1727 TATATATATA Statistics Matches: 69, Mismatches: 10, Indels: 15 0.73 0.11 0.16 Matches are distributed among these distances: 22 3 0.04 23 16 0.23 24 32 0.46 25 4 0.06 26 5 0.07 27 8 0.12 28 1 0.01 ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20 Consensus pattern (24 bp): AAAAATAAATATAATAAAAAAGTA Found at i:1730 original size:30 final size:32 Alignment explanation

Indices: 1668--1800 Score: 103 Period size: 34 Copynumber: 4.0 Consensus size: 32 1658 AATAAAACAA * 1668 ATAAAAAAATAATAAAAAAGTAAAAAATATAT 1 ATAATAAAATAATAAAAAAGTAAAAAATATAT * 1700 ATAATAAAA-AATAAAATAGTAAATATATATATAT 1 ATAATAAAATAATAAAAAAGTAAA-A-A-ATATAT * ** 1734 ATAATATAATTAATAATGAA-TAAAATAATATAT 1 ATAATA-AAATAATAAAAAAGTAAAA-AATATAT * * 1767 ATATATATATAAT-CTAAAAAAAT-AAAAATATAT 1 ATA-ATA-A-AATAATAAAAAAGTAAAAAATATAT 1800 A 1 A 1801 CTAAAGTAAA Statistics Matches: 83, Mismatches: 10, Indels: 15 0.77 0.09 0.14 Matches are distributed among these distances: 31 13 0.16 32 9 0.11 33 18 0.22 34 28 0.34 35 9 0.11 36 6 0.07 ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31 Consensus pattern (32 bp): ATAATAAAATAATAAAAAAGTAAAAAATATAT Found at i:1740 original size:43 final size:43 Alignment explanation

Indices: 1693--1777 Score: 118 Period size: 43 Copynumber: 2.0 Consensus size: 43 1683 AAAAGTAAAA * 1693 AATAT-ATATAATAAAAAATAAAATAGTAAATATATATATATAT 1 AATATAAT-TAATAAAAAATAAAATAATAAATATATATATATAT ** * 1736 AATATAATTAATAATGAATAAAATAATATATATATATATATA 1 AATATAATTAATAAAAAATAAAATAATAAATATATATATATA 1778 ATCTAAAAAA Statistics Matches: 37, Mismatches: 4, Indels: 2 0.86 0.09 0.05 Matches are distributed among these distances: 43 35 0.95 44 2 0.05 ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36 Consensus pattern (43 bp): AATATAATTAATAAAAAATAAAATAATAAATATATATATATAT Found at i:17491 original size:60 final size:58 Alignment explanation

Indices: 17363--17514 Score: 196 Period size: 60 Copynumber: 2.6 Consensus size: 58 17353 AAGCATAATG * * * * * 17363 AATAGTCGAGTGACCATTTTGTAACTTTTAAAAGTCGAGACTCAACAAAGTAACTCCC 1 AATAGTTGAGGGACCATTTTGTAACTTTTAATAGTCGAGACTCAACAAAATAACTCCA * * 17421 TATAGTTGAGGGACCATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAATAACTCTA 1 AATAGTTGAGGGACCATTTTGTAACTTTTAATAGTCGA--GACTCAACAAAATAACTCCA * * * 17481 AATAGTTGAGGAACTATTTTGTAATTTTTAATAG 1 AATAGTTGAGGGACCATTTTGTAACTTTTAATAG 17515 GTGAGAGACT Statistics Matches: 81, Mismatches: 11, Indels: 2 0.86 0.12 0.02 Matches are distributed among these distances: 58 34 0.42 60 47 0.58 ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33 Consensus pattern (58 bp): AATAGTTGAGGGACCATTTTGTAACTTTTAATAGTCGAGACTCAACAAAATAACTCCA Found at i:18748 original size:2 final size:2 Alignment explanation

Indices: 18741--18771 Score: 53 Period size: 2 Copynumber: 15.5 Consensus size: 2 18731 TATCATTTAA * 18741 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 18772 ATTATAATTA Statistics Matches: 27, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 2 27 1.00 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (2 bp): AT Found at i:20741 original size:3 final size:3 Alignment explanation

Indices: 20733--20763 Score: 62 Period size: 3 Copynumber: 10.3 Consensus size: 3 20723 CTTCCTCAAC 20733 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G 1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G 20764 GCTTGTACTG Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 28 1.00 ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00 Consensus pattern (3 bp): GAA Found at i:22176 original size:23 final size:24 Alignment explanation

Indices: 22125--22180 Score: 78 Period size: 23 Copynumber: 2.4 Consensus size: 24 22115 CATTTAAATG * 22125 ATAAACGAACACAAAAGAATGAAC 1 ATAAACGAAAACAAAAGAATGAAC * * 22149 GTAAACGAAAACAATA-AATGAAC 1 ATAAACGAAAACAAAAGAATGAAC 22172 ATAAACGAA 1 ATAAACGAA 22181 TTTGCACAAA Statistics Matches: 28, Mismatches: 4, Indels: 1 0.85 0.12 0.03 Matches are distributed among these distances: 23 15 0.54 24 13 0.46 ACGTcount: A:0.62, C:0.14, G:0.12, T:0.11 Consensus pattern (24 bp): ATAAACGAAAACAAAAGAATGAAC Found at i:22215 original size:23 final size:23 Alignment explanation

Indices: 22186--22241 Score: 76 Period size: 23 Copynumber: 2.4 Consensus size: 23 22176 ACGAATTTGC 22186 ACAAACATAACAAATGAACATAA 1 ACAAACATAACAAATGAACATAA * * * * 22209 TCGAACATAATAAATGAACGTAA 1 ACAAACATAACAAATGAACATAA 22232 ACAAACATAA 1 ACAAACATAA 22242 ACAACAACAA Statistics Matches: 27, Mismatches: 6, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 23 27 1.00 ACGTcount: A:0.61, C:0.16, G:0.07, T:0.16 Consensus pattern (23 bp): ACAAACATAACAAATGAACATAA Found at i:22452 original size:14 final size:14 Alignment explanation

Indices: 22433--22465 Score: 57 Period size: 14 Copynumber: 2.4 Consensus size: 14 22423 TGGGCTGAAT 22433 ATAAATGAACGAAC 1 ATAAATGAACGAAC * 22447 ATAAATGAATGAAC 1 ATAAATGAACGAAC 22461 ATAAA 1 ATAAA 22466 CAAATGAATT Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 14 18 1.00 ACGTcount: A:0.61, C:0.09, G:0.12, T:0.18 Consensus pattern (14 bp): ATAAATGAACGAAC Found at i:29598 original size:20 final size:19 Alignment explanation

Indices: 29573--29613 Score: 55 Period size: 20 Copynumber: 2.1 Consensus size: 19 29563 TTAGTTCATT * 29573 TTAATATTTAAACTATACAA 1 TTAATACTTAAACTAT-CAA * 29593 TTAATACTTAAATTATCAA 1 TTAATACTTAAACTATCAA 29612 TT 1 TT 29614 TTGATTCATT Statistics Matches: 19, Mismatches: 2, Indels: 1 0.86 0.09 0.05 Matches are distributed among these distances: 19 5 0.26 20 14 0.74 ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44 Consensus pattern (19 bp): TTAATACTTAAACTATCAA Found at i:37384 original size:16 final size:16 Alignment explanation

Indices: 37365--37395 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 37355 TTTAGTGCGT * 37365 TTTTATTTTATTTAAG 1 TTTTATGTTATTTAAG 37381 TTTTATGTTATTTAA 1 TTTTATGTTATTTAA 37396 TAATAATAAA Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 16 14 1.00 ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68 Consensus pattern (16 bp): TTTTATGTTATTTAAG Found at i:51846 original size:31 final size:31 Alignment explanation

Indices: 51805--51869 Score: 121 Period size: 31 Copynumber: 2.1 Consensus size: 31 51795 CTTAAAATGA * 51805 TCGGTCTAAATTAAGTCTGAGTTAATTTGAT 1 TCGGACTAAATTAAGTCTGAGTTAATTTGAT 51836 TCGGACTAAATTAAGTCTGAGTTAATTTGAT 1 TCGGACTAAATTAAGTCTGAGTTAATTTGAT 51867 TCG 1 TCG 51870 AATTAATCAA Statistics Matches: 33, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 31 33 1.00 ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40 Consensus pattern (31 bp): TCGGACTAAATTAAGTCTGAGTTAATTTGAT Found at i:55342 original size:11 final size:13 Alignment explanation

Indices: 55328--55359 Score: 50 Period size: 13 Copynumber: 2.6 Consensus size: 13 55318 ATAAATGGAG 55328 TTTAA-ATT-TTT 1 TTTAATATTATTT 55339 TTTAATATTATTT 1 TTTAATATTATTT 55352 TTTAATAT 1 TTTAATAT 55360 GATAAGTATA Statistics Matches: 19, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 11 5 0.26 12 3 0.16 13 11 0.58 ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69 Consensus pattern (13 bp): TTTAATATTATTT Found at i:55983 original size:12 final size:12 Alignment explanation

Indices: 55966--55996 Score: 53 Period size: 12 Copynumber: 2.6 Consensus size: 12 55956 ATATATATAT * 55966 ATACCCGGTCCG 1 ATACCCGGCCCG 55978 ATACCCGGCCCG 1 ATACCCGGCCCG 55990 ATACCCG 1 ATACCCG 55997 TTTAAATAAC Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 12 18 1.00 ACGTcount: A:0.19, C:0.45, G:0.23, T:0.13 Consensus pattern (12 bp): ATACCCGGCCCG Found at i:64165 original size:30 final size:30 Alignment explanation

Indices: 64121--64197 Score: 91 Period size: 30 Copynumber: 2.6 Consensus size: 30 64111 GTTTTTTAAC * * * 64121 ATTTTCAGTCATTTTTTAACTCCTAGTAAT 1 ATTTTCAGTAATTTTTTAACGCCTAATAAT * 64151 ATTTTCGGTAATTTTTTAACGCCTAATAAT 1 ATTTTCAGTAATTTTTTAACGCCTAATAAT * * * 64181 GTTTCCAGTCATTTTTT 1 ATTTTCAGTAATTTTTT 64198 TAAAAATCTA Statistics Matches: 39, Mismatches: 8, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 30 39 1.00 ACGTcount: A:0.25, C:0.16, G:0.09, T:0.51 Consensus pattern (30 bp): ATTTTCAGTAATTTTTTAACGCCTAATAAT Found at i:65084 original size:10 final size:10 Alignment explanation

Indices: 65069--65122 Score: 60 Period size: 10 Copynumber: 5.6 Consensus size: 10 65059 TATTTTTTTT 65069 AAAATAAATA 1 AAAATAAATA 65079 AAAATACAATA 1 AAAATA-AATA 65090 AAAAT---TA 1 AAAATAAATA 65097 AAAATAAATA 1 AAAATAAATA * * 65107 AAAGTCAATA 1 AAAATAAATA 65117 AAAATA 1 AAAATA 65123 TGATGTAAAG Statistics Matches: 36, Mismatches: 4, Indels: 8 0.75 0.08 0.17 Matches are distributed among these distances: 7 7 0.19 10 20 0.56 11 9 0.25 ACGTcount: A:0.74, C:0.04, G:0.02, T:0.20 Consensus pattern (10 bp): AAAATAAATA Found at i:65103 original size:28 final size:27 Alignment explanation

Indices: 65069--65121 Score: 88 Period size: 28 Copynumber: 1.9 Consensus size: 27 65059 TATTTTTTTT 65069 AAAATAAATAAAAATACAATAAAAATTA 1 AAAATAAATAAAAAT-CAATAAAAATTA * 65097 AAAATAAATAAAAGTCAATAAAAAT 1 AAAATAAATAAAAATCAATAAAAAT 65122 ATGATGTAAA Statistics Matches: 24, Mismatches: 1, Indels: 1 0.92 0.04 0.04 Matches are distributed among these distances: 27 10 0.42 28 14 0.58 ACGTcount: A:0.74, C:0.04, G:0.02, T:0.21 Consensus pattern (27 bp): AAAATAAATAAAAATCAATAAAAATTA Found at i:65109 original size:27 final size:28 Alignment explanation

Indices: 65069--65121 Score: 83 Period size: 27 Copynumber: 1.9 Consensus size: 28 65059 TATTTTTTTT 65069 AAAATAAATAAAAA-TACAATAAAAATTA 1 AAAATAAATAAAAAGT-CAATAAAAATTA 65097 AAAATAAAT-AAAAGTCAATAAAAAT 1 AAAATAAATAAAAAGTCAATAAAAAT 65122 ATGATGTAAA Statistics Matches: 24, Mismatches: 0, Indels: 3 0.89 0.00 0.11 Matches are distributed among these distances: 27 14 0.58 28 10 0.42 ACGTcount: A:0.74, C:0.04, G:0.02, T:0.21 Consensus pattern (28 bp): AAAATAAATAAAAAGTCAATAAAAATTA Found at i:66430 original size:11 final size:10 Alignment explanation

Indices: 66395--66436 Score: 50 Period size: 11 Copynumber: 4.0 Consensus size: 10 66385 TTAGTTTTAC 66395 ATTATATTTTT 1 ATTA-ATTTTT 66406 ATTGAA-TTTT 1 ATT-AATTTTT 66416 ATTAATTTTT 1 ATTAATTTTT 66426 AATTAATTTTT 1 -ATTAATTTTT 66437 TAAAAAATTG Statistics Matches: 28, Mismatches: 0, Indels: 6 0.82 0.00 0.18 Matches are distributed among these distances: 9 2 0.07 10 11 0.39 11 14 0.50 12 1 0.04 ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67 Consensus pattern (10 bp): ATTAATTTTT Found at i:66436 original size:21 final size:21 Alignment explanation

Indices: 66395--66435 Score: 59 Period size: 20 Copynumber: 2.0 Consensus size: 21 66385 TTAGTTTTAC 66395 ATTATATTTTTATTGAATTTT 1 ATTATATTTTTATTGAATTTT 66416 ATTA-ATTTTTAATT-AATTTT 1 ATTATATTTTT-ATTGAATTTT 66436 TTAAAAAATT Statistics Matches: 19, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 20 12 0.63 21 7 0.37 ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66 Consensus pattern (21 bp): ATTATATTTTTATTGAATTTT Done.