Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007489.1 Hibiscus syriacus cultivar Beakdansim tig00020681_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: 78348
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1151 original size:21 final size:21
Alignment explanation
Indices: 1127--1172 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
1117 CTTGAAATCC
*
1127 AAATAAAATAGCTCAAAATGG
1 AAATAAAAAAGCTCAAAATGG
1148 AAATAAAAAAGCTCAAAATGG
1 AAATAAAAAAGCTCAAAATGG
1169 AAAT
1 AAAT
1173 CAATTTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.61, C:0.09, G:0.13, T:0.17
Consensus pattern (21 bp):
AAATAAAAAAGCTCAAAATGG
Found at i:12502 original size:36 final size:37
Alignment explanation
Indices: 12433--12533 Score: 132
Period size: 36 Copynumber: 2.7 Consensus size: 37
12423 CGAAAATAGG
* * *
12433 TATCTTCCACCCGAACCTAACCCGACCCAAAAAATTTA
1 TATCCTCCACCCGACCCTAACCCGA-CCAAAAAATATA
*
12471 TATCCTCCATCCGACCCT-ACCCGACCAAAAAATATA
1 TATCCTCCACCCGACCCTAACCCGACCAAAAAATATA
* *
12507 TATCCTCCACCCGACTCTGACCCGACC
1 TATCCTCCACCCGACCCTAACCCGACC
12534 CAGTAAAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
36 27 0.48
37 14 0.25
38 15 0.27
ACGTcount: A:0.32, C:0.42, G:0.07, T:0.20
Consensus pattern (37 bp):
TATCCTCCACCCGACCCTAACCCGACCAAAAAATATA
Found at i:35422 original size:31 final size:31
Alignment explanation
Indices: 35384--35493 Score: 114
Period size: 31 Copynumber: 3.4 Consensus size: 31
35374 CAGTCTCTAT
35384 TGGTAATTCCTTGTATAGGTTCAACACCGAC
1 TGGTAATTCCTTGTATAGGTTCAACACCGAC
* * * *
35415 TGGTAATTCCTTATGTCTGGCAGGTTCAGTCGCTG-C
1 TGGTAATTCC-T-TGTAT---AGGTTCA-ACACCGAC
*
35451 TGGTAATTTCTTGTATAGGTTCAACACCGAC
1 TGGTAATTCCTTGTATAGGTTCAACACCGAC
35482 TGGTAATTCCTT
1 TGGTAATTCCTT
35494 ATGGACCTAA
Statistics
Matches: 62, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
30 3 0.05
31 29 0.47
32 1 0.02
33 4 0.06
34 4 0.06
35 1 0.02
36 17 0.27
37 3 0.05
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (31 bp):
TGGTAATTCCTTGTATAGGTTCAACACCGAC
Found at i:45055 original size:15 final size:15
Alignment explanation
Indices: 45036--45090 Score: 92
Period size: 15 Copynumber: 3.7 Consensus size: 15
45026 TTCATGGGGT
* *
45036 AAGAAGACAACGTCT
1 AAGAAGAAAACGTCA
45051 AAGAAGAAAACGTCA
1 AAGAAGAAAACGTCA
45066 AAGAAGAAAACGTCA
1 AAGAAGAAAACGTCA
45081 AAGAAGAAAA
1 AAGAAGAAAA
45091 AAGAAAGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.60, C:0.13, G:0.20, T:0.07
Consensus pattern (15 bp):
AAGAAGAAAACGTCA
Found at i:49199 original size:2 final size:2
Alignment explanation
Indices: 49192--49270 Score: 140
Period size: 2 Copynumber: 39.5 Consensus size: 2
49182 TCAATCTACA
49192 AT 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 AT
* *
49234 AT AT AT AT AT AT AT AT AT AT TT AT TT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
49271 ATTTCCGAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:49419 original size:85 final size:84
Alignment explanation
Indices: 49330--49625 Score: 432
Period size: 85 Copynumber: 3.5 Consensus size: 84
49320 GACGTGTGCG
* * *
49330 TCAATGACACGCAATGTAAGTCATATATGCGTGTCATAAATTTATGACACACAAATGTATGTCAA
1 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTGTGTCAA
* *
49395 ACAGATTTATGACGGGGGAT
66 TCA-ATTTATGACGGGGGCT
*
49415 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGTC-A
1 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTGTGTCAA
49479 TCTTAATTTATGACGGGGGCT
66 TC--AATTTATGACGGGGGCT
* * *
49500 TTAATGACGCGCAATGTAAGTCATAAATGCATGTCATAAATTTATGACACACAAATGTGTGTCAT
1 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTGTGTCA-
* * *
49565 ATTAATTTATGATGGAGGCT
65 ATCAATTTATGACGGGGGCT
*
49585 TCAATGACGCGCAATGTAAGTCATACATGCGCGTCATAAAT
1 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAAT
49626 GAACGTCATA
Statistics
Matches: 190, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
84 2 0.01
85 185 0.97
86 1 0.01
87 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (84 bp):
TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTGTGTCAA
TCAATTTATGACGGGGGCT
Found at i:49622 original size:13 final size:13
Alignment explanation
Indices: 49604--49648 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
49594 CGCAATGTAA
* *
49604 GTCATACATGCGC
1 GTCATAAATGAGC
*
49617 GTCATAAATGAAC
1 GTCATAAATGAGC
*
49630 GTCATAAATGTGC
1 GTCATAAATGAGC
49643 GTCATA
1 GTCATA
49649 TATTTATGAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (13 bp):
GTCATAAATGAGC
Found at i:49652 original size:85 final size:84
Alignment explanation
Indices: 49330--49658 Score: 416
Period size: 85 Copynumber: 3.9 Consensus size: 84
49320 GACGTGTGCG
* * * *
49330 TCAATGACACGCAATGTAAGTCATATATGCGTGTCATAAATTTATGACACACAAATGTATGTCA-
1 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTA-GACGCACAAATGTGTGTCAT
** *
49394 AACAGATTTATGACGGGGGAT
65 ATTA-ATTTATGACGGGGGCT
49415 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGTCAT
1 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTA-GACGCACAAATGTGTGTCAT
*
49480 CTTAATTTATGACGGGGGCT
65 ATTAATTTATGACGGGGGCT
* * * *
49500 TTAATGACGCGCAATGTAAGTCATAAATGCATGTCATAAATTTATGACACACAAATGTGTGTCAT
1 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTA-GACGCACAAATGTGTGTCAT
* *
49565 ATTAATTTATGATGGAGGCT
65 ATTAATTTATGACGGGGGCT
* * * *
49585 TCAATGACGCGCAATGTAAGTCATACATGCGCGTCATAAA-TGA-ACGTCATAAATGTGCGTCAT
1 TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTAGACG-CACAAATGTGTGTCAT
49648 A-T-ATTTATGAC
65 ATTAATTTATGAC
49659 ACACAATTGC
Statistics
Matches: 218, Mismatches: 24, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
81 8 0.04
82 3 0.01
83 15 0.07
84 2 0.01
85 189 0.87
86 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (84 bp):
TCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTAGACGCACAAATGTGTGTCATA
TTAATTTATGACGGGGGCT
Found at i:54113 original size:24 final size:24
Alignment explanation
Indices: 54079--54140 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 24
54069 TTAGCATGTT
*
54079 TAAAAATAAAACTT-AAAATAAAA
1 TAAAAATAAAACTTGAAAACAAAA
54102 TAAAAATGAAAACTTGAAAACAAAA
1 TAAAAAT-AAAACTTGAAAACAAAA
*
54127 GAAAAA-AAGAACTT
1 TAAAAATAA-AACTT
54141 TATAAAAGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 9 0.26
24 12 0.35
25 13 0.38
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.18
Consensus pattern (24 bp):
TAAAAATAAAACTTGAAAACAAAA
Found at i:57419 original size:5 final size:5
Alignment explanation
Indices: 57411--57443 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
57401 ATTTCTCAAC
57411 TAAAA TAAAA TAAAA TAAAA T-AAA -AAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
57444 AATGGGTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 6 0.23
5 20 0.77
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
TAAAA
Found at i:66917 original size:30 final size:30
Alignment explanation
Indices: 66883--66949 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
66873 TTAAGTTTAG
** *
66883 AAAAGTTTAAGGACCAAAAATGTAATTTTC
1 AAAAGTTTAAGGACCAAAAATACAATTTCC
*
66913 AAAAGTTTAAGGACCAAAATTACAATTTCC
1 AAAAGTTTAAGGACCAAAAATACAATTTCC
66943 AAAAGTT
1 AAAAGTT
66950 AGGTGTTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (30 bp):
AAAAGTTTAAGGACCAAAAATACAATTTCC
Found at i:71571 original size:41 final size:40
Alignment explanation
Indices: 71492--71598 Score: 151
Period size: 41 Copynumber: 2.6 Consensus size: 40
71482 TGAATTGAAA
* *
71492 TGTGAATTAATCCATACTACCATGACCTAATTTAATTGGTT
1 TGTGAA-TAATGCATACTACCATGACCTAATTTAATTGGGT
71533 TGTGAACTAATGCATACTACCATGACCTAATTTAATTGGGT
1 TGTGAA-TAATGCATACTACCATGACCTAATTTAATTGGGT
**
71574 TGTGAATAAATGCATGTTACCATGA
1 TGTGAAT-AATGCATACTACCATGA
71599 TTGAATTAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
40 1 0.02
41 59 0.98
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (40 bp):
TGTGAATAATGCATACTACCATGACCTAATTTAATTGGGT
Found at i:71611 original size:41 final size:40
Alignment explanation
Indices: 71520--71727 Score: 102
Period size: 41 Copynumber: 5.1 Consensus size: 40
71510 ACCATGACCT
* * ** *
71520 AATTTAATTGGTTTGTGAACTAATGCATACTACCATGACCT-
1 AATTAAATTGGATTGTGAA-TAATGCATGTTACCATGA-TTG
* *
71561 AATTTAATTGGGTTGTGAATAAATGCATGTTACCATGATTG
1 AATTAAATTGGATTGTGAAT-AATGCATGTTACCATGATTG
* * *
71602 AATTAAATT-GAATGATAAATTATTGCATGCTT-CCATGATTG
1 AATTAAATTGGATTG-TGAA-TAATGCATG-TTACCATGATTG
* * * * *
71643 AATTAAA-TCGAATGATGAACTATTGCATCCTT-TCATGATTG
1 AATTAAATTGGATTG-TGAA-TAATGCAT-GTTACCATGATTG
* * * * * *
71684 AATTGAATAGAATTGTGAATTATTGCATGCTACCATGATCG
1 AATTAAATTGGATTGTGAA-TAATGCATGTTACCATGATTG
71725 AAT
1 AAT
71728 CAAGTTTAAT
Statistics
Matches: 135, Mismatches: 23, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
40 7 0.05
41 122 0.90
42 6 0.04
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (40 bp):
AATTAAATTGGATTGTGAATAATGCATGTTACCATGATTG
Found at i:71662 original size:123 final size:123
Alignment explanation
Indices: 71535--71826 Score: 298
Period size: 123 Copynumber: 2.4 Consensus size: 123
71525 AATTGGTTTG
* * * ** *
71535 TGAACTAATGCATACTACCATGACCT-AATTTAATTGGGTTGTGAATAAATGCATGTTACCATGA
1 TGAACTATTGCATACTACCATGA-CTGAATTGAATAGAATTGTGAATAAATGCATGCTACCATGA
* * *
71599 TTGAATTAAATTGAATGATAAATTATTGCATGCTTCCATGATTGAATTAAATCGAATGA
65 TCGAATCAAATTGAATGATAAATTATTGCATGCTTCCATGATTGAATTAAATCAAATGA
* ** * * *
71658 TGAACTATTGCATCCTTTCATGATTGAATTGAATAGAATTGTGAATTATTGCATGCTACCATGAT
1 TGAACTATTGCATACTACCATGACTGAATTGAATAGAATTGTGAATAAATGCATGCTACCATGAT
* * * * ** * *
71723 CGAATCAAGTTTAATGTTGAATTATTTTATGCTTCCATGATTGAATTGAATCAAATGG
66 CGAATCAAATTGAATGATAAATTATTGCATGCTTCCATGATTGAATTAAATCAAATGA
* *** * * *
71781 TGAACTATTGCATGCTGTTAGGATTGAATTGAATTGAATTGTGAAT
1 TGAACTATTGCATACTACCATGACTGAATTGAATAGAATTGTGAAT
71827 TAGTACCTGC
Statistics
Matches: 140, Mismatches: 28, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
122 1 0.01
123 139 0.99
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (123 bp):
TGAACTATTGCATACTACCATGACTGAATTGAATAGAATTGTGAATAAATGCATGCTACCATGAT
CGAATCAAATTGAATGATAAATTATTGCATGCTTCCATGATTGAATTAAATCAAATGA
Found at i:71744 original size:41 final size:41
Alignment explanation
Indices: 71584--71828 Score: 219
Period size: 41 Copynumber: 6.0 Consensus size: 41
71574 TGTGAATAAA
*
71584 TGCATG-TTACCATGATTGAATTAAATTGAATGATAAATTAT
1 TGCATGCTT-CCATGATTGAATTAAATTGAATGATGAATTAT
* *
71625 TGCATGCTTCCATGATTGAATTAAATCGAATGATGAACTAT
1 TGCATGCTTCCATGATTGAATTAAATTGAATGATGAATTAT
* * * *
71666 TGCATCCTTTCATGATTGAATTGAATAGAATTG-TGAATTAT
1 TGCATGCTTCCATGATTGAATTAAATTGAA-TGATGAATTAT
* * * * * *
71707 TGCATGCTACCATGATCGAATCAAGTTTAATGTTGAATTAT
1 TGCATGCTTCCATGATTGAATTAAATTGAATGATGAATTAT
** * ** * *
71748 TTTATGCTTCCATGATTGAATTGAATCAAATGGTGAACTAT
1 TGCATGCTTCCATGATTGAATTAAATTGAATGATGAATTAT
* * *
71789 TGCATGCTGT-TAGGATTGAATTGAATTGAATTG-TGAATTA
1 TGCATGCT-TCCATGATTGAATTAAATTGAA-TGATGAATTA
71829 GTACCTGCTG
Statistics
Matches: 164, Mismatches: 35, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
40 2 0.01
41 155 0.95
42 7 0.04
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (41 bp):
TGCATGCTTCCATGATTGAATTAAATTGAATGATGAATTAT
Found at i:71827 original size:123 final size:123
Alignment explanation
Indices: 71573--71828 Score: 343
Period size: 123 Copynumber: 2.1 Consensus size: 123
71563 TTTAATTGGG
* * * *
71573 TTGTGAATAAATGCATGTTACCATGATTGAATTAAATTGAATGATAAATTATTGCATGCTTCCAT
1 TTGTGAATTAATGCATGCTACCATGATCGAATCAAATTGAATGATAAATTATTGCATGCTTCCAT
* *
71638 GATTGAATTAAATCGAATGATGAACTATTGCATCCTTTCATGATTGAATTGAATAGAA
66 GATTGAATTAAATCAAATGATGAACTATTGCATCCTTTCAGGATTGAATTGAATAGAA
* * * * * **
71696 TTGTGAATTATTGCATGCTACCATGATCGAATCAAGTTTAATGTTGAATTATTTTATGCTTCCAT
1 TTGTGAATTAATGCATGCTACCATGATCGAATCAAATTGAATGATAAATTATTGCATGCTTCCAT
* * * *
71761 GATTGAATTGAATCAAATGGTGAACTATTGCATGCTGTT-AGGATTGAATTGAATTGAA
66 GATTGAATTAAATCAAATGATGAACTATTGCATCCT-TTCAGGATTGAATTGAATAGAA
71819 TTGTGAATTA
1 TTGTGAATTA
71829 GTACCTGCTG
Statistics
Matches: 115, Mismatches: 17, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
123 113 0.98
124 2 0.02
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (123 bp):
TTGTGAATTAATGCATGCTACCATGATCGAATCAAATTGAATGATAAATTATTGCATGCTTCCAT
GATTGAATTAAATCAAATGATGAACTATTGCATCCTTTCAGGATTGAATTGAATAGAA
Found at i:71838 original size:41 final size:41
Alignment explanation
Indices: 71761--71838 Score: 93
Period size: 41 Copynumber: 1.9 Consensus size: 41
71751 ATGCTTCCAT
* *
71761 GATTGAATTGAATCAAATGGTGAACTATTGCATGCTGTTAG
1 GATTGAATTGAATCAAATGGTGAACTAGTACATGCTGTTAG
** * * *
71802 GATTGAATTGAATTGAATTGTGAATTAGTACCTGCTG
1 GATTGAATTGAATCAAATGGTGAACTAGTACATGCTG
71839 CCAAGGTCAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 30 1.00
ACGTcount: A:0.31, C:0.09, G:0.24, T:0.36
Consensus pattern (41 bp):
GATTGAATTGAATCAAATGGTGAACTAGTACATGCTGTTAG
Found at i:75793 original size:59 final size:58
Alignment explanation
Indices: 75643--75793 Score: 248
Period size: 58 Copynumber: 2.6 Consensus size: 58
75633 AGGTAAGATG
* *
75643 TTATATATGCATGTGTTTTCGACCCCAATATATAGTTTACAGACTGTGTTTAATCTCATT
1 TTATATATGCATGTGTATTCGACCCC-A-ATATAGGTTACAGACTGTGTTTAATCTCATT
75703 TTATATATGCATGTGTATTCGACCCCAATATAGGTTACAGACTGTGTTTAATCTCATT
1 TTATATATGCATGTGTATTCGACCCCAATATAGGTTACAGACTGTGTTTAATCTCATT
*
75761 TATATATATGCATGTGTATTCGACACCAATATA
1 T-TATATATGCATGTGTATTCGACCCCAATATA
75794 TATAGGTTAC
Statistics
Matches: 87, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
58 31 0.36
59 31 0.36
60 25 0.29
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (58 bp):
TTATATATGCATGTGTATTCGACCCCAATATAGGTTACAGACTGTGTTTAATCTCATT
Done.