Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002137.1 Hibiscus syriacus cultivar Beakdansim tig00004371_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: 71844
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:2727 original size:27 final size:27
Alignment explanation
Indices: 2666--2727 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
2656 AGCAAAACGA
*
2666 TAAAAAAGGATTGTTCATGGCAACTTC
1 TAAAAAATGATTGTTCATGGCAACTTC
2693 TAAAAAATGATTGTTCATGGCAACTTC
1 TAAAAAATGATTGTTCATGGCAACTTC
2720 TAAAAAAT
1 TAAAAAAT
2728 TTATAGTTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.31
Consensus pattern (27 bp):
TAAAAAATGATTGTTCATGGCAACTTC
Found at i:2751 original size:4 final size:4
Alignment explanation
Indices: 2742--2766 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2732 AGTTGTTTAT
2742 AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA A
2767 CCTACATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:8129 original size:21 final size:21
Alignment explanation
Indices: 8080--8129 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
8070 GATCTGATAT
*
8080 AAAATAAGGACTTAATTTTAA
1 AAAATAATGACTTAATTTTAA
8101 AAAATAATGACTTAATTTTAA
1 AAAATAATGACTTAATTTTAA
8122 AAAATAAT
1 AAAATAAT
8130 AAAATTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (21 bp):
AAAATAATGACTTAATTTTAA
Found at i:9142 original size:31 final size:32
Alignment explanation
Indices: 9107--9178 Score: 119
Period size: 31 Copynumber: 2.2 Consensus size: 32
9097 TGTGATGACA
*
9107 ATATCTTAATTATATAAAAAC-AAAAGTGATC
1 ATATCTTAATTATATAAAAACAAAAAATGATC
9138 ATATCTTAATTATATAAAAACAAAAAAATGATC
1 ATATCTTAATTATATAAAAAC-AAAAAATGATC
9171 ATATCTTA
1 ATATCTTA
9179 TGTTTGTTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
31 21 0.55
33 17 0.45
ACGTcount: A:0.53, C:0.10, G:0.04, T:0.33
Consensus pattern (32 bp):
ATATCTTAATTATATAAAAACAAAAAATGATC
Found at i:14705 original size:6 final size:6
Alignment explanation
Indices: 14694--14730 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
14684 ACACGTATTA
14694 CCACGG CCACGG CCACGG CCACGG CCACGG CCACGG C
1 CCACGG CCACGG CCACGG CCACGG CCACGG CCACGG C
14731 TCGAGACGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.16, C:0.51, G:0.32, T:0.00
Consensus pattern (6 bp):
CCACGG
Found at i:17596 original size:19 final size:20
Alignment explanation
Indices: 17569--17610 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
17559 CCAATTAATT
* *
17569 ATCTTAATT-AAAATACATA
1 ATCTGAATTGAAAATAAATA
17588 ATCTGAATTGAAAATAAATA
1 ATCTGAATTGAAAATAAATA
17608 ATC
1 ATC
17611 GAGTAAATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.52, C:0.10, G:0.05, T:0.33
Consensus pattern (20 bp):
ATCTGAATTGAAAATAAATA
Found at i:28134 original size:20 final size:20
Alignment explanation
Indices: 28119--28167 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
28109 AAACCGATTC
28119 GAACCGGTTGAAACCGGTCA
1 GAACCGGTTGAAACCGGTCA
* *
28139 GAATCGGTTGAAACCCGGTTA
1 GAACCGGTTGAAA-CCGGTCA
28160 -AACCGGTT
1 GAACCGGTT
28168 TCCAGCAGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (20 bp):
GAACCGGTTGAAACCGGTCA
Found at i:30708 original size:37 final size:36
Alignment explanation
Indices: 30633--30709 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
30623 TTTTTATATT
*
30633 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
30669 TTTAATTTTTTAAATAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
30706 TTTA
1 TTTA
30710 TAATATTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 26 0.72
37 10 0.28
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:30729 original size:18 final size:18
Alignment explanation
Indices: 30685--30732 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
30675 TTTTTAAATA
*
30685 AAATATATAAATATTTTAC
1 AAATATAT-AATATTATAC
*
30704 -AATTTATAATATTATAC
1 AAATATATAATATTATAC
30721 AAATATATAATA
1 AAATATATAATA
30733 AAGACAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATATAATATTATAC
Found at i:53214 original size:28 final size:27
Alignment explanation
Indices: 53179--53235 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
53169 CTCGCCGGAA
*
53179 TCTATTTTCCCT-TTTAACTTTTCTCTC
1 TCTATTTTCCCTCTCT-ACTTTTCTCTC
*
53206 TCTACTTTTCTCTCTCTACTTTTCTCTC
1 TCTA-TTTTCCCTCTCTACTTTTCTCTC
53234 TC
1 TC
53236 CCATGTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 4 0.15
28 20 0.77
29 2 0.08
ACGTcount: A:0.09, C:0.33, G:0.00, T:0.58
Consensus pattern (27 bp):
TCTATTTTCCCTCTCTACTTTTCTCTC
Found at i:53219 original size:12 final size:14
Alignment explanation
Indices: 53195--53235 Score: 82
Period size: 14 Copynumber: 2.9 Consensus size: 14
53185 TTCCCTTTTA
53195 ACTTTTCTCTCTCT
1 ACTTTTCTCTCTCT
53209 ACTTTTCTCTCTCT
1 ACTTTTCTCTCTCT
53223 ACTTTTCTCTCTC
1 ACTTTTCTCTCTC
53236 CCATGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.07, C:0.37, G:0.00, T:0.56
Consensus pattern (14 bp):
ACTTTTCTCTCTCT
Found at i:60576 original size:39 final size:39
Alignment explanation
Indices: 60501--60579 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
60491 CAACTATGAG
* *
60501 GGAGGTTTTTAACGAGACCTCCTATTCCTATAAAAAAAA
1 GGAGGTTTTTAACGAGACCTCCAAATCCTATAAAAAAAA
* * * *
60540 GGAGGTTTTTAATGAGGCCTTCAAATCTTATCAAAAAAAA
1 GGAGGTTTTTAACGAGACCTCCAAATCCTAT-AAAAAAAA
60580 AATCAGTCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
39 25 0.76
40 8 0.24
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.29
Consensus pattern (39 bp):
GGAGGTTTTTAACGAGACCTCCAAATCCTATAAAAAAAA
Found at i:66390 original size:2 final size:2
Alignment explanation
Indices: 66383--66419 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
66373 TGATTTATTT
66383 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
66420 TATTTTTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:66658 original size:23 final size:23
Alignment explanation
Indices: 66615--66658 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
66605 ATTTGATTAT
* *
66615 ATTTCTATTTTAATTTTTAATAA
1 ATTTCTATTTCAATTTGTAATAA
66638 ATTT-TATTTCAATTATGTAAT
1 ATTTCTATTTCAATT-TGTAAT
66659 TTGAATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (23 bp):
ATTTCTATTTCAATTTGTAATAA
Found at i:71827 original size:28 final size:32
Alignment explanation
Indices: 71768--71827 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 32
71758 CAGTTATATG
* *
71768 TATTAAACTATTACAAATTAATTATTATATTT
1 TATTAAACTATTACAAATTAATTATCAAATTT
71800 TATTAAA-TA-TA-AAA-TAATTATCAAATTT
1 TATTAAACTATTACAAATTAATTATCAAATTT
71828 ATTTTACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 12 0.46
29 3 0.12
30 2 0.08
31 2 0.08
32 7 0.27
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (32 bp):
TATTAAACTATTACAAATTAATTATCAAATTT
Done.