Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006897.1 Hibiscus syriacus cultivar Beakdansim tig00017613_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: 88468
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:2862 original size:21 final size:20
Alignment explanation
Indices: 2819--2863 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
2809 AAAAGTGATT
*
2819 TAAAGTGAAAATAAAGAATG
1 TAAAGTGAAAATAAAGAAGG
* *
2839 TAAAGTTGAAAATGAATAAGG
1 TAAAG-TGAAAATAAAGAAGG
2860 TAAA
1 TAAA
2864 AATAGCCTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.58, C:0.00, G:0.20, T:0.22
Consensus pattern (20 bp):
TAAAGTGAAAATAAAGAAGG
Found at i:3432 original size:23 final size:25
Alignment explanation
Indices: 3406--3457 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
3396 TTAACATGTT
*
3406 TAAAAAT-AAAACTT-AAGATAAAA
1 TAAAAATGAAAACTTGAAAATAAAA
3429 T-AAAATGAAAACTTGAAAATAAAA
1 TAAAAATGAAAACTTGAAAATAAAA
3453 TAAAA
1 TAAAA
3458 GAGAGAACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 5 0.20
23 8 0.32
24 9 0.36
25 3 0.12
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.21
Consensus pattern (25 bp):
TAAAAATGAAAACTTGAAAATAAAA
Found at i:12397 original size:15 final size:15
Alignment explanation
Indices: 12373--12404 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12363 TGGCAGATCG
*
12373 AAATCCAGAACGGGA
1 AAATCAAGAACGGGA
12388 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
12403 AA
1 AA
12405 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.16, G:0.25, T:0.06
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:15582 original size:28 final size:27
Alignment explanation
Indices: 15551--15624 Score: 114
Period size: 26 Copynumber: 2.7 Consensus size: 27
15541 GTAGGACCAT
*
15551 TATGTCCCATAGGACCACGTAGAACACA
1 TATGTCCCGTAGGACCAC-TAGAACACA
15579 TATGTCCCGTA-GACCACTAGAACACA
1 TATGTCCCGTAGGACCACTAGAACACA
*
15605 TATGTCCCGTTGGACCACTA
1 TATGTCCCGTAGGACCACTA
15625 TGTCCCGTAG
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 19 0.44
27 14 0.33
28 10 0.23
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.22
Consensus pattern (27 bp):
TATGTCCCGTAGGACCACTAGAACACA
Found at i:15628 original size:18 final size:18
Alignment explanation
Indices: 15605--15640 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
15595 CTAGAACACA
*
15605 TATGTCCCGTTGGACCAC
1 TATGTCCCGTAGGACCAC
15623 TATGTCCCGTAGGACCAC
1 TATGTCCCGTAGGACCAC
15641 GTAGAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.33, G:0.22, T:0.25
Consensus pattern (18 bp):
TATGTCCCGTAGGACCAC
Found at i:16328 original size:25 final size:25
Alignment explanation
Indices: 16300--16349 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
16290 TTTAGCACTA
*
16300 TATCACTACGTGTTTATGCTTCAGT
1 TATCACTACATGTTTATGCTTCAGT
*
16325 TATCACTATATGTTTATGCTTCAGT
1 TATCACTACATGTTTATGCTTCAGT
16350 ACCCCTGATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.46
Consensus pattern (25 bp):
TATCACTACATGTTTATGCTTCAGT
Found at i:20800 original size:15 final size:15
Alignment explanation
Indices: 20780--20809 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
20770 CTAGAGCGGG
20780 TTTGTGAGTTCCAAA
1 TTTGTGAGTTCCAAA
20795 TTTGTGAGTTCCAAA
1 TTTGTGAGTTCCAAA
20810 ACTATCATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (15 bp):
TTTGTGAGTTCCAAA
Found at i:22103 original size:29 final size:29
Alignment explanation
Indices: 22071--22129 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
22061 CCTAAATTAA
*
22071 TTTGATGTCATTGTTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
22100 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
22129 T
1 T
22130 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.51
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:26746 original size:29 final size:29
Alignment explanation
Indices: 26714--26772 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
26704 CTTAAATTAA
26714 TTTGATGCCATTACTTACATCAATTTAGT
1 TTTGATGCCATTACTTACATCAATTTAGT
* *
26743 TTTGATGGCATTGCTTACATCAATTTAGT
1 TTTGATGCCATTACTTACATCAATTTAGT
26772 T
1 T
26773 AGGTGAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (29 bp):
TTTGATGCCATTACTTACATCAATTTAGT
Found at i:33705 original size:20 final size:18
Alignment explanation
Indices: 33670--33712 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 18
33660 TTAGCATTGT
*
33670 GAAAAGAAAATAATGAAA
1 GAAAAGAAAAAAATGAAA
33688 GAAAAGTAAAAAAGATGAAA
1 GAAAAG-AAAAAA-ATGAAA
33708 GAAAA
1 GAAAA
33713 TAGAACTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
19 5 0.23
20 11 0.50
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (18 bp):
GAAAAGAAAAAAATGAAA
Found at i:46297 original size:12 final size:12
Alignment explanation
Indices: 46280--46313 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
46270 GAAAATAAAG
46280 AAAACTTAATGT
1 AAAACTTAATGT
*
46292 AAAACTTGATGT
1 AAAACTTAATGT
46304 AAAAC-TAATG
1 AAAACTTAATG
46314 GCTCTAGCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (12 bp):
AAAACTTAATGT
Found at i:52534 original size:21 final size:20
Alignment explanation
Indices: 52491--52535 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
52481 AAAAGTGATT
*
52491 TAAAGTGAAAATAAAGAATG
1 TAAAGTGAAAATAAAGAAGG
* *
52511 TAAAGTTGAAAATGAATAAGG
1 TAAAG-TGAAAATAAAGAAGG
52532 TAAA
1 TAAA
52536 AATAGCCTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.58, C:0.00, G:0.20, T:0.22
Consensus pattern (20 bp):
TAAAGTGAAAATAAAGAAGG
Found at i:53142 original size:25 final size:24
Alignment explanation
Indices: 53080--53132 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 24
53070 TTAACATGTT
*
53080 TAAAAAT-AAAACTTAAGATAAAA
1 TAAAAATGAAAACTTAAAATAAAA
53103 TAAAAATGAAAACTTGAAAATAAAA
1 TAAAAATGAAAACTT-AAAATAAAA
53128 TAAAA
1 TAAAA
53133 GAGAGAACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 7 0.26
24 7 0.26
25 13 0.48
ACGTcount: A:0.70, C:0.04, G:0.06, T:0.21
Consensus pattern (24 bp):
TAAAAATGAAAACTTAAAATAAAA
Found at i:62079 original size:15 final size:15
Alignment explanation
Indices: 62055--62086 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
62045 TGGCAGATCG
*
62055 AAATCCAGAACGGGA
1 AAATCAAGAACGGGA
62070 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
62085 AA
1 AA
62087 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.16, G:0.25, T:0.06
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:64981 original size:2 final size:2
Alignment explanation
Indices: 64944--64968 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
64934 ACATTCATTC
64944 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 A
64969 CATTAACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:65275 original size:28 final size:27
Alignment explanation
Indices: 65244--65317 Score: 114
Period size: 26 Copynumber: 2.7 Consensus size: 27
65234 GTAGGACCAT
*
65244 TATGTCCCATAGGACCACGTAGAACACA
1 TATGTCCCGTAGGACCAC-TAGAACACA
65272 TATGTCCCGTA-GACCACTAGAACACA
1 TATGTCCCGTAGGACCACTAGAACACA
*
65298 TATGTCCCGTTGGACCACTA
1 TATGTCCCGTAGGACCACTA
65318 TGTCCCGTAG
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 19 0.44
27 14 0.33
28 10 0.23
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.22
Consensus pattern (27 bp):
TATGTCCCGTAGGACCACTAGAACACA
Found at i:65321 original size:18 final size:18
Alignment explanation
Indices: 65298--65333 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
65288 CTAGAACACA
*
65298 TATGTCCCGTTGGACCAC
1 TATGTCCCGTAGGACCAC
65316 TATGTCCCGTAGGACCAC
1 TATGTCCCGTAGGACCAC
65334 GTAGAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.33, G:0.22, T:0.25
Consensus pattern (18 bp):
TATGTCCCGTAGGACCAC
Found at i:66024 original size:25 final size:25
Alignment explanation
Indices: 65996--66045 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
65986 TTTAGCACTA
*
65996 TATCACTACGTGTTTATGCTTCAGT
1 TATCACTACATGTTTATGCTTCAGT
*
66021 TATCACTATATGTTTATGCTTCAGT
1 TATCACTACATGTTTATGCTTCAGT
66046 ACCCCTGATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.46
Consensus pattern (25 bp):
TATCACTACATGTTTATGCTTCAGT
Found at i:70499 original size:15 final size:15
Alignment explanation
Indices: 70479--70508 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
70469 CTAGAGCGGG
70479 TTTGTGAGTTCCAAA
1 TTTGTGAGTTCCAAA
70494 TTTGTGAGTTCCAAA
1 TTTGTGAGTTCCAAA
70509 ACTATCATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (15 bp):
TTTGTGAGTTCCAAA
Found at i:71803 original size:29 final size:29
Alignment explanation
Indices: 71771--71829 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
71761 CCTAAATTAA
*
71771 TTTGATGTCATTGTTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
71800 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
71829 T
1 T
71830 GGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.51
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:76452 original size:29 final size:29
Alignment explanation
Indices: 76420--76478 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
76410 CTTAAATTAA
76420 TTTGATGCCATTACTTACATCAATTTAGT
1 TTTGATGCCATTACTTACATCAATTTAGT
* *
76449 TTTGATGGCATTGCTTACATCAATTTAGT
1 TTTGATGCCATTACTTACATCAATTTAGT
76478 T
1 T
76479 AGGTGAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (29 bp):
TTTGATGCCATTACTTACATCAATTTAGT
Found at i:83405 original size:18 final size:17
Alignment explanation
Indices: 83380--83417 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
83370 AGCATTGTGA
83380 AAAGAAAATA-ATGAAAG
1 AAAGAAAA-AGATGAAAG
83397 AAAGTAAAAAGATGAAAG
1 AAAG-AAAAAGATGAAAG
83415 AAA
1 AAA
83418 ATAGAACTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.11
Consensus pattern (17 bp):
AAAGAAAAAGATGAAAG
Done.