Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001995.1 Hibiscus syriacus cultivar Beakdansim tig00004085_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: 62550
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1469 original size:21 final size:22
Alignment explanation
Indices: 1436--1478 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
1426 TTTTCCCATA
*
1436 TTTTGTTACAAAACAA-AGACTT
1 TTTTATTACAAAA-AATAGACTT
1458 TTTTATTA-AAAAAATAGACTT
1 TTTTATTACAAAAAATAGACTT
1479 GTTCAAAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 2 0.11
21 10 0.53
22 7 0.37
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (22 bp):
TTTTATTACAAAAAATAGACTT
Found at i:3963 original size:3 final size:3
Alignment explanation
Indices: 3955--3980 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3945 AACGTAACAT
3955 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
3981 TCAATAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:11718 original size:28 final size:29
Alignment explanation
Indices: 11638--11718 Score: 82
Period size: 28 Copynumber: 2.9 Consensus size: 29
11628 AAATTTTATA
* *
11638 AGTAACTTCAAGACTTCAAA-TATC-TTAG
1 AGTAACTTCAATACTTCAAAGT-TCATTAC
11666 AGTAACTTCAATAC-T-AAAGATTTCATT-C
1 AGTAACTTCAATACTTCAAAG--TTCATTAC
11694 AGTAACTTCAATACTTCAAAGTTCA
1 AGTAACTTCAATACTTCAAAGTTCA
11719 AAACAAATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
26 3 0.07
27 1 0.02
28 33 0.73
29 4 0.09
30 4 0.09
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.33
Consensus pattern (29 bp):
AGTAACTTCAATACTTCAAAGTTCATTAC
Found at i:12669 original size:24 final size:24
Alignment explanation
Indices: 12640--12688 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
12630 CGTGATTTTT
12640 AGAATGTTTTCAACTTCGTTCCAA
1 AGAATGTTTTCAACTTCGTTCCAA
12664 AGAATGTTTTCAACTTCGTTCCAA
1 AGAATGTTTTCAACTTCGTTCCAA
12688 A
1 A
12689 AATCATCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (24 bp):
AGAATGTTTTCAACTTCGTTCCAA
Found at i:17973 original size:30 final size:30
Alignment explanation
Indices: 17937--17996 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
17927 CTTATGTTTG
17937 TCAAATGTAAACAAGTCATAAAAACAATAA
1 TCAAATGTAAACAAGTCATAAAAACAATAA
17967 TCAAATGTAAACAAGTCATAAAAACAATAA
1 TCAAATGTAAACAAGTCATAAAAACAATAA
17997 GGACATGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.60, C:0.13, G:0.07, T:0.20
Consensus pattern (30 bp):
TCAAATGTAAACAAGTCATAAAAACAATAA
Found at i:20734 original size:29 final size:29
Alignment explanation
Indices: 20701--20770 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 29
20691 GAATTTTATA
20701 ATTATTAAAAAATATAAAATAATTATTTG
1 ATTATTAAAAAATATAAAATAATTATTTG
* * * * * *
20730 ATTATTTAAATATTCTAAATTCATTATTTT
1 ATTA-TTAAAAAATATAAAATAATTATTTG
20760 ATTATTAAAAA
1 ATTATTAAAAA
20771 TTAATTATAT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
29 10 0.30
30 23 0.70
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (29 bp):
ATTATTAAAAAATATAAAATAATTATTTG
Found at i:26632 original size:12 final size:12
Alignment explanation
Indices: 26617--26661 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
26607 TTCGAACTTG
26617 AATCGAGCTCAA
1 AATCGAGCTCAA
*
26629 AATCGAGCTC-G
1 AATCGAGCTCAA
*
26640 AGTCGAGCTCAA
1 AATCGAGCTCAA
26652 AATCGAGCTC
1 AATCGAGCTC
26662 TTGAAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 9 0.32
12 19 0.68
ACGTcount: A:0.33, C:0.27, G:0.22, T:0.18
Consensus pattern (12 bp):
AATCGAGCTCAA
Found at i:32941 original size:14 final size:15
Alignment explanation
Indices: 32915--32943 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
32905 CATGTTATAT
32915 TATAAAAATATATTC
1 TATAAAAATATATTC
32930 TATAAAAA-ATATTC
1 TATAAAAATATATTC
32944 AGAATTCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
TATAAAAATATATTC
Found at i:33677 original size:30 final size:31
Alignment explanation
Indices: 33641--33700 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
33631 AACTAACAAG
* *
33641 AATTAATAAC-TCAGTGACCAAAATTTAATA
1 AATTAATAACGTAAGTGACCAAAACTTAATA
33671 AATTAATAACGTAAGTGACCAAAACTTAAT
1 AATTAATAACGTAAGTGACCAAAACTTAAT
33701 TTTTTAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.50, C:0.13, G:0.08, T:0.28
Consensus pattern (31 bp):
AATTAATAACGTAAGTGACCAAAACTTAATA
Found at i:36189 original size:2 final size:2
Alignment explanation
Indices: 36182--36213 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
36172 ATGCGTGTGC
36182 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
36214 GAGTCCTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40556 original size:59 final size:60
Alignment explanation
Indices: 40451--40614 Score: 233
Period size: 59 Copynumber: 2.8 Consensus size: 60
40441 AAATACAACT
* * * *
40451 TAAATTGGTCC-CTAAACTTTTAAATGTTTCAATTTCATCCCTAAACTATAATTATCATTC
1 TAAATTAGTCCTC-AAACTTCTAAATATTTCAATTTCATCCCTAAACTATAATTACCATTC
* *
40511 TAAATTAGTCTTCAAACTTCTAAATATTT-AATTTCATCCCTAAACTATGATTACCATTC
1 TAAATTAGTCCTCAAACTTCTAAATATTTCAATTTCATCCCTAAACTATAATTACCATTC
* *
40570 TAAATTAGTCCTCAAACTTCTAAACATTTCAAATTCATCCCTAAA
1 TAAATTAGTCCTCAAACTTCTAAATATTTCAATTTCATCCCTAAA
40615 ATATGACCTT
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
59 55 0.59
60 37 0.40
61 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.04, T:0.39
Consensus pattern (60 bp):
TAAATTAGTCCTCAAACTTCTAAATATTTCAATTTCATCCCTAAACTATAATTACCATTC
Found at i:40635 original size:60 final size:58
Alignment explanation
Indices: 40451--40678 Score: 221
Period size: 60 Copynumber: 3.8 Consensus size: 58
40441 AAATACAACT
* * * *
40451 TAAATTGGTCC-CTAAACTTTTAAATGTTTCAATTTCATCCCTAAACTATAATTATCATTC
1 TAAATTAGTCCTC-AAACTTCTAAATATTTCAATTTCATCCCTAAACTATGA-T-TCATTC
*
40511 TAAATTAGTCTTCAAACTTCTAAATATTT-AATTTCATCCCTAAACTATGATTACCATTC
1 TAAATTAGTCCTCAAACTTCTAAATATTTCAATTTCATCCCTAAACTATGATT--CATTC
* * *
40570 TAAATTAGTCCTCAAACTTCTAAACATTTCAAATTCATCCCTAAAATATGACCTTCATTC
1 TAAATTAGTCCTCAAACTTCTAAATATTTCAATTTCATCCCTAAACTATGA--TTCATTC
* * * * * *
40630 TAAATT-GATCCCCTAACTTTTTGAAGATTCCAATTTCATCCC-AAACTAT
1 TAAATTAG-TCCTCAAAC-TTCTAAATATTTCAATTTCATCCCTAAACTAT
40679 ACATATACAC
Statistics
Matches: 143, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
57 1 0.01
58 1 0.01
59 53 0.37
60 66 0.46
61 20 0.14
62 2 0.01
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (58 bp):
TAAATTAGTCCTCAAACTTCTAAATATTTCAATTTCATCCCTAAACTATGATTCATTC
Found at i:48570 original size:22 final size:23
Alignment explanation
Indices: 48521--48570 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
48511 TTGATATGAT
* *
48521 ACTAATATTTTAAGAACTTAAAT
1 ACTAGTATTTTAAGAACTTAAAA
*
48544 A-TAGTATTTTAA-AAGTTAAAA
1 ACTAGTATTTTAAGAACTTAAAA
48565 ACTAGT
1 ACTAGT
48571 TTAAATTCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 8 0.35
22 14 0.61
23 1 0.04
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.38
Consensus pattern (23 bp):
ACTAGTATTTTAAGAACTTAAAA
Found at i:49333 original size:21 final size:21
Alignment explanation
Indices: 49304--49351 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
49294 GAATAATCCT
* *
49304 TAATTTTTTTTTAATTTTTAA
1 TAATATTTTTTTAATTTTAAA
49325 TAATATTTTTTTAATTTTAAA
1 TAATATTTTTTTAATTTTAAA
*
49346 TTATAT
1 TAATAT
49352 ATTTAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TAATATTTTTTTAATTTTAAA
Found at i:49394 original size:22 final size:22
Alignment explanation
Indices: 49352--49404 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
49342 TAAATTATAT
49352 ATTTAATTTTGTAGTAATTTAA
1 ATTTAATTTTGTAGTAATTTAA
* * *
49374 ATTTTATTTT-TAGTATTTTTAT
1 ATTTAATTTTGTAGTA-ATTTAA
49396 ATTTAATTT
1 ATTTAATTT
49405 ATTGAATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 5 0.19
22 21 0.81
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (22 bp):
ATTTAATTTTGTAGTAATTTAA
Found at i:49400 original size:21 final size:21
Alignment explanation
Indices: 49344--49400 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
49334 TTTAATTTTA
49344 AATTATATATTTAATTTTGTAGT
1 AATT-TATATTT-ATTTTGTAGT
*
49367 AATTTAAATTTTATTTT-TAGT
1 AATTTATA-TTTATTTTGTAGT
*
49388 ATTTTTATATTTA
1 A-ATTTATATTTA
49401 ATTTATTGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 9 0.31
22 13 0.45
23 7 0.24
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.61
Consensus pattern (21 bp):
AATTTATATTTATTTTGTAGT
Found at i:50979 original size:133 final size:133
Alignment explanation
Indices: 50741--51008 Score: 412
Period size: 133 Copynumber: 2.0 Consensus size: 133
50731 GTTTAAAATA
* * * * * *
50741 TTTCTTAGTTATTAATAATACAAACATGCCATGTAGACATAGCCGTTCAAACTCGAAATCTTTAA
1 TTTCTCAGTTATCAATAACACAAACATGCCATGTAGACACAACCGTTCAAACTCGAAATCTTCAA
*
50806 GGAGAACAACACTCTCTTTTACTACTGAAGTCGTTTGATAGGTTCTTACTAACGGAGAAAGTTGA
66 GGAGAACAACACTCTCTTTTACTACTGAAGTCGTTTGATAGGTTCTTACTAACGGAGAAAGTCGA
50871 GTG
131 GTG
* * *
50874 TTTCTCAGTTATCAATAACGCAAACATGTCAT-TCAGACACAACCTTTCAAACTCGAAATCTTCA
1 TTTCTCAGTTATCAATAACACAAACATGCCATGT-AGACACAACCGTTCAAACTCGAAATCTTCA
* *
50938 AGGAGAACAACATTCTCTTTTATTACTGAAGTCGTTTGATAGGTTCTTACTAACGGAGAAAGTCG
65 AGGAGAACAACACTCTCTTTTACTACTGAAGTCGTTTGATAGGTTCTTACTAACGGAGAAAGTCG
51003 AGTG
130 AGTG
51007 TT
1 TT
51009 AGATAAAAGA
Statistics
Matches: 122, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
132 1 0.01
133 121 0.99
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (133 bp):
TTTCTCAGTTATCAATAACACAAACATGCCATGTAGACACAACCGTTCAAACTCGAAATCTTCAA
GGAGAACAACACTCTCTTTTACTACTGAAGTCGTTTGATAGGTTCTTACTAACGGAGAAAGTCGA
GTG
Done.