Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009850.1 Corchorus capsularis cultivar CVL-1 contig09871, 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: 53496
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1141 original size:32 final size:32
Alignment explanation
Indices: 1100--1282 Score: 154
Period size: 32 Copynumber: 5.7 Consensus size: 32
1090 ATACAATAGG
* * *
1100 GGCGTTTCACATGTAGAATGCCCCTATTTAGA
1 GGCGTTTCACATATAAAACGCCCCTATTTAGA
* * *
1132 GGCGTTTCACATCTAAAACGCCCTTATTTTGA
1 GGCGTTTCACATATAAAACGCCCCTATTTAGA
* * *
1164 GGCGTTTCTCATATAAAACGTCCCTATTTAGC
1 GGCGTTTCACATATAAAACGCCCCTATTTAGA
* *
1196 GGCGTATT-TCATATAAAACGCCCCTATTTTAGC
1 GGCGT-TTCACATATAAAACGCCCCTA-TTTAGA
* * * * ** *
1229 GGCGTTT-ACGTTTAAAATGCCACTAAATAGG
1 GGCGTTTCACATATAAAACGCCCCTATTTAGA
*
1260 GGCGTTTCACTTAATAAAACGCC
1 GGCGTTTCACAT-ATAAAACGCC
1283 GGGAAACAAT
Statistics
Matches: 124, Mismatches: 23, Indels: 7
0.81 0.15 0.05
Matches are distributed among these distances:
31 10 0.08
32 93 0.75
33 21 0.17
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (32 bp):
GGCGTTTCACATATAAAACGCCCCTATTTAGA
Found at i:13111 original size:1 final size:1
Alignment explanation
Indices: 13105--13134 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
13095 AGATAAATTT
13105 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
13135 CCTGAAACTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:15685 original size:18 final size:18
Alignment explanation
Indices: 15633--15687 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 18
15623 ATATAAGTTG
15633 AAAATTATAATGA-TTTT
1 AAAATTATAATGATTTTT
* * * * *
15650 GACATTGT-GTGATGTTT
1 AAAATTATAATGATTTTT
15667 AAAATTATAATGATTTTT
1 AAAATTATAATGATTTTT
15685 AAA
1 AAA
15688 CCTCTTCCCA
Statistics
Matches: 26, Mismatches: 10, Indels: 3
0.67 0.26 0.08
Matches are distributed among these distances:
16 3 0.12
17 13 0.50
18 10 0.38
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.45
Consensus pattern (18 bp):
AAAATTATAATGATTTTT
Found at i:17641 original size:10 final size:11
Alignment explanation
Indices: 17621--17646 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
17611 TCCCTCTTTC
17621 TTTCTTTTTTT
1 TTTCTTTTTTT
17632 TTTCTTTTTTT
1 TTTCTTTTTTT
17643 TTTC
1 TTTC
17647 CCAGATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:19800 original size:2 final size:2
Alignment explanation
Indices: 19751--19784 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
19741 TTTGAATTGC
19751 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
19785 GAACTAAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35539 original size:36 final size:36
Alignment explanation
Indices: 35492--35597 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
35482 AAAGGAACCA
* * *
35492 TCGAAGGAGCAGATGAAGCTGAGCAATGAAAATCCG
1 TCGAAGAAGCAGATGAAGCCGAGCAAGGAAAATCCG
35528 TCGAAGAAGCAGATGAAGCCGAGCAAGGAAAATCCG
1 TCGAAGAAGCAGATGAAGCCGAGCAAGGAAAATCCG
35564 TCGAAGAAGCAGATGAAGCCGAGCAAGGAAAATC
1 TCGAAGAAGCAGATGAAGCCGAGCAAGGAAAATC
35598 ATGATAGGGG
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 67 1.00
ACGTcount: A:0.42, C:0.18, G:0.30, T:0.10
Consensus pattern (36 bp):
TCGAAGAAGCAGATGAAGCCGAGCAAGGAAAATCCG
Found at i:37712 original size:3 final size:3
Alignment explanation
Indices: 37704--37747 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
37694 GATTTGAGGG
37704 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
37748 CAAAATACAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:39250 original size:31 final size:30
Alignment explanation
Indices: 39195--39292 Score: 99
Period size: 31 Copynumber: 3.2 Consensus size: 30
39185 TAATTAAGTA
* *
39195 CCTAACATTGCAAAATAAGCTCAAATCGATC
1 CCTAACATTGCAAAAT-CGTTCAAATCGATC
* * *
39226 CCTAACGTTGCAAAATCTGTTCAAATTGATT
1 CCTAACATTGCAAAATC-GTTCAAATCGATC
*
39257 TCTAACATTGCAAAATCGATTCAAATC-AGTC
1 CCTAACATTGCAAAATCG-TTCAAATCGA-TC
39288 CCTAA
1 CCTAA
39293 AGTAAATTGA
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
30 2 0.04
31 52 0.96
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (30 bp):
CCTAACATTGCAAAATCGTTCAAATCGATC
Found at i:46088 original size:2 final size:2
Alignment explanation
Indices: 46081--46110 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
46071 ACCATCATTC
46081 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
46111 TTTATAAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50477 original size:46 final size:46
Alignment explanation
Indices: 50410--50498 Score: 160
Period size: 46 Copynumber: 1.9 Consensus size: 46
50400 GTTCCTCAGC
* *
50410 TTGCTTGCTTCACTGACAAGTGACAGGCATGCCTAGATACATGATA
1 TTGCTTGCTTCACTGACAAGTGACAGCCATGCCTAAATACATGATA
50456 TTGCTTGCTTCACTGACAAGTGACAGCCATGCCTAAATACATG
1 TTGCTTGCTTCACTGACAAGTGACAGCCATGCCTAAATACATG
50499 GTAAAATATG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (46 bp):
TTGCTTGCTTCACTGACAAGTGACAGCCATGCCTAAATACATGATA
Found at i:51358 original size:2 final size:2
Alignment explanation
Indices: 51353--51382 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
51343 TCTTTTTTAT
51353 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
51383 CTCCTTTGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:51534 original size:20 final size:21
Alignment explanation
Indices: 51509--51550 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
51499 AAAATAAAAT
*
51509 TAAAATGAT-AATTGAAATAG
1 TAAAATGATAAATTAAAATAG
*
51529 TAAAATGGTAAATTAAAATAG
1 TAAAATGATAAATTAAAATAG
51550 T
1 T
51551 TATAAGGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.31
Consensus pattern (21 bp):
TAAAATGATAAATTAAAATAG
Found at i:51616 original size:70 final size:69
Alignment explanation
Indices: 51526--51674 Score: 228
Period size: 70 Copynumber: 2.1 Consensus size: 69
51516 ATAATTGAAA
* * *
51526 TAGTAAAATGGTAAATTAAAATAGTTATAAGGATATTAGGTTTAATTAAATAAAAATAGAGTTTT
1 TAGTAAAATAGTAAATTAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTT
51591 TAGT
66 TAGT
*
51595 CTAGTAAAATAGTGAAA-TAAAATAGTTATAAAGATATTAGATTTAATTAAATAAATATAGAGTT
1 -TAGTAAAATAGT-AAATTAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTT
51659 TTTAGT
64 TTTAGT
51665 TAAGTAAAAT
1 T-AGTAAAAT
51675 TATAAAAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
69 1 0.01
70 69 0.95
71 3 0.04
ACGTcount: A:0.48, C:0.01, G:0.14, T:0.37
Consensus pattern (69 bp):
TAGTAAAATAGTAAATTAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTT
TAGT
Found at i:51946 original size:215 final size:215
Alignment explanation
Indices: 51575--51990 Score: 744
Period size: 215 Copynumber: 1.9 Consensus size: 215
51565 GTTTAATTAA
51575 ATAAAAATAGAGTTTTTAGTCTAGTAAAATAGTGAAATAAAATAGTTATAAAGATATTAGATTTA
1 ATAAAAATAGAGTTTTTAGTCTAGTAAAATAGTGAAATAAAATAGTTATAAAGATATTAGATTTA
**
51640 ATTAAATAAATATAGAGTTTTTAGTTAAGTAAAATTATAAAAGTGTAAATAATGGTATTTTTGAA
66 ATTAAATAAATATAGAGTTTTTAGTTAAGTAAAATTATAAAAGTGTAAATAATGACATTTTTGAA
* *
51705 ATATATTCGAAAAATAAGGGTATAATAGACGATTCAAAAGTTTTACAGGTGAATGTACTTTTTAA
131 ATATATTCGAAAAATAAGGGTATAATAGACGATTCAAAAATTTTACAGGTGAACGTACTTTTTAA
51770 TATAGTGTATGTATATGTAT
196 TATAGTGTATGTATATGTAT
* *
51790 ATAAAAATAGAGTTTTTAGT-TGAGTAAAATAGTGGAATAAAATAGTTATAAAGATATTATATTT
1 ATAAAAATAGAGTTTTTAGTCT-AGTAAAATAGTGAAATAAAATAGTTATAAAGATATTAGATTT
*
51854 AATTAAATAAATATAGAGTTTTTAGTTGAGTAAAATTATAAAAGTGTAAATAATGACATTTTTGA
65 AATTAAATAAATATAGAGTTTTTAGTTAAGTAAAATTATAAAAGTGTAAATAATGACATTTTTGA
*
51919 AATATGTTCGAAAAATAAGGGTATAATAGACGATTCAAAAATTTTACAGGTGAACGTACTTTTTA
130 AATATATTCGAAAAATAAGGGTATAATAGACGATTCAAAAATTTTACAGGTGAACGTACTTTTTA
51984 ATATAGT
195 ATATAGT
51991 ATAGATATAG
Statistics
Matches: 192, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
214 1 0.01
215 191 0.99
ACGTcount: A:0.44, C:0.03, G:0.15, T:0.37
Consensus pattern (215 bp):
ATAAAAATAGAGTTTTTAGTCTAGTAAAATAGTGAAATAAAATAGTTATAAAGATATTAGATTTA
ATTAAATAAATATAGAGTTTTTAGTTAAGTAAAATTATAAAAGTGTAAATAATGACATTTTTGAA
ATATATTCGAAAAATAAGGGTATAATAGACGATTCAAAAATTTTACAGGTGAACGTACTTTTTAA
TATAGTGTATGTATATGTAT
Done.