Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014394.1 Corchorus capsularis cultivar CVL-1 contig14415, 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: 47585
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:4096 original size:15 final size:15
Alignment explanation
Indices: 4076--4107 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4066 ACTCGCTTTC
4076 TCTTCCTCTTTATTT
1 TCTTCCTCTTTATTT
*
4091 TCTTCCTTTTTATTT
1 TCTTCCTCTTTATTT
4106 TC
1 TC
4108 ACCAACAAAT
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:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (15 bp):
TCTTCCTCTTTATTT
Found at i:6531 original size:2 final size:2
Alignment explanation
Indices: 6526--6552 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6516 TAAACCTAGC
6526 AT 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 AT A
6553 CACCTCATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16561 original size:51 final size:51
Alignment explanation
Indices: 16495--16601 Score: 137
Period size: 54 Copynumber: 2.1 Consensus size: 51
16485 TTGAGACTTC
* *
16495 TTTTCTTCTTCTCTTC-TCATCACCA-TCTTTCCAAGAAAACAAGAGCCTACT
1 TTTTCTTCCTCTCTTCATCATCACCATTC-TTCCAAGAAAACAAGACCCTA-T
*
16546 TTTTGTTCCTCTCTTCTGATCATCACCATTCTTCCAAGAAAACAAGACCCTAT
1 TTTTCTTCCTCTCTTC--ATCATCACCATTCTTCCAAGAAAACAAGACCCTAT
16599 TTT
1 TTT
16602 ATTATGTTTC
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
51 14 0.29
53 4 0.08
54 29 0.59
55 2 0.04
ACGTcount: A:0.25, C:0.30, G:0.07, T:0.38
Consensus pattern (51 bp):
TTTTCTTCCTCTCTTCATCATCACCATTCTTCCAAGAAAACAAGACCCTAT
Found at i:17433 original size:20 final size:20
Alignment explanation
Indices: 17408--17446 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
17398 ATGCAAATGT
17408 TGCTCAATTGGAGGTTCAAG
1 TGCTCAATTGGAGGTTCAAG
17428 TGCTCAATTGGAGGTTCAA
1 TGCTCAATTGGAGGTTCAA
17447 AGTGATTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (20 bp):
TGCTCAATTGGAGGTTCAAG
Found at i:17959 original size:14 final size:14
Alignment explanation
Indices: 17940--17967 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17930 ATTACTAGTA
17940 CTAATTATAATGTG
1 CTAATTATAATGTG
17954 CTAATTATAATGTG
1 CTAATTATAATGTG
17968 AAGTCCTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (14 bp):
CTAATTATAATGTG
Found at i:18202 original size:138 final size:137
Alignment explanation
Indices: 17954--18226 Score: 519
Period size: 138 Copynumber: 2.0 Consensus size: 137
17944 TTATAATGTG
*
17954 CTAATTATAATGTGAAGTCCTGAGTTTGTGTCACGAGTTGACTCGGAGACAAACTCGGTGACTCA
1 CTAATTATAATGTGAAGTCCTGAGTTTGTGTCACGAGTTGACTCGGAAACAAACTCGGTGACTCA
*
18019 CAACTAAATTATTTGGAAATTAATATTTTATGAAGTTGGTTAACAAAACTAAAATAAAAAACTGC
66 CAACTAAATTATTTGAAAATTAATATTTTATGAAGTTGGTTAACAAAACTAAAATAAAAAACT-C
18084 TATCTATA
130 TATCTATA
18092 CTAATTATAATGTGAAGTCCTGAGTTTGTGTCACGAGTTGACTCGGAAACAAACTCGGTGACTCA
1 CTAATTATAATGTGAAGTCCTGAGTTTGTGTCACGAGTTGACTCGGAAACAAACTCGGTGACTCA
18157 CAACTAAATTATTTGAAAATTAATATTTTATGAAGTTGGTTAACAAAACTAAAATAAAAAACTCT
66 CAACTAAATTATTTGAAAATTAATATTTTATGAAGTTGGTTAACAAAACTAAAATAAAAAACTCT
18222 ATCTA
131 ATCTA
18227 GATTTTATGA
Statistics
Matches: 133, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
137 7 0.05
138 126 0.95
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (137 bp):
CTAATTATAATGTGAAGTCCTGAGTTTGTGTCACGAGTTGACTCGGAAACAAACTCGGTGACTCA
CAACTAAATTATTTGAAAATTAATATTTTATGAAGTTGGTTAACAAAACTAAAATAAAAAACTCT
ATCTATA
Found at i:18580 original size:51 final size:51
Alignment explanation
Indices: 18525--18622 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
18515 CATTGATAAT
* *
18525 CAACAACATACACATTTTGCTGAAA-AGTTTTTAAGATTGGGAGCCATTCAC
1 CAACAACATACACATTTTGCT-AAAGAGTTTTGAAGATTGGAAGCCATTCAC
* * *
18576 CAACAGCATACTCATTTTGGTAAAGAGTTTTGAAGATTGGAAGCCAT
1 CAACAACATACACATTTTGCTAAAGAGTTTTGAAGATTGGAAGCCAT
18623 GCACATTACA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
50 3 0.07
51 38 0.93
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (51 bp):
CAACAACATACACATTTTGCTAAAGAGTTTTGAAGATTGGAAGCCATTCAC
Found at i:18670 original size:2 final size:2
Alignment explanation
Indices: 18663--18689 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18653 CTTTAATACT
18663 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 T
18690 TTGGCAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19085 original size:40 final size:41
Alignment explanation
Indices: 19011--19109 Score: 182
Period size: 40 Copynumber: 2.4 Consensus size: 41
19001 TTTCCTTAAC
19011 TTGATTTCTCATGTTTATTTTTTTATTTTTTTGACGTCATTT
1 TTGATTTCTCATGTTTA-TTTTTTATTTTTTTGACGTCATTT
19053 TTGATTTCTCATGTTTA-TTTTTATTTTTTTGACGTCATTT
1 TTGATTTCTCATGTTTATTTTTTATTTTTTTGACGTCATTT
19093 TTGATTTCTCATGTTTA
1 TTGATTTCTCATGTTTA
19110 CTCTTCTTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
40 40 0.70
42 17 0.30
ACGTcount: A:0.15, C:0.10, G:0.10, T:0.65
Consensus pattern (41 bp):
TTGATTTCTCATGTTTATTTTTTATTTTTTTGACGTCATTT
Found at i:28734 original size:107 final size:108
Alignment explanation
Indices: 28612--28826 Score: 328
Period size: 109 Copynumber: 2.0 Consensus size: 108
28602 AATGTAAAAA
* *
28612 TTAATTAACAATATCCTT-ATCAATTTTTTTTGTTTTTTTTTTT-CGAATATCTCAGACTTATAA
1 TTAATTAACAATATCCTTAATCAA-TTTTTTTGTTTTTTTTTTTCCGAATATCCCAGACTTAAAA
*
28675 TTTATAATATAAAGTAC-GATTGTTTTGTTCAAGAATTAATATAC
65 TTTATAATATAAAGT-CGGATTATTTTGTTCAAGAATTAATATAC
*
28719 TTAATTAACAATATCCTTAAATCAATTTTTTTGTTTTTTTTTTTCCGAATATCCCAGCCTTAAAA
1 TTAATTAACAATATCCTT-AATCAATTTTTTTGTTTTTTTTTTTCCGAATATCCCAGACTTAAAA
* *
28784 TTTATAATGTAAAGTCGGATTATTTTGTTGAAGAATTAATATA
65 TTTATAATATAAAGTCGGATTATTTTGTTCAAGAATTAATATA
28827 TCTGATTAAT
Statistics
Matches: 98, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
107 18 0.18
108 20 0.20
109 60 0.61
ACGTcount: A:0.33, C:0.11, G:0.08, T:0.48
Consensus pattern (108 bp):
TTAATTAACAATATCCTTAATCAATTTTTTTGTTTTTTTTTTTCCGAATATCCCAGACTTAAAAT
TTATAATATAAAGTCGGATTATTTTGTTCAAGAATTAATATAC
Found at i:28905 original size:17 final size:17
Alignment explanation
Indices: 28883--28919 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
28873 TTACTATACA
*
28883 TTAATATTGATGAAATT
1 TTAATATAGATGAAATT
28900 TTAATATAGATGAAATT
1 TTAATATAGATGAAATT
28917 TTA
1 TTA
28920 TACTCACCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (17 bp):
TTAATATAGATGAAATT
Found at i:36971 original size:22 final size:22
Alignment explanation
Indices: 36913--36972 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
36903 GTGGAATTTG
* *
36913 GGCCAGATGT-TGATTT-AGCA
1 GGCCAGATGTAAGTTTTGAGCA
* *
36933 GGCTAGGTGTCAA-TTTTGAGCA
1 GGCCAGATGT-AAGTTTTGAGCA
36955 GGCCAGATGTAAGTTTTG
1 GGCCAGATGTAAGTTTTG
36973 GGCAAGTGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
20 8 0.27
21 5 0.17
22 17 0.57
ACGTcount: A:0.23, C:0.13, G:0.32, T:0.32
Consensus pattern (22 bp):
GGCCAGATGTAAGTTTTGAGCA
Found at i:46393 original size:3 final size:3
Alignment explanation
Indices: 46387--46433 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
46377 AAAAAAAATT
* *
46387 TTA TTA TTA TTA TTA ATA AT- TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
46434 ATAGCTGTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 1 0.02
3 40 0.98
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:47116 original size:20 final size:21
Alignment explanation
Indices: 47091--47133 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
47081 AAAAAGTGAA
47091 TTACTAAATACCGCCC-CCTT
1 TTACTAAATACCGCCCTCCTT
**
47111 TTACTAGCTACCGCCCTCCTT
1 TTACTAAATACCGCCCTCCTT
47132 TT
1 TT
47134 GGACTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.19, C:0.40, G:0.07, T:0.35
Consensus pattern (21 bp):
TTACTAAATACCGCCCTCCTT
Done.