Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007992.1 Corchorus capsularis cultivar CVL-1 contig08013, 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: 13824
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:3238 original size:7 final size:7
Alignment explanation
Indices: 3226--3266 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
3216 AAATTCTAAC
3226 TAATAAT
1 TAATAAT
3233 TAATAAT
1 TAATAAT
3240 TACATAAT
1 TA-ATAAT
3248 TAATAA-
1 TAATAAT
3254 TAATCAA-
1 TAAT-AAT
3261 TAATAA
1 TAATAA
3267 AAAAAAAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.19
7 19 0.59
8 7 0.22
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (7 bp):
TAATAAT
Found at i:3248 original size:28 final size:25
Alignment explanation
Indices: 3207--3264 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
3197 ATTAAATTTC
* *
3207 ATAATTTCAAAATTCTAACTAATAATTA
1 ATAATTACAAAA-T-TAA-TAATAATCA
*
3235 ATAATTACATAATTAATAATAATCA
1 ATAATTACAAAATTAATAATAATCA
3260 ATAAT
1 ATAAT
3265 AAAAAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 13 0.48
26 3 0.11
27 1 0.04
28 10 0.37
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (25 bp):
ATAATTACAAAATTAATAATAATCA
Found at i:3339 original size:33 final size:33
Alignment explanation
Indices: 3300--3387 Score: 92
Period size: 33 Copynumber: 2.7 Consensus size: 33
3290 TGTCCATGGA
*
3300 CAGTGCCGCCCTCCTGGGGCGGCATG-CCATGC
1 CAGTGCCGCCCTCCTGGGGCGGCATGTCAATGC
** * * *
3332 CATGTGCCGCCCTAGTGGGACGGCTTGTCAATGG
1 CA-GTGCCGCCCTCCTGGGGCGGCATGTCAATGC
3366 CA-TGCCGCCCTCCT-GGGCGGCA
1 CAGTGCCGCCCTCCTGGGGCGGCA
3388 CTATCCATGG
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
31 6 0.14
32 12 0.27
33 20 0.45
34 6 0.14
ACGTcount: A:0.11, C:0.36, G:0.34, T:0.18
Consensus pattern (33 bp):
CAGTGCCGCCCTCCTGGGGCGGCATGTCAATGC
Found at i:3398 original size:32 final size:31
Alignment explanation
Indices: 3292--3408 Score: 94
Period size: 32 Copynumber: 3.6 Consensus size: 31
3282 CAAACTGTTG
3292 TCCATGGACAGTGCCGCCCTCCTGGGGCGGCAT
1 TCCATGG-CAGTGCCGCCCTCCT-GGGCGGCAT
* * ** *
3325 GCCATGCCATGTGCCGCCCTAGTGGGACGGCTT
1 TCCATGGCA-GTGCCGCCCTCCTGGG-CGGCAT
*
3358 GTCAATGGCA-TGCCGCCCTCCTGGGCGGCACT
1 -TCCATGGCAGTGCCGCCCTCCTGGGCGGCA-T
*
3390 ATCCATGGCA-TGTCGCCCT
1 -TCCATGGCAGTGCCGCCCT
3409 AGGAGGGCGG
Statistics
Matches: 66, Mismatches: 14, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
31 4 0.06
32 35 0.53
33 21 0.32
34 6 0.09
ACGTcount: A:0.13, C:0.36, G:0.31, T:0.21
Consensus pattern (31 bp):
TCCATGGCAGTGCCGCCCTCCTGGGCGGCAT
Found at i:4291 original size:33 final size:33
Alignment explanation
Indices: 4249--4314 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
4239 ATAGACCCTA
4249 AGCTTTTTAACTCGATTGCCAATTGAGGTTTGT
1 AGCTTTTTAACTCGATTGCCAATTGAGGTTTGT
4282 AGCTTTTTAACTCGATTGCCAATTGAGGTTTGT
1 AGCTTTTTAACTCGATTGCCAATTGAGGTTTGT
4315 GGAGTTCGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.42
Consensus pattern (33 bp):
AGCTTTTTAACTCGATTGCCAATTGAGGTTTGT
Found at i:4327 original size:33 final size:33
Alignment explanation
Indices: 4257--4327 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
4247 TAAGCTTTTT
** **
4257 AACTCGATTGCCAATTGAGGTTTGTAGCTTTTT
1 AACTCGATTGCCAATTGAGGTTTGTAGAGTTCG
*
4290 AACTCGATTGCCAATTGAGGTTTGTGGAGTTCG
1 AACTCGATTGCCAATTGAGGTTTGTAGAGTTCG
4323 AACTC
1 AACTC
4328 TGATCTCATA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.37
Consensus pattern (33 bp):
AACTCGATTGCCAATTGAGGTTTGTAGAGTTCG
Found at i:4593 original size:32 final size:32
Alignment explanation
Indices: 4556--4660 Score: 113
Period size: 32 Copynumber: 3.3 Consensus size: 32
4546 AGATCGGACA
* * *
4556 AACCCGTGACCCGAATGACCTGCAACCTAGAT
1 AACCCGAGACCCGAATGACCCGCAACCCAGAT
* *
4588 GACCCGAGACCCGAATGACCCGTAACCCAGAT
1 AACCCGAGACCCGAATGACCCGCAACCCAGAT
* * * *
4620 AACCCGAAACCTGAATGACCCGAAACCC-GAAA
1 AACCCGAGACCCGAATGACCCGCAACCCAG-AT
4652 AACCCGAGA
1 AACCCGAGA
4661 AGTTAATCCG
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
31 1 0.02
32 60 0.98
ACGTcount: A:0.36, C:0.35, G:0.19, T:0.10
Consensus pattern (32 bp):
AACCCGAGACCCGAATGACCCGCAACCCAGAT
Found at i:4605 original size:16 final size:16
Alignment explanation
Indices: 4564--4650 Score: 79
Period size: 16 Copynumber: 5.4 Consensus size: 16
4554 CAAACCCGTG
* *
4564 ACCCGAATGACCTGCA
1 ACCCGAATGACCCGAA
* *
4580 A-CCTAGATGACCCGAG
1 ACCCGA-ATGACCCGAA
*
4596 ACCCGAATGACCCGTA
1 ACCCGAATGACCCGAA
*
4612 ACCC-AGATAACCCGAA
1 ACCCGA-ATGACCCGAA
*
4628 ACCTGAATGACCCGAA
1 ACCCGAATGACCCGAA
4644 ACCCGAA
1 ACCCGAA
4651 AAACCCGAGA
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
15 4 0.07
16 47 0.85
17 4 0.07
ACGTcount: A:0.36, C:0.36, G:0.18, T:0.10
Consensus pattern (16 bp):
ACCCGAATGACCCGAA
Found at i:4656 original size:16 final size:16
Alignment explanation
Indices: 4589--4658 Score: 70
Period size: 16 Copynumber: 4.4 Consensus size: 16
4579 AACCTAGATG
* *
4589 ACCCGAGACCCGAATG
1 ACCCGAAACCCGAATA
*
4605 ACCCGTAACCC-AGATA
1 ACCCGAAACCCGA-ATA
* *
4621 ACCCGAAACCTGAATG
1 ACCCGAAACCCGAATA
*
4637 ACCCGAAACCCGAAAA
1 ACCCGAAACCCGAATA
4653 ACCCGA
1 ACCCGA
4659 GAAGTTAATC
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
15 1 0.02
16 41 0.95
17 1 0.02
ACGTcount: A:0.39, C:0.37, G:0.17, T:0.07
Consensus pattern (16 bp):
ACCCGAAACCCGAATA
Found at i:5239 original size:42 final size:42
Alignment explanation
Indices: 5179--5260 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
5169 TGTTGACACA
*
5179 TACCCCACCTAATGATTAATTATGTATTTAATATTCAAAACT
1 TACCCCACCTAATAATTAATTATGTATTTAATATTCAAAACT
*
5221 TACCCCACCTGATAATTAATTATGTATTTAATATTCAAAA
1 TACCCCACCTAATAATTAATTATGTATTTAATATTCAAAA
5261 TTAATATCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.38
Consensus pattern (42 bp):
TACCCCACCTAATAATTAATTATGTATTTAATATTCAAAACT
Found at i:5752 original size:16 final size:16
Alignment explanation
Indices: 5696--5769 Score: 64
Period size: 16 Copynumber: 4.6 Consensus size: 16
5686 CCCGCCCAAT
*
5696 CCGAGACCCGGTA-GAT
1 CCGAGACCC-GTATGAC
* * *
5712 CCGAGACCTGAATGAT
1 CCGAGACCCGTATGAC
5728 CCG-GAACCCGTATGAC
1 CCGAG-ACCCGTATGAC
5744 CCGAGACCC-TACTGAC
1 CCGAGACCCGTA-TGAC
5760 CCGAGACCCG
1 CCGAGACCCG
5770 AATAACCTGA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
15 5 0.10
16 42 0.88
17 1 0.02
ACGTcount: A:0.26, C:0.36, G:0.26, T:0.12
Consensus pattern (16 bp):
CCGAGACCCGTATGAC
Found at i:8036 original size:2 final size:2
Alignment explanation
Indices: 8024--8058 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
8014 AAGCATCATG
8024 AT AT AT A- 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 AT
8059 TTAAGGAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13412 original size:27 final size:27
Alignment explanation
Indices: 13374--13429 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
13364 TAAACTGTCT
13374 TTTCACCTTCTTAGATTGAAAAGTCGA
1 TTTCACCTTCTTAGATTGAAAAGTCGA
13401 TTTCACCTTCTTAGATTGAAAAGTCGA
1 TTTCACCTTCTTAGATTGAAAAGTCGA
13428 TT
1 TT
13430 ATACCCTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (27 bp):
TTTCACCTTCTTAGATTGAAAAGTCGA
Done.