Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011047.1 Corchorus capsularis cultivar CVL-1 contig11068, 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: 28604
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4541 original size:20 final size:21
Alignment explanation
Indices: 4516--4554 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
4506 TGGGTTCTAC
4516 TCTCACGGAA-TGTGAGTTAT
1 TCTCACGGAATTGTGAGTTAT
4536 TCTCACGGAATTGTGAGTT
1 TCTCACGGAATTGTGAGTT
4555 TTATTTGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (21 bp):
TCTCACGGAATTGTGAGTTAT
Found at i:9248 original size:21 final size:21
Alignment explanation
Indices: 9222--9263 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
9212 CTCCATCATT
9222 TTAGATTTAATATATAAACTA
1 TTAGATTTAATATATAAACTA
9243 TTAGATTTAATATATAAACTA
1 TTAGATTTAATATATAAACTA
9264 ATATGCCACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (21 bp):
TTAGATTTAATATATAAACTA
Found at i:16268 original size:22 final size:22
Alignment explanation
Indices: 16243--16308 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 22
16233 TGACTTGGAA
16243 TGAGCTTGACTCGAGATGAGTT
1 TGAGCTTGACTCGAGATGAGTT
* *
16265 TGAGCTCGACTTG-GA--A---
1 TGAGCTTGACTCGAGATGAGTT
16281 TGAGCTTGACTCGAGATGAGTT
1 TGAGCTTGACTCGAGATGAGTT
16303 TGAGCT
1 TGAGCT
16309 ACTCAAACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
16 11 0.32
17 2 0.06
19 2 0.06
21 2 0.06
22 17 0.50
ACGTcount: A:0.23, C:0.15, G:0.32, T:0.30
Consensus pattern (22 bp):
TGAGCTTGACTCGAGATGAGTT
Found at i:16285 original size:38 final size:38
Alignment explanation
Indices: 16229--16308 Score: 151
Period size: 38 Copynumber: 2.1 Consensus size: 38
16219 CTCGAGCTCA
*
16229 AGCTTGACTTGGAATGAGCTTGACTCGAGATGAGTTTG
1 AGCTCGACTTGGAATGAGCTTGACTCGAGATGAGTTTG
16267 AGCTCGACTTGGAATGAGCTTGACTCGAGATGAGTTTG
1 AGCTCGACTTGGAATGAGCTTGACTCGAGATGAGTTTG
16305 AGCT
1 AGCT
16309 ACTCAAACTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.24, C:0.15, G:0.31, T:0.30
Consensus pattern (38 bp):
AGCTCGACTTGGAATGAGCTTGACTCGAGATGAGTTTG
Found at i:16299 original size:16 final size:17
Alignment explanation
Indices: 16229--16305 Score: 61
Period size: 16 Copynumber: 4.4 Consensus size: 17
16219 CTCGAGCTCA
*
16229 AGCTTGACTTG-GAATG
1 AGCTTGACTCGAGAATG
16245 AGCTTGACTCGAG-ATG
1 AGCTTGACTCGAGAATG
*
16261 AGTTTGAGCTCGACTTGGAATG
1 AGCTTGA-CTCGA----GAATG
16283 AGCTTGACTCGAG-ATG
1 AGCTTGACTCGAGAATG
*
16299 AGTTTGA
1 AGCTTGA
16306 GCTACTCAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
16 28 0.56
17 7 0.14
21 6 0.12
22 9 0.18
ACGTcount: A:0.25, C:0.14, G:0.31, T:0.30
Consensus pattern (17 bp):
AGCTTGACTCGAGAATG
Found at i:17129 original size:6 final size:6
Alignment explanation
Indices: 17118--17148 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
17108 TCCATGTTAA
17118 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT T
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT T
17149 GTCAAATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTCTT
Found at i:20865 original size:3 final size:3
Alignment explanation
Indices: 20857--20897 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
20847 CTTAAACTAA
20857 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 AT
20898 CCATCGATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:22444 original size:27 final size:27
Alignment explanation
Indices: 22406--22458 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
22396 ACTCCCTCTG
*
22406 TTCCTTTTTAATTGTCTCTTTCCCTTA
1 TTCCTTTTTAATAGTCTCTTTCCCTTA
*
22433 TTCCTTTTTAATAGTCTTTTTCCCTT
1 TTCCTTTTTAATAGTCTCTTTCCCTT
22459 GTTTTCCAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.11, C:0.25, G:0.04, T:0.60
Consensus pattern (27 bp):
TTCCTTTTTAATAGTCTCTTTCCCTTA
Found at i:23308 original size:3 final size:3
Alignment explanation
Indices: 23300--23333 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
23290 TAATATTAGC
23300 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
23334 TTTTTTGGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:26450 original size:2 final size:2
Alignment explanation
Indices: 26443--26469 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
26433 AAGTAAAGAA
26443 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
26470 AGTAAGAAAT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28113 original size:2 final size:2
Alignment explanation
Indices: 28106--28146 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
28096 TCTGAAGGAC
28106 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
28147 GAGACTTATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.