Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013444.1 Corchorus capsularis cultivar CVL-1 contig13465, 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: 18716
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Found at i:637 original size:14 final size:15
Alignment explanation
Indices: 609--641 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
599 ATTTTTAGTT
*
609 TAATTGTTTTCTTTA
1 TAATTGTTATCTTTA
624 TAATTGTTAT-TTTA
1 TAATTGTTATCTTTA
638 TAAT
1 TAAT
642 CCCCTGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (15 bp):
TAATTGTTATCTTTA
Found at i:4087 original size:11 final size:11
Alignment explanation
Indices: 4071--4144 Score: 130
Period size: 11 Copynumber: 6.7 Consensus size: 11
4061 AAGCCAGTAT
*
4071 GCCCGGCTGCA
1 GCCCGGCCGCA
*
4082 GCCCGGCTGCA
1 GCCCGGCCGCA
4093 GCCCGGCCGCA
1 GCCCGGCCGCA
4104 GCCCGGCCGCA
1 GCCCGGCCGCA
4115 GCCCGGCCGCA
1 GCCCGGCCGCA
4126 GCCCGGCCGCA
1 GCCCGGCCGCA
4137 GCCCGGCC
1 GCCCGGCC
4145 ATCGACACCA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
11 62 1.00
ACGTcount: A:0.08, C:0.53, G:0.36, T:0.03
Consensus pattern (11 bp):
GCCCGGCCGCA
Found at i:7762 original size:14 final size:15
Alignment explanation
Indices: 7734--7766 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
7724 ATTTTTAGTT
*
7734 TAATTGTTTTCTTTA
1 TAATTGTTATCTTTA
7749 TAATTGTTAT-TTTA
1 TAATTGTTATCTTTA
7763 TAAT
1 TAAT
7767 CCCCTGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (15 bp):
TAATTGTTATCTTTA
Found at i:9115 original size:21 final size:21
Alignment explanation
Indices: 9075--9115 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
9065 CCCTGTACTC
**
9075 ATCATTCCTGAATCTTTCTCG
1 ATCATTCCTGAATCGATCTCG
*
9096 ATCATTTCTGAATCGATCTC
1 ATCATTCCTGAATCGATCTC
9116 TTTTCTGGCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.27, G:0.10, T:0.41
Consensus pattern (21 bp):
ATCATTCCTGAATCGATCTCG
Found at i:11800 original size:5 final size:5
Alignment explanation
Indices: 11792--11849 Score: 71
Period size: 5 Copynumber: 11.2 Consensus size: 5
11782 TTTTTAAAAC
* * *
11792 AGAAT AGAAT AGAAT AGAAT AGAGT AGAGT ACAAT AGAAT AGAAT AGACAAT
1 AGAAT AGAAT AGAAT AGAAT AGAAT AGAAT AGAAT AGAAT AGAAT AG--AAT
11844 AGAAT A
1 AGAAT A
11850 AGATTGATAG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
5 42 0.89
7 5 0.11
ACGTcount: A:0.57, C:0.03, G:0.21, T:0.19
Consensus pattern (5 bp):
AGAAT
Found at i:12491 original size:105 final size:104
Alignment explanation
Indices: 12340--12569 Score: 266
Period size: 105 Copynumber: 2.2 Consensus size: 104
12330 TTTGAAGTCT
* * ** *
12340 AACATCAATCGACTAAAACTCCAAGTCTTCACTGTAGCAAAATGGCAGTATTGACA-ACATCTCC
1 AACATTAATCGATTAAAACTCCAAAACTTCACTGCAGCAAAATGGCAGTATTGA-AGACATCTCC
* *
12404 GAAGGA-AGTATTAATCAATGAATACTGAATTTTCACGCTTC
65 G--GGAGAGTATTAATCAATGAATACTCAAATTTCACGCTTC
* * * * *
12445 AACATTAATCGATTAAAACTCTAAAACTTCACTGCATCAAAGTGGCAGTGTTGAAGACATCTCTG
1 AACATTAATCGATTAAAACTCCAAAACTTCACTGCAGCAAAATGGCAGTATTGAAGACATCTCCG
* * * *
12510 GGAGTAGTTTTAATCGATGAATACTCAAATTTCATGTTTC
66 GGAG-AGTATTAATCAATGAATACTCAAATTTCACGCTTC
12550 AACATTAATCGATTAAAACT
1 AACATTAATCGATTAAAACT
12570 TCCTTTCATT
Statistics
Matches: 106, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
103 3 0.03
104 1 0.01
105 102 0.96
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (104 bp):
AACATTAATCGATTAAAACTCCAAAACTTCACTGCAGCAAAATGGCAGTATTGAAGACATCTCCG
GGAGAGTATTAATCAATGAATACTCAAATTTCACGCTTC
Found at i:15465 original size:18 final size:18
Alignment explanation
Indices: 15442--15476 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
15432 CTGCAAAGCT
15442 GCCATATTCCGACAATTG
1 GCCATATTCCGACAATTG
15460 GCCATATTCCGACAATT
1 GCCATATTCCGACAATT
15477 TAATACTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (18 bp):
GCCATATTCCGACAATTG
Done.