Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004049.1 Corchorus capsularis cultivar CVL-1 contig04057, 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: 5524
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:750 original size:12 final size:12
Alignment explanation
Indices: 729--758 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
719 CGACCCGCTG
*
729 TTCTTCTTCTTC
1 TTCTTTTTCTTC
741 TTCTTTTTCTTC
1 TTCTTTTTCTTC
753 TTCTTT
1 TTCTTT
759 AAAGGCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
TTCTTTTTCTTC
Found at i:2871 original size:26 final size:27
Alignment explanation
Indices: 2808--2871 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 27
2798 GTGGCATTTT
* *
2808 TACACGTGGTGTGCCACGTGTCCTTTTG
1 TACACGTGGCGTGCCACGTGT-CTTTGG
* *
2836 TACACATGGCGTGCCATGTGT-TTTGG
1 TACACGTGGCGTGCCACGTGTCTTTGG
2862 TACACGTGGC
1 TACACGTGGC
2872 ATACCACATC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 13 0.42
28 18 0.58
ACGTcount: A:0.14, C:0.23, G:0.30, T:0.33
Consensus pattern (27 bp):
TACACGTGGCGTGCCACGTGTCTTTGG
Found at i:4477 original size:33 final size:33
Alignment explanation
Indices: 4432--4506 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
4422 GCGCGCAACT
*
4432 TGGGCGGCTAGCCATGGGCCATGCCACCCACGC
1 TGGGCGGCTAGCCATGGACCATGCCACCCACGC
* * *
4465 TGGGCGGTTAGCCATGGACTATGCCGCCCACGC
1 TGGGCGGCTAGCCATGGACCATGCCACCCACGC
4498 TGGGCGGCT
1 TGGGCGGCT
4507 CCATTTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.13, C:0.35, G:0.36, T:0.16
Consensus pattern (33 bp):
TGGGCGGCTAGCCATGGACCATGCCACCCACGC
Found at i:4564 original size:25 final size:25
Alignment explanation
Indices: 4531--4588 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
4521 TTTTTTTAAT
*
4531 ATTAATTAGTTTATGATTAGTTTTA
1 ATTAGTTAGTTTATGATTAGTTTTA
4556 ATTAGTTAGTTTATGATTAGTTTTA
1 ATTAGTTAGTTTATGATTAGTTTTA
4581 ATTAGTTA
1 ATTAGTTA
4589 ATTAAAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (25 bp):
ATTAGTTAGTTTATGATTAGTTTTA
Found at i:4566 original size:14 final size:14
Alignment explanation
Indices: 4547--4627 Score: 57
Period size: 14 Copynumber: 6.1 Consensus size: 14
4537 TAGTTTATGA
4547 TTAGTTTTAATTAG
1 TTAGTTTTAATTAG
*
4561 TTAG-TTT-ATGA-
1 TTAGTTTTAATTAG
4572 TTAGTTTTAATTAG
1 TTAGTTTTAATTAG
* ** *
4586 TTAATTAAAATTAC
1 TTAGTTTTAATTAG
4600 TTAG-TTT-ATTAG
1 TTAGTTTTAATTAG
4612 TTTA-TGTTTAATTAG
1 -TTAGT-TTTAATTAG
4627 T
1 T
4628 ATCTAATTAG
Statistics
Matches: 50, Mismatches: 10, Indels: 14
0.68 0.14 0.19
Matches are distributed among these distances:
11 4 0.08
12 10 0.20
13 10 0.20
14 21 0.42
15 5 0.10
ACGTcount: A:0.31, C:0.01, G:0.12, T:0.56
Consensus pattern (14 bp):
TTAGTTTTAATTAG
Found at i:5362 original size:165 final size:165
Alignment explanation
Indices: 4981--5382 Score: 558
Period size: 165 Copynumber: 2.4 Consensus size: 165
4971 TGAGTCATTT
* *
4981 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATAAAAAATTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * * ** * *
5046 TTAAGTAATCTGCCAAGTAGGTAAAGACGAAAAAGATTAGTTCTCTAGCTCATCATCAATCCTTG
65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAGATAAGTTCTCTAACTCAAAAGCAAGCCTTG
* * * *
5111 AAGGGGATCTTTTATTAGTTCCACTACTCAATTCAA
130 AAGGGGACCTTTTAGTAATTCCACTACTCAATTAAA
* * * * *
5147 GTCCATTGAGAAATGACCAAAAAGATTACTTATTTAATTCCCTAAAGAATCAAAAGTTTGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
5212 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAA-A-AAGTTCTCTAACTCCAAAAGCAAGCCTT
65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAGATAAGTTCTCTAACT-CAAAAGCAAGCCTT
* *
5275 GGTA-GGGACCTTTTAGTAATTCCACTACTCTATTAAA
129 -GAAGGGGACCTTTTAGTAATTCCACTACTCAATTAAA
5312 GTCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAGT-TAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
5377 TTAAGT
65 TTAAGT
5383 TTAAACTTTA
Statistics
Matches: 207, Mismatches: 26, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
164 12 0.06
165 103 0.50
166 92 0.44
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (165 bp):
GTCAATTGAGAAATGACCAAAAAGTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATT
TAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAGATAAGTTCTCTAACTCAAAAGCAAGCCTTGA
AGGGGACCTTTTAGTAATTCCACTACTCAATTAAA
Done.