Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007724.1 Corchorus capsularis cultivar CVL-1 contig07745, 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: 55056
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:777 original size:24 final size:24
Alignment explanation
Indices: 728--777 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
718 CTATTGCATT
* * *
728 ATTTGATACTGTTAAATGTTATTG
1 ATTTGATACTGATAAATGTGACTG
752 ATTTGAT-CTGATAAATGTGAGCTG
1 ATTTGATACTGATAAATGTGA-CTG
776 AT
1 AT
778 GTTTTTGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.30, C:0.06, G:0.20, T:0.44
Consensus pattern (24 bp):
ATTTGATACTGATAAATGTGACTG
Found at i:4929 original size:43 final size:43
Alignment explanation
Indices: 4882--4967 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
4872 CTAGGAGCTG
*
4882 CCTTTTCATTCTTTGAATTGAAACCTAACAATCCAAAACACCT
1 CCTTTTCATCCTTTGAATTGAAACCTAACAATCCAAAACACCT
* *
4925 CCTTTTTATCCTTTGAATTGAAACTTAACAATCCAAAACACCT
1 CCTTTTCATCCTTTGAATTGAAACCTAACAATCCAAAACACCT
4968 TAAAATTCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.34
Consensus pattern (43 bp):
CCTTTTCATCCTTTGAATTGAAACCTAACAATCCAAAACACCT
Found at i:6083 original size:109 final size:109
Alignment explanation
Indices: 5904--6130 Score: 386
Period size: 109 Copynumber: 2.1 Consensus size: 109
5894 CTAATATCTT
**
5904 TATCTTTATAATTACTTTATTTTTACCAAAAAATTTGGATACACTAAAATTTTTTCTAATATACA
1 TATCTTTATAATTACTTTATTTTTACCAAAAAAAATGGATACACTAAAATTTTTTCTAATATACA
5969 ATTTTATTCTACTAAAAACTCAATTTTCATTTAATTAAA-TCTAA
66 ATTTTATTCTACTAAAAACTCAATTTTCATTTAATTAAATTC-AA
* *
6013 TATCTTTATAATTACTTTATTTTTACCAAAAAAAATGGATATATTAAAATTTTTTCTAATATACA
1 TATCTTTATAATTACTTTATTTTTACCAAAAAAAATGGATACACTAAAATTTTTTCTAATATACA
*
6078 ATTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATTCAA
66 ATTTTATTCTACTAAAAACTCAATTTTCATTTAATTAAATTCAA
6122 TAT-TTTATA
1 TATCTTTATA
6131 TTTTTTTTTA
Statistics
Matches: 112, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
108 6 0.05
109 104 0.93
110 2 0.02
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (109 bp):
TATCTTTATAATTACTTTATTTTTACCAAAAAAAATGGATACACTAAAATTTTTTCTAATATACA
ATTTTATTCTACTAAAAACTCAATTTTCATTTAATTAAATTCAA
Found at i:6827 original size:18 final size:18
Alignment explanation
Indices: 6804--6838 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
6794 ATGAAATTTT
6804 GTAGTATGCTTAAGATTA
1 GTAGTATGCTTAAGATTA
6822 GTAGTATGCTTAAGATT
1 GTAGTATGCTTAAGATT
6839 TTAATCTTCA
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:0.31, C:0.06, G:0.23, T:0.40
Consensus pattern (18 bp):
GTAGTATGCTTAAGATTA
Found at i:8185 original size:30 final size:30
Alignment explanation
Indices: 8145--8203 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
8135 TGTCTTCAAG
8145 TCCATAATAAGTCCTT-GGCGCATCATTCCT
1 TCCATAATAAG-CCTTGGGCGCATCATTCCT
* *
8175 TCCATGATAAGCCTTGGGTGCATCATTCC
1 TCCATAATAAGCCTTGGGCGCATCATTCC
8204 CTCCCCTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32
Consensus pattern (30 bp):
TCCATAATAAGCCTTGGGCGCATCATTCCT
Found at i:11611 original size:14 final size:15
Alignment explanation
Indices: 11592--11622 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
11582 AGGGCTGAAA
11592 ATAATAATTA-TATT
1 ATAATAATTATTATT
11606 ATAATAATTATTATT
1 ATAATAATTATTATT
11621 AT
1 AT
11623 CAAGTCAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATAATAATTATTATT
Found at i:13303 original size:14 final size:15
Alignment explanation
Indices: 13272--13309 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
13262 CTTTCACTTC
*
13272 TAATT-AATATTTAT
1 TAATTGAATATTTAG
13286 TAATTGAATATTT-G
1 TAATTGAATATTTAG
13300 TAATTGAATA
1 TAATTGAATA
13310 CAAACGTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (15 bp):
TAATTGAATATTTAG
Found at i:14336 original size:19 final size:22
Alignment explanation
Indices: 14309--14354 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 22
14299 GAGTGAGTTT
*
14309 TGAATTTTGAG-GTG-TTGGG-
1 TGAAGTTTGAGAGTGTTTGGGA
14328 TGAAGTTTGAGAGTGTTTGGGA
1 TGAAGTTTGAGAGTGTTTGGGA
14350 TGAAG
1 TGAAG
14355 ATGGTTGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 10 0.43
20 3 0.13
21 5 0.22
22 5 0.22
ACGTcount: A:0.22, C:0.00, G:0.41, T:0.37
Consensus pattern (22 bp):
TGAAGTTTGAGAGTGTTTGGGA
Found at i:16265 original size:21 final size:20
Alignment explanation
Indices: 16239--16280 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
16229 TCTTGAAGGT
*
16239 TTGAAGTCCATTGAAGATCAA
1 TTGAAGACCATTGAAGA-CAA
*
16260 TTGAAGAGCATTGAAGACAA
1 TTGAAGACCATTGAAGACAA
16280 T
1 T
16281 AAGCAAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.26
Consensus pattern (20 bp):
TTGAAGACCATTGAAGACAA
Found at i:28052 original size:12 final size:13
Alignment explanation
Indices: 28029--28060 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
28019 AATTATTGTT
28029 TGCTTTATTAATC
1 TGCTTTATTAATC
28042 TGCTTTA-TAATC
1 TGCTTTATTAATC
28054 TGCTTTA
1 TGCTTTA
28061 GATTTAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.22, C:0.16, G:0.09, T:0.53
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:28068 original size:6 final size:6
Alignment explanation
Indices: 28057--28090 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
28047 TATAATCTGC
28057 TTTAGA TTTAGA TTTAAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTT-AGA TTTAGA TTTAGA TTT
28091 GGTTTGCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (6 bp):
TTTAGA
Found at i:28078 original size:13 final size:12
Alignment explanation
Indices: 28057--28090 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 12
28047 TATAATCTGC
28057 TTTAGATTTAGA
1 TTTAGATTTAGA
28069 TTTAAGATTTAGA
1 TTT-AGATTTAGA
28082 TTTAGATTT
1 TTTAGATTT
28091 GGTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (12 bp):
TTTAGATTTAGA
Found at i:28139 original size:14 final size:15
Alignment explanation
Indices: 28111--28143 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
28101 ATTTTTAGTT
*
28111 TAATTGTTTTCTTCA
1 TAATTGTTATCTTCA
28126 TAATTGTTAT-TTCA
1 TAATTGTTATCTTCA
28140 TAAT
1 TAAT
28144 CCCTGTTTTC
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:0.09, G:0.06, T:0.58
Consensus pattern (15 bp):
TAATTGTTATCTTCA
Found at i:38187 original size:27 final size:28
Alignment explanation
Indices: 38157--38227 Score: 90
Period size: 27 Copynumber: 2.5 Consensus size: 28
38147 TCACCTAGGA
38157 GCATTTTGGTCATTTTTACATTCA-GGG
1 GCATTTTGGTCATTTTTACATTCAGGGG
* * * *
38184 GCATTTTTGTCATTCTTGCATTTAGGGGG
1 GCATTTTGGTCATTTTTACATTCA-GGGG
38213 GCATTTTGGTCATTT
1 GCATTTTGGTCATTT
38228 GGTCCCTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
27 20 0.56
29 16 0.44
ACGTcount: A:0.15, C:0.14, G:0.24, T:0.46
Consensus pattern (28 bp):
GCATTTTGGTCATTTTTACATTCAGGGG
Done.