Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016105.1 Corchorus capsularis cultivar CVL-1 contig16126, 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: 25173
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:8 original size:3 final size:3
Alignment explanation
Indices: 1--27 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
28 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1940 original size:39 final size:38
Alignment explanation
Indices: 1897--2003 Score: 124
Period size: 39 Copynumber: 2.7 Consensus size: 38
1887 GCCCAATGTC
* * *
1897 TTATATGTGTTTAGGGACTTTAATATAGATGCCTTTATG
1 TTATATGTGTTT-GGGACTTTAAGAGAGATGCCCTTATG
* * *
1936 TTATATGTGTTTGAGGACTTTGAGAGAGTTGCCCTTGTG
1 TTATATGTGTTTG-GGACTTTAAGAGAGATGCCCTTATG
*
1975 TTATATGTGTTTGGGAACATTAAGAGAGA
1 TTATATGTGTTTGGG-ACTTTAAGAGAGA
2004 GAAATGTCCT
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
38 3 0.05
39 54 0.95
ACGTcount: A:0.25, C:0.07, G:0.26, T:0.41
Consensus pattern (38 bp):
TTATATGTGTTTGGGACTTTAAGAGAGATGCCCTTATG
Found at i:4559 original size:16 final size:16
Alignment explanation
Indices: 4538--4603 Score: 57
Period size: 16 Copynumber: 4.3 Consensus size: 16
4528 TGTATATTTC
*
4538 GCTGCGGTGACATTCT
1 GCTGCGGTAACATTCT
*
4554 GCTGCGGTAACATTTT
1 GCTGCGGTAACATTCT
* * *
4570 GCTGTGGCAAGATT-T
1 GCTGCGGTAACATTCT
*
4585 --TGCGGTAGCATTCT
1 GCTGCGGTAACATTCT
4599 GCTGC
1 GCTGC
4604 TATGATTGTT
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
13 8 0.21
14 1 0.03
15 1 0.03
16 28 0.74
ACGTcount: A:0.15, C:0.21, G:0.30, T:0.33
Consensus pattern (16 bp):
GCTGCGGTAACATTCT
Found at i:5336 original size:72 final size:72
Alignment explanation
Indices: 5214--5562 Score: 409
Period size: 72 Copynumber: 4.9 Consensus size: 72
5204 GTAGTAGCAT
* *
5214 GGATTGTGCGAAGGACTGCC-AATGTGGGAACTGTCTCGACTACAATCGCAATGAGGAAGATAAT
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAGATAAT
5278 CACATAA
66 CACATAA
* * * *
5285 GGATTGTGTGAAGGACTGCCAAATGTGGGAACTGCCTCAGCTACAACCGCAAT-ATGGAAGATTA
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGA-GGAAGATAA
***
5349 TCATGGAA
65 TCACATAA
* * * *
5357 GGCTTGTGCGAAGGACTGCCAAATGTGGGAACAGCCTCGGCTACAATCGCAATGAATG-TGATAA
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATG-AGGAAGATAA
*
5421 TCGCATAA
65 TCACATAA
* * * * *
5429 GGGTTGTGCGAAGGACTGCCATATGTGCGAACTGCCTCGGCTACAACCGCAAT-ATGGAAGACAA
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGA-GGAAGATAA
* **
5493 TTATGTAA
65 TCACATAA
* * * *
5501 GGATTGTGCGAAGGACTGCCAAATGTGAGAACTGCGTCGGCTACAATCGTAATGAAGAAGAT
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAGAT
5563 GACCATGTGA
Statistics
Matches: 230, Mismatches: 41, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
70 1 0.00
71 21 0.09
72 205 0.89
73 2 0.01
74 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.21
Consensus pattern (72 bp):
GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAGATAAT
CACATAA
Found at i:5508 original size:144 final size:145
Alignment explanation
Indices: 5214--5562 Score: 499
Period size: 144 Copynumber: 2.4 Consensus size: 145
5204 GTAGTAGCAT
* *
5214 GGATTGTGCGAAGGACTGCC-AATGTGGGAACTGTCTCGACTACAATCGCAATG-AGGAAGATAA
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAAGGAAGATAA
* *
5277 TCACATAAGGATTGTGTGAAGGACTGCCAAATGTGGGAACTGCCTCAGCTACAACCGCAATATGG
66 TCACATAAGGATTGTGCGAAGGACTGCCAAATGTGCGAACTGCCTCAGCTACAACCGCAATATGG
**
5342 AAGATTATCATGGAA
131 AAGACAATCATGGAA
* * * *
5357 GGCTTGTGCGAAGGACTGCCAAATGTGGGAACAGCCTCGGCTACAATCGCAATGAATG-TGATAA
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAAGGAAGATAA
* * * *
5421 TCGCATAAGGGTTGTGCGAAGGACTGCCATATGTGCGAACTGCCTCGGCTACAACCGCAATATGG
66 TCACATAAGGATTGTGCGAAGGACTGCCAAATGTGCGAACTGCCTCAGCTACAACCGCAATATGG
* *
5486 AAGACAATTATGTAA
131 AAGACAATCATGGAA
* * *
5501 GGATTGTGCGAAGGACTGCCAAATGTGAGAACTGCGTCGGCTACAATCGTAATGAA-GAAGAT
1 GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAAGGAAGAT
5563 GACCATGTGA
Statistics
Matches: 181, Mismatches: 22, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
143 20 0.11
144 159 0.88
145 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.21
Consensus pattern (145 bp):
GGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAAGGAAGATAA
TCACATAAGGATTGTGCGAAGGACTGCCAAATGTGCGAACTGCCTCAGCTACAACCGCAATATGG
AAGACAATCATGGAA
Found at i:7280 original size:18 final size:17
Alignment explanation
Indices: 7253--7288 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
7243 TTTCTCTTCA
7253 TCTATTTTTCTTCTAGT
1 TCTATTTTTCTTCTAGT
7270 TCTAGTTTTTCTTCTAGT
1 TCTA-TTTTTCTTCTAGT
7288 T
1 T
7289 TTAGGTTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (17 bp):
TCTATTTTTCTTCTAGT
Found at i:8053 original size:21 final size:20
Alignment explanation
Indices: 8029--8076 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
8019 TAGATTTAGA
* *
8029 TTTAATTTACTTTGCTTAGTT
1 TTTAATTTA-ATTGCTTACTT
* *
8050 TTTAGTTTAATTGCTTTCTT
1 TTTAATTTAATTGCTTACTT
8070 TTTAATT
1 TTTAATT
8077 GATAATTTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.19, C:0.08, G:0.08, T:0.65
Consensus pattern (20 bp):
TTTAATTTAATTGCTTACTT
Found at i:10003 original size:52 final size:52
Alignment explanation
Indices: 9920--10027 Score: 189
Period size: 52 Copynumber: 2.1 Consensus size: 52
9910 CCACCCACGC
9920 GCCACGCCCAACCACAACCGCGTCAACCTATGCCATAGCCGCGCCAACACCG
1 GCCACGCCCAACCACAACCGCGTCAACCTATGCCATAGCCGCGCCAACACCG
* * *
9972 GCCACGCCCAGCCACAGCCGCGTCAATCTATGCCATAGCCGCGCCAACACCG
1 GCCACGCCCAACCACAACCGCGTCAACCTATGCCATAGCCGCGCCAACACCG
10024 GCCA
1 GCCA
10028 TCACCATGCC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.25, C:0.47, G:0.19, T:0.08
Consensus pattern (52 bp):
GCCACGCCCAACCACAACCGCGTCAACCTATGCCATAGCCGCGCCAACACCG
Found at i:13385 original size:21 final size:20
Alignment explanation
Indices: 13361--13408 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
13351 TAGATTTAGA
*
13361 TTTAATTTACTTTGCTTAGTT
1 TTTAATTTA-ATTGCTTAGTT
* *
13382 TTTAGTTTAATTGCTTTGTT
1 TTTAATTTAATTGCTTAGTT
13402 TTTAATT
1 TTTAATT
13409 GATAATTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.19, C:0.06, G:0.10, T:0.65
Consensus pattern (20 bp):
TTTAATTTAATTGCTTAGTT
Found at i:14540 original size:40 final size:40
Alignment explanation
Indices: 14461--14540 Score: 90
Period size: 40 Copynumber: 2.0 Consensus size: 40
14451 GTGCTCTGCC
** *
14461 ACCCATTGATTGAGAAAAGTGTCGACGTCTGCAGCAGGAA
1 ACCCATTGATTGAGAAAAGCATCGACGTCTACAGCAGGAA
* * *
14501 ACCCATTGATTGA-AAAGAGCATCGACTTTTACAGTAGGAA
1 ACCCATTGATTGAGAAA-AGCATCGACGTCTACAGCAGGAA
14541 GTTGGAGTGG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
39 3 0.09
40 30 0.91
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.23
Consensus pattern (40 bp):
ACCCATTGATTGAGAAAAGCATCGACGTCTACAGCAGGAA
Found at i:16775 original size:39 final size:38
Alignment explanation
Indices: 16732--16842 Score: 123
Period size: 39 Copynumber: 2.8 Consensus size: 38
16722 CAAGACCCAA
* * *
16732 TGTGTTATATGTGTTTATGGACTTTAATATAGATGCCTC
1 TGTGTTATATGTGTTTA-GGACTTTAAGAGAGATGCCCC
* *
16771 TGTGTTATATGTGTTTGAGGACTTTGAGAGAGTTGCCCC
1 TGTGTTATATGTGTTT-AGGACTTTAAGAGAGATGCCCC
* * *
16810 AGTGTTATATGTGTTTGGGGACTTTGAGAGAGA
1 TGTGTTATATGTGTTT-AGGACTTTAAGAGAGA
16843 GAAATGCCCT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
39 62 0.98
40 1 0.02
ACGTcount: A:0.22, C:0.09, G:0.29, T:0.41
Consensus pattern (38 bp):
TGTGTTATATGTGTTTAGGACTTTAAGAGAGATGCCCC
Found at i:18300 original size:11 final size:11
Alignment explanation
Indices: 18286--18323 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
18276 ATTAATAACA
18286 AATTTATAATT
1 AATTTATAATT
18297 AATTTATAATT
1 AATTTATAATT
18308 -ATTTGATAATT
1 AATTT-ATAATT
*
18319 TATTT
1 AATTT
18324 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:20413 original size:19 final size:20
Alignment explanation
Indices: 20375--20421 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
20365 GTTTTACAAG
* *
20375 GATTCAAAAAGTTTTCAGTT
1 GATTGAAAAAATTTTCAGTT
20395 GATTGAAAAAATTTT-AGTT
1 GATTGAAAAAATTTTCAGTT
20414 GATTGAAA
1 GATTGAAA
20422 TTCAACCAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.40, C:0.04, G:0.17, T:0.38
Consensus pattern (20 bp):
GATTGAAAAAATTTTCAGTT
Found at i:21245 original size:30 final size:28
Alignment explanation
Indices: 21176--21245 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
21166 TTTTGCCAAC
* **
21176 GGTCAAATAAGCCCCTGAACTTTAATTTT
1 GGTC-AATAAGCCCCTAAACTCCAATTTT
*
21205 GGCCTAATAAGCCCCTAAACTACCAATTTT
1 GGTC-AATAAGCCCCTAAACT-CCAATTTT
21235 GGTCAGATAAG
1 GGTCA-ATAAG
21246 ATCTTCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
29 19 0.58
30 14 0.42
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.29
Consensus pattern (28 bp):
GGTCAATAAGCCCCTAAACTCCAATTTT
Found at i:22368 original size:2 final size:2
Alignment explanation
Indices: 22361--22392 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
22351 GATCTTAGTA
22361 AT AT 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
22393 CCGAGCCAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24446 original size:18 final size:18
Alignment explanation
Indices: 24423--24458 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
24413 CATATGAAAT
*
24423 TCCAAAAAATTTTCAAAA
1 TCCAAAAAATCTTCAAAA
24441 TCCAAAAAATCTTCAAAA
1 TCCAAAAAATCTTCAAAA
24459 AACATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.25
Consensus pattern (18 bp):
TCCAAAAAATCTTCAAAA
Done.