Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007476.1 Corchorus capsularis cultivar CVL-1 contig07497, 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: 29763
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Found at i:2081 original size:62 final size:62
Alignment explanation
Indices: 2011--2136 Score: 234
Period size: 62 Copynumber: 2.0 Consensus size: 62
2001 GTCATCACTT
*
2011 ACTTGAAGCTCTGATAAAAATGCTGAGGTCTATTTAACTTGAAATAAATAACGTTATTCCTA
1 ACTTGAAGCTCTGATAAAAATGCTGAGGCCTATTTAACTTGAAATAAATAACGTTATTCCTA
*
2073 ACTTGAAGCTCTGATAAAAATGCTGAGGCCTATTTAACTTGAAATAAATAATGTTATTCCTA
1 ACTTGAAGCTCTGATAAAAATGCTGAGGCCTATTTAACTTGAAATAAATAACGTTATTCCTA
2135 AC
1 AC
2137 GCTCAAATGA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Consensus pattern (62 bp):
ACTTGAAGCTCTGATAAAAATGCTGAGGCCTATTTAACTTGAAATAAATAACGTTATTCCTA
Found at i:2120 original size:30 final size:31
Alignment explanation
Indices: 2024--2125 Score: 79
Period size: 30 Copynumber: 3.3 Consensus size: 31
2014 TGAAGCTCTG
*
2024 ATAAA-AATGCTGAGGTCTATTTAACTTGAA
1 ATAAATAATGCTGAGGCCTATTTAACTTGAA
* * ** *
2054 ATAAATAACG-TTATTCCTAACTTGAAGCTCTG--
1 ATAAATAATGCTGAGGCCT-A-TTTAA-CT-TGAA
2086 ATAAA-AATGCTGAGGCCTATTTAACTTGAA
1 ATAAATAATGCTGAGGCCTATTTAACTTGAA
2116 ATAAATAATG
1 ATAAATAATG
2126 TTATTCCTAA
Statistics
Matches: 52, Mismatches: 11, Indels: 17
0.65 0.14 0.21
Matches are distributed among these distances:
28 2 0.04
29 2 0.04
30 18 0.35
31 12 0.23
32 14 0.27
33 2 0.04
34 2 0.04
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (31 bp):
ATAAATAATGCTGAGGCCTATTTAACTTGAA
Found at i:2382 original size:4 final size:4
Alignment explanation
Indices: 2373--2450 Score: 156
Period size: 4 Copynumber: 19.5 Consensus size: 4
2363 AAAATTAATA
2373 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
2421 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
2451 GTAATGTATA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 74 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:3312 original size:11 final size:9
Alignment explanation
Indices: 3290--3314 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3280 GTTAAAAATA
3290 ATATATAGT
1 ATATATAGT
3299 ATATATAGT
1 ATATATAGT
3308 ATATATA
1 ATATATA
3315 ATAATAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (9 bp):
ATATATAGT
Found at i:3541 original size:15 final size:14
Alignment explanation
Indices: 3523--3588 Score: 57
Period size: 15 Copynumber: 4.8 Consensus size: 14
3513 ACTTAAAATT
*
3523 ATAATTTATTTATAA
1 ATAATTTATTAAT-A
3538 ATAATTTATTAATA
1 ATAATTTATTAATA
* *
3552 AT--TTTA-AAATT
1 ATAATTTATTAATA
*
3563 ATAATTTATTTATAA
1 ATAATTTATTAAT-A
3578 ATAATTTATTA
1 ATAATTTATTA
3589 GTAACATAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
11 5 0.12
12 4 0.10
13 4 0.10
14 5 0.12
15 22 0.55
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATAATTTATTAATA
Found at i:3584 original size:11 final size:11
Alignment explanation
Indices: 3530--3586 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
3520 ATTATAATTT
3530 ATTTATAAATA
1 ATTTATAAATA
*
3541 ATTTATTAATA
1 ATTTATAAATA
3552 ATTT-T-AA-A
1 ATTTATAAATA
* *
3560 A-TTATAATTT
1 ATTTATAAATA
3570 ATTTATAAATA
1 ATTTATAAATA
3581 ATTTAT
1 ATTTAT
3587 TAGTAACATA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
7 2 0.05
8 3 0.08
9 3 0.08
10 2 0.05
11 27 0.73
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
ATTTATAAATA
Found at i:3772 original size:16 final size:16
Alignment explanation
Indices: 3751--3781 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3741 TAGAAAAATA
*
3751 TTACTAAATTTTTATT
1 TTACTAAATCTTTATT
3767 TTACTAAATCTTTAT
1 TTACTAAATCTTTAT
3782 AATTTATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.58
Consensus pattern (16 bp):
TTACTAAATCTTTATT
Found at i:4427 original size:18 final size:20
Alignment explanation
Indices: 4400--4447 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
4390 TCTTAGAGAT
*
4400 TTTTAATAACTTGA-TAAA-
1 TTTTAGTAACTTGATTAAAC
*
4418 TTTTAGTAACTTTATTAAAC
1 TTTTAGTAACTTGATTAAAC
4438 TTTTAGTAAC
1 TTTTAGTAAC
4448 ATTATTGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 12 0.46
19 4 0.15
20 10 0.38
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.48
Consensus pattern (20 bp):
TTTTAGTAACTTGATTAAAC
Found at i:4443 original size:20 final size:19
Alignment explanation
Indices: 4400--4453 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
4390 TCTTAGAGAT
* *
4400 TTTTAATAACTTGA-TAAA
1 TTTTAGTAACTTTATTAAA
4418 TTTTAGTAACTTTATTAAA
1 TTTTAGTAACTTTATTAAA
*
4437 CTTTTAGTAACATTATT
1 -TTTTAGTAACTTTATT
4454 GATTTATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 12 0.39
19 4 0.13
20 15 0.48
ACGTcount: A:0.37, C:0.07, G:0.06, T:0.50
Consensus pattern (19 bp):
TTTTAGTAACTTTATTAAA
Found at i:5667 original size:26 final size:26
Alignment explanation
Indices: 5635--5690 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
5625 TGTACATAAA
* * *
5635 TTTAGTAATCTTACATTCTTAGAAAT
1 TTTAGTAATCCTACATTCATACAAAT
*
5661 TTTAGTAATCCTGCATTCATACAAAT
1 TTTAGTAATCCTACATTCATACAAAT
5687 TTTA
1 TTTA
5691 TAAGTAACAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (26 bp):
TTTAGTAATCCTACATTCATACAAAT
Found at i:7911 original size:26 final size:26
Alignment explanation
Indices: 7882--7931 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
7872 ATAAATTCAA
*
7882 TAACCTCACATTCTTAGAATTTTTGG
1 TAACCTCACATTCTTAGAAATTTTGG
***
7908 TAACCTTGTATTCTTAGAAATTTT
1 TAACCTCACATTCTTAGAAATTTT
7932 AGTATAGTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (26 bp):
TAACCTCACATTCTTAGAAATTTTGG
Found at i:15522 original size:11 final size:11
Alignment explanation
Indices: 15479--15516 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
15469 TTCCTATATA
*
15479 AAATAAATTAT
1 AAATTAATTAT
15490 CAAA-TAATTAT
1 -AAATTAATTAT
15501 AAATTAATTAT
1 AAATTAATTAT
15512 AAATT
1 AAATT
15517 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:17381 original size:16 final size:16
Alignment explanation
Indices: 17360--17390 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
17350 GTAACCTTAT
17360 AAACATTTTATTAAAA
1 AAACATTTTATTAAAA
17376 AAACATTTTATTAAA
1 AAACATTTTATTAAA
17391 GAAGTTTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (16 bp):
AAACATTTTATTAAAA
Found at i:17750 original size:107 final size:105
Alignment explanation
Indices: 17519--17780 Score: 393
Period size: 107 Copynumber: 2.5 Consensus size: 105
17509 AAATTTTCTA
* * ** *
17519 ACCCTCAAAATAAAATTTTAATTTTAATTT-GGACTAAACTTAGTG-AATTAGTTATATATTTCA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTCA
*
17582 TTTCTAAAACCCTATAACAATATTATTAATCATGGAATTT
66 TTTCTAAAACCCTATAACAATATTATTAATCATGAAATTT
* * *
17622 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTCA
**
17687 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
66 TTTCTAAAACCCTATAACAAT--ATTATTAATCATGAAATTT
17729 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
17781 AGGCTAAACT
Statistics
Matches: 144, Mismatches: 11, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
103 26 0.18
104 14 0.10
105 36 0.25
107 68 0.47
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (105 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTCA
TTTCTAAAACCCTATAACAATATTATTAATCATGAAATTT
Found at i:19310 original size:21 final size:21
Alignment explanation
Indices: 19286--19331 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
19276 TCCCATACGA
*
19286 TGGCGCGGCTACTCCTTGCTT
1 TGGCGCGGCTACTCCATGCTT
*
19307 TGGCGCGGCTCCTCCATGCTT
1 TGGCGCGGCTACTCCATGCTT
19328 TGGC
1 TGGC
19332 CGGTCATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.04, C:0.35, G:0.30, T:0.30
Consensus pattern (21 bp):
TGGCGCGGCTACTCCATGCTT
Found at i:19573 original size:27 final size:27
Alignment explanation
Indices: 19535--19594 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
19525 CTGCAAAAGC
19535 AGTCCCGCAGACTGAATTTCTCACAGG
1 AGTCCCGCAGACTGAATTTCTCACAGG
19562 AGTCCCGCAGACTGAATTTCTCACAGG
1 AGTCCCGCAGACTGAATTTCTCACAGG
*
19589 TGTCCC
1 AGTCCC
19595 AAAATTCAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.23, C:0.32, G:0.22, T:0.23
Consensus pattern (27 bp):
AGTCCCGCAGACTGAATTTCTCACAGG
Found at i:22039 original size:2 final size:2
Alignment explanation
Indices: 22032--22061 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
22022 TTAGATGATG
22032 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
22062 CTGTGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22199 original size:16 final size:16
Alignment explanation
Indices: 22178--22237 Score: 102
Period size: 16 Copynumber: 3.8 Consensus size: 16
22168 CAGTTTTTTT
22178 GGGTCATTCGGGTTTC
1 GGGTCATTCGGGTTTC
*
22194 GGGTCATTCGGGTCTC
1 GGGTCATTCGGGTTTC
*
22210 GGGTCATACGGGTTTC
1 GGGTCATTCGGGTTTC
22226 GGGTCATTCGGG
1 GGGTCATTCGGG
22238 GTTGGGCGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.08, C:0.20, G:0.40, T:0.32
Consensus pattern (16 bp):
GGGTCATTCGGGTTTC
Found at i:22203 original size:9 final size:9
Alignment explanation
Indices: 22178--22237 Score: 69
Period size: 9 Copynumber: 7.3 Consensus size: 9
22168 CAGTTTTTTT
22178 GGGTCATTC
1 GGGTCATTC
22187 GGGT--TTC
1 GGGTCATTC
22194 GGGTCATTC
1 GGGTCATTC
22203 GGGTC--TC
1 GGGTCATTC
*
22210 GGGTCATAC
1 GGGTCATTC
22219 GGGT--TTC
1 GGGTCATTC
22226 GGGTCATTC
1 GGGTCATTC
22235 GGG
1 GGG
22238 GTTGGGCGTG
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
7 20 0.47
9 23 0.53
ACGTcount: A:0.08, C:0.20, G:0.40, T:0.32
Consensus pattern (9 bp):
GGGTCATTC
Found at i:22849 original size:15 final size:15
Alignment explanation
Indices: 22829--22857 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
22819 AATTTTAGTG
22829 ATTGTTCATATAATT
1 ATTGTTCATATAATT
22844 ATTGTTCATATAAT
1 ATTGTTCATATAAT
22858 GAATTTTAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (15 bp):
ATTGTTCATATAATT
Done.