Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007887.1 Corchorus capsularis cultivar CVL-1 contig07908, 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: 19826
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:555 original size:31 final size:31
Alignment explanation
Indices: 519--578 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
509 TGTTCATAAG
519 TGAACAATTATAAAGAGACTTATTTGTCTTA
1 TGAACAATTATAAAGAGACTTATTTGTCTTA
*
550 TGAACAATTATGAAGAGACTTATTTGTCT
1 TGAACAATTATAAAGAGACTTATTTGTCT
579 ATAATAGGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (31 bp):
TGAACAATTATAAAGAGACTTATTTGTCTTA
Found at i:670 original size:37 final size:37
Alignment explanation
Indices: 607--677 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
597 ATATGATTAT
* * * *
607 TCATAAAGTTATGTTTATTTGGAAAGACATGTATTGA
1 TCATAAAGTTATATCTATATGAAAAGACATGTATTGA
644 TCATAAAGTTATATCTATATGAAAAGACATGTAT
1 TCATAAAGTTATATCTATATGAAAAGACATGTAT
678 GTTGATCAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.38
Consensus pattern (37 bp):
TCATAAAGTTATATCTATATGAAAAGACATGTATTGA
Found at i:5229 original size:2 final size:2
Alignment explanation
Indices: 5222--5260 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
5212 ATAATTAATA
*
5222 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5261 GCAATAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6942 original size:133 final size:133
Alignment explanation
Indices: 6666--7024 Score: 412
Period size: 133 Copynumber: 2.7 Consensus size: 133
6656 TCACTATCCT
* * * * *
6666 TTCTGTGAAGGTTAACGCTTTTAAAGAGGAATACCATGAAATCTCCCCTGTTTTAAACTTGAGAA
1 TTCTTTGAAGGTGAACGCTTTCAAAGAGGAATCCCTTGAAATCT-CCCTGTTTTAAACTTGAGAA
* ** * * * *
6731 TCATTTCAAAGGGAGGCTGTTGGTATTTGCTCAATCGTTGTTCCAATGTTGTCTTTCAGAAGCAT
65 TCATCTCAAA-GGAGGCCCTTGGTATTTGCTAAATCGTTATTCCAATATTGTCTTCCAGAAGCAT
*
6796 CAATC
129 AAATC
* **
6801 TTCTTTGAAGGTGAACGCTTTCAAAGAGGAATCCCTTGAATTCTCCCTGTCCTAAACTTGAGAAT
1 TTCTTTGAAGGTGAACGCTTTCAAAGAGGAATCCCTTGAAATCTCCCTGTTTTAAACTTGAGAAT
* * * ** * * ** *
6866 CATCACAAAGGAGGCCCTTGGTTTTTGTTAAATCGTTATTTTAGTATTTTCTTCCATCAGTATAA
66 CATCTCAAAGGAGGCCCTTGGTATTTGCTAAATCGTTATTCCAATATTGTCTTCCAGAAGCATAA
6931 ATC
131 ATC
* * *
6934 TTCTTTGAAGGTGAAGGCTTTCAAAGAGGAATCCCTTAAAATCTTCCCTGTTTTAAATTTGAGAA
1 TTCTTTGAAGGTGAACGCTTTCAAAGAGGAATCCCTTGAAATC-TCCCTGTTTTAAACTTGAGAA
*
6999 TCATCTTAAAGGAAGGCCCTTGGTAT
65 TCATCTCAAAGG-AGGCCCTTGGTAT
7025 GTTCCAGTCA
Statistics
Matches: 187, Mismatches: 35, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
133 83 0.44
134 54 0.29
135 50 0.27
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (133 bp):
TTCTTTGAAGGTGAACGCTTTCAAAGAGGAATCCCTTGAAATCTCCCTGTTTTAAACTTGAGAAT
CATCTCAAAGGAGGCCCTTGGTATTTGCTAAATCGTTATTCCAATATTGTCTTCCAGAAGCATAA
ATC
Found at i:7393 original size:23 final size:21
Alignment explanation
Indices: 7341--7393 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 21
7331 TCAGATTTCA
*
7341 TATG-TTTAGTATTGTAGTTT
1 TATGTTTTAGAATTGTAGTTT
7361 TATAGTTTTTAGAATTGTAGTAGTT
1 TAT-G-TTTTAGAATTGTAGT--TT
7386 TATGTTTT
1 TATGTTTT
7394 CTTGTATACA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
20 3 0.11
21 1 0.04
23 17 0.63
24 1 0.04
25 5 0.19
ACGTcount: A:0.23, C:0.00, G:0.19, T:0.58
Consensus pattern (21 bp):
TATGTTTTAGAATTGTAGTTT
Found at i:14231 original size:31 final size:31
Alignment explanation
Indices: 14193--14251 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
14183 TATGTTAGAC
* *
14193 AAATAAGGATATAATTGGCGTTTCAAAAATT
1 AAATAAGGACATAATAGGCGTTTCAAAAATT
*
14224 AAATAAGGACATAATAGGTGTTTCAAAA
1 AAATAAGGACATAATAGGCGTTTCAAAA
14252 GTTTTACAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.29
Consensus pattern (31 bp):
AAATAAGGACATAATAGGCGTTTCAAAAATT
Found at i:14319 original size:12 final size:12
Alignment explanation
Indices: 14302--14339 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
14292 ATAATATTAG
14302 ATATATATAATT
1 ATATATATAATT
*
14314 ATATATATAATA
1 ATATATATAATT
14326 ATATATATAATT
1 ATATATATAATT
14338 AT
1 AT
14340 TAAATGGTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATATATAATT
Found at i:14319 original size:14 final size:14
Alignment explanation
Indices: 14272--14334 Score: 55
Period size: 14 Copynumber: 4.6 Consensus size: 14
14262 ACTCGTACTT
14272 TTATATATAGTATAGA
1 TTATATATA-TATA-A
14288 -TATA-ATA-AT-A
1 TTATATATATATAA
*
14298 TTAGATATATATAA
1 TTATATATATATAA
14312 TTATATATATAATAA
1 TTATATATAT-ATAA
14327 -TATATATA
1 TTATATATA
14335 ATTATTAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
10 1 0.03
11 3 0.08
12 5 0.12
13 2 0.05
14 21 0.52
15 8 0.20
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (14 bp):
TTATATATATATAA
Found at i:14620 original size:11 final size:11
Alignment explanation
Indices: 14604--14637 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
14594 TACTCGTGAT
*
14604 GGGTTCAGGTA
1 GGGTTCGGGTA
14615 GGGTTCGGGTA
1 GGGTTCGGGTA
14626 GGGTTCGGGTA
1 GGGTTCGGGTA
14637 G
1 G
14638 TGACCTTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.12, C:0.09, G:0.53, T:0.26
Consensus pattern (11 bp):
GGGTTCGGGTA
Found at i:14701 original size:19 final size:19
Alignment explanation
Indices: 14683--14719 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
14673 TATTAATTAT
*
14683 TTTA-ATATTATATTTTTA
1 TTTATATATTACATTTTTA
14701 TTTATATATTACATTTTTA
1 TTTATATATTACATTTTTA
14720 CTTAAAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATATATTACATTTTTA
Found at i:14853 original size:13 final size:13
Alignment explanation
Indices: 14835--14864 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
14825 TTTAAATATA
14835 ATGAATATGATTT
1 ATGAATATGATTT
14848 ATGAATATGATTT
1 ATGAATATGATTT
14861 ATGA
1 ATGA
14865 GGTTATAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (13 bp):
ATGAATATGATTT
Done.