Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016230.1 Corchorus capsularis cultivar CVL-1 contig16251, 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: 16741
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Found at i:545 original size:49 final size:50
Alignment explanation
Indices: 492--603 Score: 174
Period size: 49 Copynumber: 2.3 Consensus size: 50
482 ATTTGTAATT
* * *
492 TATTT-ATTATGTTTGGTAGTTATAGATGAAATTAGAGATTTGGCAATCC
1 TATTTGATTATGTTTGGCAGTTATAGATGAAATTAGAGATTTGACAATCA
541 TATTTGA-TATGTTTGGCAGTTATAGATGAAATTAGAGATTTGACAATCA
1 TATTTGATTATGTTTGGCAGTTATAGATGAAATTAGAGATTTGACAATCA
590 TATTTGATTTATGT
1 TATTTGA-TTATGT
604 ACGCTTCAAC
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
49 51 0.89
50 1 0.02
51 5 0.09
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (50 bp):
TATTTGATTATGTTTGGCAGTTATAGATGAAATTAGAGATTTGACAATCA
Found at i:729 original size:20 final size:20
Alignment explanation
Indices: 706--746 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
696 TACCGATCTC
*
706 TGATTA-TTGATTAATAAAAT
1 TGATTATTTGA-TAAAAAAAT
726 TGATTATTTGATAAAAAAAT
1 TGATTATTTGATAAAAAAAT
746 T
1 T
747 TACATATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (20 bp):
TGATTATTTGATAAAAAAAT
Found at i:1344 original size:31 final size:29
Alignment explanation
Indices: 1303--1395 Score: 107
Period size: 29 Copynumber: 3.2 Consensus size: 29
1293 CGGACATCCG
1303 ACGTGGCATGCCACGTGTACCAAAAAATGCC
1 ACGTGGCATGCCACGTGTA-C-AAAAATGCC
* * * *
1334 ACGTGACATGCCACGTATACAAAAAGGAC
1 ACGTGGCATGCCACGTGTACAAAAATGCC
* *
1363 ACATGGCACGCCACGTGT-CAAAAATGCC
1 ACGTGGCATGCCACGTGTACAAAAATGCC
1391 ACGTG
1 ACGTG
1396 CCACATGTCA
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
28 12 0.24
29 21 0.41
30 1 0.02
31 17 0.33
ACGTcount: A:0.34, C:0.28, G:0.23, T:0.15
Consensus pattern (29 bp):
ACGTGGCATGCCACGTGTACAAAAATGCC
Found at i:3883 original size:7 final size:7
Alignment explanation
Indices: 3871--3905 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
3861 GTTGAGGGTA
3871 TTTATAT
1 TTTATAT
3878 TTTATAT
1 TTTATAT
3885 TTTATAT
1 TTTATAT
3892 TTTATAT
1 TTTATAT
3899 TTTATAT
1 TTTATAT
3906 ATAATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTATAT
Found at i:3912 original size:21 final size:21
Alignment explanation
Indices: 3871--3912 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3861 GTTGAGGGTA
* *
3871 TTTATATTTTATATTTTATAT
1 TTTATATTTTATATATAATAT
3892 TTTATATTTTATATATAATAT
1 TTTATATTTTATATATAATAT
3913 ATATAGTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTATATTTTATATATAATAT
Found at i:4090 original size:3 final size:3
Alignment explanation
Indices: 4084--4111 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4074 GGCAGGAGGA
4084 TGG TGG TGG TGG TGG TGG TGG TGG TGG T
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG T
4112 TGTTGTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.64, T:0.36
Consensus pattern (3 bp):
TGG
Found at i:10263 original size:23 final size:23
Alignment explanation
Indices: 10208--10270 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
10198 ACAACTCACA
*
10208 ACAAATTTCAGAATTCACAAATC
1 ACAAAATTCAGAATTCACAAATC
* * *
10231 ACAAATTTCAGAATTCACAATTT
1 ACAAAATTCAGAATTCACAAATC
* *
10254 TCAGAATTCAGAATTCA
1 ACAAAATTCAGAATTCA
10271 GTTCAGAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.30
Consensus pattern (23 bp):
ACAAAATTCAGAATTCACAAATC
Found at i:10268 original size:16 final size:16
Alignment explanation
Indices: 10229--10268 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
10219 AATTCACAAA
*
10229 TCACAAATTTCAGAAT
1 TCACAATTTTCAGAAT
10245 TCACAATTTTCAGAAT
1 TCACAATTTTCAGAAT
*
10261 TCAGAATT
1 TCACAATT
10269 CAGTTCAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.35
Consensus pattern (16 bp):
TCACAATTTTCAGAAT
Found at i:15782 original size:14 final size:14
Alignment explanation
Indices: 15723--15787 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
15713 AACAATATTT
*
15723 ATATTTCAGAACCAC
1 ATATTTCAGAATC-C
15738 ATATTTCCA-AATCC
1 ATATTT-CAGAATCC
* * *
15752 -TGAATTCGGAATGC
1 AT-ATTTCAGAATCC
15766 ATATTTCAGAATCC
1 ATATTTCAGAATCC
15780 ATATTTCA
1 ATATTTCA
15788 ACTCAATCAT
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
13 2 0.05
14 25 0.64
15 10 0.26
16 2 0.05
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.34
Consensus pattern (14 bp):
ATATTTCAGAATCC
Found at i:16490 original size:29 final size:30
Alignment explanation
Indices: 16417--16504 Score: 124
Period size: 29 Copynumber: 2.9 Consensus size: 30
16407 GGTGGCTAAA
* * *
16417 TGCTCAATTTCGTCCTAAACCTTTGAGCGAG
1 TGCTCAATTTGGTCCTAAACCTTTGAAC-AC
*
16448 TGCTCAATTTGGTCCTAAAACTTTGAAC-C
1 TGCTCAATTTGGTCCTAAACCTTTGAACAC
16477 TGCTCAATTTGGTCCTAAACCTTTGAAC
1 TGCTCAATTTGGTCCTAAACCTTTGAAC
16505 GGTCGCTCAA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
29 27 0.52
31 25 0.48
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (30 bp):
TGCTCAATTTGGTCCTAAACCTTTGAACAC
Found at i:16524 original size:31 final size:30
Alignment explanation
Indices: 16417--16516 Score: 139
Period size: 31 Copynumber: 3.3 Consensus size: 30
16407 GGTGGCTAAA
* *
16417 TGCTCAATTTCGTCCTAAACCTTTGAGCGAG
1 TGCTCAATTTGGTCCTAAACCTTTGAACG-G
* *
16448 TGCTCAATTTGGTCCTAAAACTTTGAAC-C
1 TGCTCAATTTGGTCCTAAACCTTTGAACGG
16477 TGCTCAATTTGGTCCTAAACCTTTGAACGG
1 TGCTCAATTTGGTCCTAAACCTTTGAACGG
16507 TCGCTCAATT
1 T-GCTCAATT
16517 CAATCCTATT
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
29 27 0.44
30 1 0.02
31 33 0.54
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (30 bp):
TGCTCAATTTGGTCCTAAACCTTTGAACGG
Done.