Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014848.1 Corchorus capsularis cultivar CVL-1 contig14869, 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: 7046
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Found at i:573 original size:294 final size:295
Alignment explanation
Indices: 33--622 Score: 1049
Period size: 294 Copynumber: 2.0 Consensus size: 295
23 ATATATAAGT
* * * *
33 ACGAGTTTCGTAAAACTTTTGAATCGACCTTTATATCCTTATTGTTTTTAATATATTTTTTAAAA
1 ACGAGTTTCGTAAAACTTTTGAATCGACCATTACACCCTTATTGTTTTTAATATATTTCTTAAAA
* * *
98 TGCCCTTGCTTAAACTATTTTAGTTTTATTCTACTAAAAACTCTATTTTTATTCAATTATTAATT
66 TGCCCTTGCTTAAACTATTGTAGTTTTATTCTACTAAAAAATCTATTTTTATTCAATTATTAAAT
*
163 CTAATATCTTTATAATTTCTTTATTTTTACCATTTTACTATTTTTCAATAAAAATTGGATATATT
131 CTAATATCTTTATAATTTCTTTATTTTTACAATTTTACTATTTTTCAATAAAAATTGGATATATT
*
228 TAAATTTTTAATATACAATTTTATTCTACTAAAAACTATATTTTCATTTAATTAAATTCAATATT
196 TAAATTTTTAATATACAATTTTATTCTACTAAAAACTACATTTTCATTTAATTAAATTCAATATT
293 ATATAATTATTTTATTTTTACCATTTTAATTTAAA
261 ATATAATTATTTTATTTTTACCATTTTAATTTAAA
*
328 ACGAGTTTCTTAAAACTTTTGAATCGACCATTACACCCTTATT-TTTTTGAATATATTTCTT-AA
1 ACGAGTTTCGTAAAACTTTTGAATCGACCATTACACCCTTATTGTTTTT-AATATATTTCTTAAA
391 ATGCCCTTGCTTAAACTATTGTAGTTTTATTCTACTAAAAAATCTATTTTTATTCAATTATTAAA
65 ATGCCCTTGCTTAAACTATTGTAGTTTTATTCTACTAAAAAATCTATTTTTATTCAATTATTAAA
456 TCTAATATCTTTATAATTTCTTTATTTTTACAATTTTACTATTTTTCAATAAAAATTGGATATAT
130 TCTAATATCTTTATAATTTCTTTATTTTTACAATTTTACTATTTTTCAATAAAAATTGGATATAT
* *
521 TTAAATTTTTAATATACAGTTTTATTCTACTAAAAACTACATTTTTATTTAATTAAATTCAATAT
195 TTAAATTTTTAATATACAATTTTATTCTACTAAAAACTACATTTTCATTTAATTAAATTCAATAT
586 TATATAATTATTTTATTTTTACCATTTTAATTTAAA
260 TATATAATTATTTTATTTTTACCATTTTAATTTAAA
622 A
1 A
623 GGTTATTGTG
Statistics
Matches: 282, Mismatches: 12, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
294 232 0.82
295 50 0.18
ACGTcount: A:0.34, C:0.11, G:0.04, T:0.50
Consensus pattern (295 bp):
ACGAGTTTCGTAAAACTTTTGAATCGACCATTACACCCTTATTGTTTTTAATATATTTCTTAAAA
TGCCCTTGCTTAAACTATTGTAGTTTTATTCTACTAAAAAATCTATTTTTATTCAATTATTAAAT
CTAATATCTTTATAATTTCTTTATTTTTACAATTTTACTATTTTTCAATAAAAATTGGATATATT
TAAATTTTTAATATACAATTTTATTCTACTAAAAACTACATTTTCATTTAATTAAATTCAATATT
ATATAATTATTTTATTTTTACCATTTTAATTTAAA
Found at i:2733 original size:19 final size:19
Alignment explanation
Indices: 2709--2765 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
2699 ATTTAGGTAT
2709 TGTACAGATGAGATTATAC
1 TGTACAGATGAGATTATAC
* * *
2728 TGTACAGATCAAATTAGATAT
1 TGTACAGATGAGATT--ATAC
*
2749 TGTACATATGAGATTAT
1 TGTACAGATGAGATTAT
2766 TATAGCAGCG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
19 15 0.50
21 15 0.50
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.35
Consensus pattern (19 bp):
TGTACAGATGAGATTATAC
Found at i:2764 original size:21 final size:21
Alignment explanation
Indices: 2701--2764 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
2691 TTGGCTCCAT
*
2701 TTAGGTATTGTACAGATGAGA
1 TTAGATATTGTACAGATGAGA
* * *
2722 TT--ATACTGTACAGATCAAA
1 TTAGATATTGTACAGATGAGA
*
2741 TTAGATATTGTACATATGAGA
1 TTAGATATTGTACAGATGAGA
2762 TTA
1 TTA
2765 TTATAGCAGC
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 15 0.45
21 18 0.55
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.36
Consensus pattern (21 bp):
TTAGATATTGTACAGATGAGA
Found at i:4669 original size:22 final size:24
Alignment explanation
Indices: 4644--4687 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
4634 AAAAGTTATC
*
4644 ATAAT-TCTTAAAATC-ATATTCA
1 ATAATATCCTAAAATCTATATTCA
4666 ATAATATCCTAAAATCTATATT
1 ATAATATCCTAAAATCTATATT
4688 TTACCTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 9 0.47
24 5 0.26
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (24 bp):
ATAATATCCTAAAATCTATATTCA
Found at i:6369 original size:11 final size:11
Alignment explanation
Indices: 6326--6363 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
6316 TTCCTATATA
*
6326 AAATAAATTAT
1 AAATTAATTAT
6337 CAAA-TAATTAT
1 -AAATTAATTAT
6348 AAATTAATTAT
1 AAATTAATTAT
6359 AAATT
1 AAATT
6364 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:6750 original size:41 final size:42
Alignment explanation
Indices: 6678--6761 Score: 161
Period size: 41 Copynumber: 2.0 Consensus size: 42
6668 CAAAAATTTC
6678 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
6720 ATTTCTTAACTGAA-TTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
6761 A
1 A
6762 CAGCCGCACG
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 28 0.67
42 14 0.33
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (42 bp):
ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
Done.