Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006242.1 Corchorus capsularis cultivar CVL-1 contig06261, 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: 43430
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30
Found at i:297 original size:2 final size:2
Alignment explanation
Indices: 290--319 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
280 TATTTACTAG
290 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
320 GAAAAATATT
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):
TA
Found at i:27477 original size:22 final size:22
Alignment explanation
Indices: 27435--27477 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
27425 ATTTTTTGAT
*
27435 TTTTCCATTTTTTCCATTTTTC
1 TTTTCCATTTTTTCCAATTTTC
*
27457 TTTT-CATTTTTCTTCAATTTT
1 TTTTCCATTTTT-TCCAATTTT
27478 TGACCTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTCCATTTTTTCCAATTTTC
Found at i:38033 original size:25 final size:26
Alignment explanation
Indices: 38005--38053 Score: 91
Period size: 25 Copynumber: 1.9 Consensus size: 26
37995 CAAGAAATTT
38005 CCAGGGGCATTTTCGTCAT-TTTACG
1 CCAGGGGCATTTTCGTCATCTTTACG
38030 CCAGGGGCATTTTCGTCATCTTTA
1 CCAGGGGCATTTTCGTCATCTTTA
38054 GACTAGACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.37
Consensus pattern (26 bp):
CCAGGGGCATTTTCGTCATCTTTACG
Found at i:41378 original size:36 final size:36
Alignment explanation
Indices: 41300--41370 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
41290 AATTTCGAAG
*
41300 ACTTAATTTCACAAGAATTAAGTAAAATTAGCAAAA
1 ACTTAATTTCACAAGAATTAAGTAAAATCAGCAAAA
*
41336 ACTTAATTTCACAAGAATTAAGTAAAGTCAGCAAA
1 ACTTAATTTCACAAGAATTAAGTAAAATCAGCAAA
41371 TATTTAATCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.51, C:0.13, G:0.10, T:0.27
Consensus pattern (36 bp):
ACTTAATTTCACAAGAATTAAGTAAAATCAGCAAAA
Found at i:41453 original size:11 final size:11
Alignment explanation
Indices: 41437--41548 Score: 152
Period size: 11 Copynumber: 10.2 Consensus size: 11
41427 TTAGGCAAAG
*
41437 GACTGAAATAA
1 GACTGAAATTA
41448 GACTGAAATTA
1 GACTGAAATTA
*
41459 GACTAAAATTA
1 GACTGAAATTA
*
41470 GACTAAAATTA
1 GACTGAAATTA
41481 GACTGAAATTA
1 GACTGAAATTA
*
41492 GACTGAAATAA
1 GACTGAAATTA
*
41503 GACTGAAATTG
1 GACTGAAATTA
*
41514 GACTGAAATTG
1 GACTGAAATTA
**
41525 GACTGAAAGAA
1 GACTGAAATTA
41536 GACTGAAATTA
1 GACTGAAATTA
41547 GA
1 GA
41549 TTGATAAAAG
Statistics
Matches: 90, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 90 1.00
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.23
Consensus pattern (11 bp):
GACTGAAATTA
Found at i:41559 original size:22 final size:22
Alignment explanation
Indices: 41437--41562 Score: 146
Period size: 22 Copynumber: 5.7 Consensus size: 22
41427 TTAGGCAAAG
41437 GACTGAAATAAGACTGAAATTA
1 GACTGAAATAAGACTGAAATTA
* * *
41459 GACTAAAATTAGACTAAAATTA
1 GACTGAAATAAGACTGAAATTA
* *
41481 GACTGAAATTAGACTGAAATAA
1 GACTGAAATAAGACTGAAATTA
** *
41503 GACTGAAATTGGACTGAAATTG
1 GACTGAAATAAGACTGAAATTA
*
41525 GACTGAAAGAAGACTGAAATTA
1 GACTGAAATAAGACTGAAATTA
*
41547 GATTGATAA-AAGACTG
1 GACTGA-AATAAGACTG
41563 GCTTAGTTTC
Statistics
Matches: 89, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
22 87 0.98
23 2 0.02
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.24
Consensus pattern (22 bp):
GACTGAAATAAGACTGAAATTA
Found at i:41562 original size:33 final size:32
Alignment explanation
Indices: 41437--41562 Score: 126
Period size: 33 Copynumber: 3.8 Consensus size: 32
41427 TTAGGCAAAG
* * **
41437 GACTGAAATAAGACTGAAATTAGACTAAAATTA
1 GACTGAAATTAGACTGAAA-TAGACTGAAAGAA
* *
41470 GACTAAAATTAGACTGAAATTAGACTGAAATAA
1 GACTGAAATTAGACTGAAA-TAGACTGAAAGAA
* *
41503 GACTGAAATTGGACTGAAATTGGACTGAAAGAA
1 GACTGAAATTAGACTGAAA-TAGACTGAAAGAA
* *
41536 GACTGAAATTAGATTGATAAAAGACTG
1 GACTGAAATTAGACTGA-AATAGACTG
41563 GCTTAGTTTC
Statistics
Matches: 80, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
33 78 0.98
34 2 0.03
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.24
Consensus pattern (32 bp):
GACTGAAATTAGACTGAAATAGACTGAAAGAA
Found at i:41594 original size:36 final size:36
Alignment explanation
Indices: 41554--41874 Score: 423
Period size: 36 Copynumber: 9.0 Consensus size: 36
41544 TTAGATTGAT
41554 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
1 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
41590 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
1 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
* *
41626 AAAGGAGTGGCTTAGTTTCAAGGAAACTAGGTAAAG
1 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
* * * *
41662 AAAAGACAGGCTTAATTTCAAGGAAATTAGGTAAGG
1 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
* * *
41698 GAAAGACTGACTTAATTTCAAGGAAA-TCAGGTAAAG
1 AAAAGACTGGCTTAGTTTCAAGGAAACT-AGGTAAAG
* * * * *
41734 -ATAGATTGGGTTAATTTCAAGGAAATTAGGTAAAG
1 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
**
41769 -ATGGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
1 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
* * *
41804 AAAAGATTGGCTTAATTTCAAGGAAACTAGGTAAAT
1 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
* *
41840 AAAAGACTGGCTTAGTTTCAAGGAAATTAAGTAAA
1 AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAA
41875 AAGGCACAGG
Statistics
Matches: 252, Mismatches: 30, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
35 60 0.24
36 192 0.76
ACGTcount: A:0.42, C:0.09, G:0.25, T:0.25
Consensus pattern (36 bp):
AAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAG
Found at i:41890 original size:142 final size:141
Alignment explanation
Indices: 41552--41896 Score: 458
Period size: 142 Copynumber: 2.4 Consensus size: 141
41542 AATTAGATTG
* *
41552 ATAAAAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTGGCTTAGTTTCAAGGAAAC
1 ATAAAAGACTGGCTTAGTTTCAAGGAAATTAGGT--A-AAAAGACTGGCTTAATTTCAAGGAAAC
*
41617 TAGGTAAAGAAAGGAGTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACAGGCTTAATTTCA
63 TAGGTAAAGAAAGGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACAGGCTTAATTTCA
*
41682 AGGAAATTAGGTAA
128 AGGAAACTAGGTAA
*** * * * * * *
41696 GGGAAAGACTGACTTAATTTCAAGGAAATCAGGTAAAGATAGATTGGGTTAATTTCAAGGAAATT
1 ATAAAAGACTGGCTTAGTTTCAAGGAAATTAGGTAAA-A-AGACTGGCTTAATTTCAAGGAAACT
* **
41761 AGGTAAAG-ATGGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGATTGGCTTAATTTCAA
64 AGGTAAAGAAAGGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACAGGCTTAATTTCAA
41825 GGAAACTAGGTAA
129 GGAAACTAGGTAA
* *
41838 ATAAAAGACTGGCTTAGTTTCAAGGAAATTAAGTAAAAAGGCACAGGCTTAATTTCAAG
1 ATAAAAGACTGGCTTAGTTTCAAGGAAATTAGGTAAAAA-G-ACTGGCTTAATTTCAAG
41897 CGAGGAAATT
Statistics
Matches: 171, Mismatches: 26, Indels: 10
0.83 0.13 0.05
Matches are distributed among these distances:
140 1 0.01
141 4 0.02
142 110 0.64
143 29 0.17
144 27 0.16
ACGTcount: A:0.41, C:0.10, G:0.24, T:0.25
Consensus pattern (141 bp):
ATAAAAGACTGGCTTAGTTTCAAGGAAATTAGGTAAAAAGACTGGCTTAATTTCAAGGAAACTAG
GTAAAGAAAGGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACAGGCTTAATTTCAAGG
AAACTAGGTAA
Done.