Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012639.1 Corchorus capsularis cultivar CVL-1 contig12660, 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: 1842
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:66 original size:37 final size:37
Alignment explanation
Indices: 2--351 Score: 350
Period size: 37 Copynumber: 9.5 Consensus size: 37
1 T
** * *
2 CTTAAACAA-GATTTTGACGAGACACCTAAACAGGGAC
1 CTTAAACAAGGA-TTTGATAAGAAACCTAAACAGGAAC
* *
39 CTTAAACAAGGATTTAATAAGAAACCTAAACAGGAAT
1 CTTAAACAAGGATTTGATAAGAAACCTAAACAGGAAC
** * *
76 CTTAAACAA-GATTTTGACGAGACACCTAAACAGGGAC
1 CTTAAACAAGGA-TTTGATAAGAAACCTAAACAGGAAC
* * *
113 CTTAAACAAGGATTTCATAAGAAACCTAAACAGGTAT
1 CTTAAACAAGGATTTGATAAGAAACCTAAACAGGAAC
* * *
150 CTTAAACAA-GATTTTGATGAGACACCTAAACAGGGAC
1 CTTAAACAAGGA-TTTGATAAGAAACCTAAACAGGAAC
* *
187 CTTAAACAAGGATTTAATAAGAAACCTAAACAGGAAT
1 CTTAAACAAGGATTTGATAAGAAACCTAAACAGGAAC
* * * *
224 CTTAAATAA-GATTTTGATGAGACACCTAAACAGGGAC
1 CTTAAACAAGGA-TTTGATAAGAAACCTAAACAGGAAC
* * * *
261 CTTAAAAAAGGATTTCATAAGAAACCTAAATAGGAAT
1 CTTAAACAAGGATTTGATAAGAAACCTAAACAGGAAC
* * *
298 CTTAAACAA-AATTTTGATGAGACACCTAAACAGGAAC
1 CTTAAACAAGGA-TTTGATAAGAAACCTAAACAGGAAC
*
335 CTTGAACAAGGATTTGA
1 CTTAAACAAGGATTTGA
352 CGAGAATGAA
Statistics
Matches: 254, Mismatches: 50, Indels: 18
0.79 0.16 0.06
Matches are distributed among these distances:
36 7 0.03
37 238 0.94
38 9 0.04
ACGTcount: A:0.45, C:0.17, G:0.16, T:0.22
Consensus pattern (37 bp):
CTTAAACAAGGATTTGATAAGAAACCTAAACAGGAAC
Found at i:122 original size:74 final size:74
Alignment explanation
Indices: 1--349 Score: 599
Period size: 74 Copynumber: 4.7 Consensus size: 74
*
1 TCTTAAACAAGATTTTGACGAGACACCTAAACAGGGACCTTAAACAAGGATTTAATAAGAAACCT
1 TCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTTAATAAGAAACCT
66 AAACAGGAA
66 AAACAGGAA
* *
75 TCTTAAACAAGATTTTGACGAGACACCTAAACAGGGACCTTAAACAAGGATTTCATAAGAAACCT
1 TCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTTAATAAGAAACCT
*
140 AAACAGGTA
66 AAACAGGAA
149 TCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTTAATAAGAAACCT
1 TCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTTAATAAGAAACCT
214 AAACAGGAA
66 AAACAGGAA
* * *
223 TCTTAAATAAGATTTTGATGAGACACCTAAACAGGGACCTTAAAAAAGGATTTCATAAGAAACCT
1 TCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTTAATAAGAAACCT
*
288 AAATAGGAA
66 AAACAGGAA
* * *
297 TCTTAAACAAAATTTTGATGAGACACCTAAACAGGAACCTTGAACAAGGATTT
1 TCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTT
350 GACGAGAATG
Statistics
Matches: 261, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 261 1.00
ACGTcount: A:0.45, C:0.17, G:0.16, T:0.23
Consensus pattern (74 bp):
TCTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCTTAAACAAGGATTTAATAAGAAACCT
AAACAGGAA
Found at i:552 original size:127 final size:126
Alignment explanation
Indices: 302--558 Score: 496
Period size: 127 Copynumber: 2.0 Consensus size: 126
292 AGGAATCTTA
302 AACAAAATTTTGATGAGACACCTAAACAGGAACCTTGAACAAGGATTTGACGAGAATGAATTTTT
1 AACAAAATTTTGATGAGACACCTAAACAGGAACCTTGAACAAGGATTTGACGAGAATGAATTTTT
367 CATGAAAAAGGATTTTGAGGTTTTACATAACAAGTAAGCTCAAACGAGGGGAGAAATTTGC
66 CATGAAAAAGGATTTTGAGGTTTTACATAACAAGTAAGCTCAAACGAGGGGAGAAATTTGC
*
428 AACAAAATTTTGATGAGACACCTAAACAGGGACCTTGAACAAGGATTTGACGAGAATGAATTTTT
1 AACAAAATTTTGATGAGACACCTAAACAGGAACCTTGAACAAGGATTTGACGAGAATGAA-TTTT
493 TCATGAAAAAGGATTTTGAGGTTTTACATAACAAGTAAGCTCAAACGAGGGGAGAAATTTGC
65 TCATGAAAAAGGATTTTGAGGTTTTACATAACAAGTAAGCTCAAACGAGGGGAGAAATTTGC
555 AACA
1 AACA
559 TGCTCAAGCT
Statistics
Matches: 129, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
126 59 0.46
127 70 0.54
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.25
Consensus pattern (126 bp):
AACAAAATTTTGATGAGACACCTAAACAGGAACCTTGAACAAGGATTTGACGAGAATGAATTTTT
CATGAAAAAGGATTTTGAGGTTTTACATAACAAGTAAGCTCAAACGAGGGGAGAAATTTGC
Found at i:661 original size:6 final size:6
Alignment explanation
Indices: 652--679 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
642 ATAAATATTG
652 ATGATT ATGATT ATGATT ATGATT ATGA
1 ATGATT ATGATT ATGATT ATGATT ATGA
680 GATGCAATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (6 bp):
ATGATT
Found at i:1347 original size:87 final size:87
Alignment explanation
Indices: 1197--1366 Score: 250
Period size: 87 Copynumber: 2.0 Consensus size: 87
1187 TGATTGATGC
* * ** *
1197 CCCAAACCTTCTTCCAATTTGGTCATGCATTGATATTCCCAACTCAATTGATGGTTCTAGATCAA
1 CCCAAACCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATCAACGGTTCTAGATCAA
*
1262 CTTCCCACTTTAAGAAATATTT
66 CTTCCCACCTTAAGAAATATTT
* * * *
1284 CCCAAATCTTCCTCCAATTTGATTATGCATTGATATTCCCAATTCAATCAACGGTTCTGGATCAA
1 CCCAAACCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATCAACGGTTCTAGATCAA
1349 CTTCCCACCTTAAGAAAT
66 CTTCCCACCTTAAGAAAT
1367 GTTCAAACAT
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.34
Consensus pattern (87 bp):
CCCAAACCTTCCTCCAATTTGATCATGCATTGATATTCCCAACTCAATCAACGGTTCTAGATCAA
CTTCCCACCTTAAGAAATATTT
Done.