Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007024.1 Corchorus capsularis cultivar CVL-1 contig07045, 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: 47806
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:11612 original size:14 final size:14
Alignment explanation
Indices: 11593--11620 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11583 TTGAAAACCA
11593 TTACGTAACGGCCG
1 TTACGTAACGGCCG
11607 TTACGTAACGGCCG
1 TTACGTAACGGCCG
11621 ATATTTAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.29, G:0.29, T:0.21
Consensus pattern (14 bp):
TTACGTAACGGCCG
Found at i:22614 original size:539 final size:534
Alignment explanation
Indices: 21445--22657 Score: 1645
Period size: 539 Copynumber: 2.3 Consensus size: 534
21435 AGCCCGTGAC
* * * * * * *
21445 AGTATTTACTACTTAAAGAGTCCCTCCGTATATCGTGGTGGACGAGCATGGAATCTCCTGCGAGA
1 AGTAGTTACTACCTACAGAGTCCCTCTGTATAACGTGGTGGACGAGCATGGAATCTCCTGCGGGG
* * * * *
21510 CCTGCAAATCTGCCAGCGAGTTATC-T-TTTTTTT-GTTTTTTT-TTGGCACAAAGTTTTCTCCT
66 CCTGCAAATCTGCCGGTGAGTTATCTTGTTTTTTTGGTTTTTTTGTTGGCGCAGAGTTTTCTCGT
* *
21571 T-TACTAGGGTTTTTTCAGAAAATAAAATTATTTCAAGAGACTGACAATCCCTGTTCAAAAAACA
131 TAT-CTAGGGTTTTTTCAGAAAACAAAATTATTTCAAGAAACTGACAATCCCTGTTCAAAAAACA
*
21635 AAAGATTTACCGAGATGTTGGGTAGTAAGTTGAACTTTTAAATCAGGAGAGTGGAACCCCTTAAT
195 AAAGATTTACCGAGATGTTGGGTAGTAAGTTGAACTCTTAAATCAGGAGAGTGGAACCCCTTAAT
* * *
21700 ATGTAAAGACAAAACCAAAGCGGAAAATCAGAAGTGGAGTATAAAGTAAGAAAGAAACAGAAAAT
260 ATGCAAAGACAAAACCAAAGCGGAAAATCAGAAATGGAGTATAAAGTAAGAAAGAAACAGAAAAC
* * * *
21765 TGACTGCATTAGTCAAAACCCAAAAACCAAGAAAAATAGACACAGGGTTAAAGCATAGAAAGACA
325 TGACTGCATTAGTCAAAACCCAAAAACCAAGAAAAATAGACACAGAGCTAAAGCAAAAAAAGACA
* * * * * *** *
21830 AAGAAAACCTAGGAGGAAAAAGAAAATCTAGAAAGATGTTGAAGAATCTGAGTAGATGTGGGCTC
390 AAGAAAACCTAGGACGAAAAAAAAAAACTAGAAAGATGTCGAAGAATCTGAGTAGACGTCAACCC
* * *
21895 TTTAGAGAGAACATTAAAACCTTCTTGAAGAAATGCAAAAGTGTAAAAGTCGGTAGAAGTGCAGT
455 TTTAAAGAGAACATTAAAACCTTCTTGAAGAAAAGCAAAAGTGTAAAAGTCGGTAGAAATGCAGT
21960 AAAGATTTGGAAGAG
520 AAAGATTTGGAAGAG
* * * * *
21975 CGTAGTTACTACTTACAGAGTCCCTCTGTATACCGTGGTGGACCAGCATGGAATCTCCTGTGGGG
1 AGTAGTTACTACCTACAGAGTCCCTCTGTATAACGTGGTGGACGAGCATGGAATCTCCTGCGGGG
* * **
22040 CCTACAAATCTGCCGGTGAGTTATCTTGCTTTTTTGGTTTTATTTGTTGGCGTTGAGTTTTCTCG
66 CCTGCAAATCTGCCGGTGAGTTATCTTGTTTTTTTGGTTTT-TTTGTTGGCGCAGAGTTTTCTCG
22105 TTATCTAGGGTTTTTTCAGAAAAACAAAATTATTTCAAGAAACT-ATCAATCCCTGTTCAAAAAA
130 TTATCTAGGGTTTTTTCAG-AAAACAAAATTATTTCAAGAAACTGA-CAATCCCTGTTCAAAAAA
* * * *
22169 CAAAGGGTTTACCGAGATGTTGGGTAGTAAGTTGAACTCTTAAATCGGGAGAGTGGAACGCCTTA
193 CAAAAGATTTACCGAGATGTTGGGTAGTAAGTTGAACTCTTAAATCAGGAGAGTGGAACCCCTTA
* * *
22234 ATATGCAAAGTCAAAACCAAAAGCGGAAAATCATAAATGGAGTATAAAGTAAGACAGAAACAGAA
258 ATATGCAAAGACAAAACC-AAAGCGGAAAATCAGAAATGGAGTATAAAGTAAGAAAGAAACAG-A
* * *
22299 AACAGCTGACTGCCTTAGTCAATACCC-AAAACCAAGAAAAATAGACGCAGAGCTAAAGCAAAAA
321 AA-A-CTGACTGCATTAGTCAAAACCCAAAAACCAAGAAAAATAGACACAGAGCTAAAGCAAAAA
* *
22363 AAGACAAAGAAAACCTAGGACGAAAAAAAAAAACGTAGAAAGTTGTCGAAGAATCTGAGTAGCCG
384 AAGACAAAGAAAACCTAGGACGAAAAAAAAAAAC-TAGAAAGATGTCGAAGAATCTGAGTAGACG
* * * * *
22428 -CAACCCTTTAAAGAGAAGATTAAAACCTTTTTGAAGAAAAGCGAAAGTG-AAGAAGTCTGTGGA
448 TCAACCCTTTAAAGAGAACATTAAAACCTTCTTGAAGAAAAGCAAAAGTGTAA-AAGTCGGTAGA
* *
22491 AATGCGGTAAAGATTTGGAAGTG
512 AATGCAGTAAAGATTTGGAAGAG
* *
22514 AGTAGTT-CTCCCCTACAGAGTCCCTCTGTATAACGTGGTGGATGAGCATGGAATCTCCTGCGGG
1 AGTAGTTACT-ACCTACAGAGTCCCTCTGTATAACGTGGTGGACGAGCATGGAATCTCCTGCGGG
* *
22578 GCCTGCAAATCTGCCGGTGAATTATCTTGTTTTTTTGTTTTTGTTTGTTGGCGCAGAGTTTTCTC
65 GCCTGCAAATCTGCCGGTGAGTTATCTTGTTTTTTTGGTTTT-TTTGTTGGCGCAGAGTTTTCTC
*
22643 GTTATCTATGGTTTT
129 GTTATCTAGGGTTTT
22658 GACCGCAAAA
Statistics
Matches: 594, Mismatches: 74, Indels: 21
0.86 0.11 0.03
Matches are distributed among these distances:
530 78 0.13
531 1 0.00
532 6 0.01
533 5 0.01
534 3 0.01
535 32 0.05
536 117 0.20
537 41 0.07
538 7 0.01
539 259 0.44
540 45 0.08
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.27
Consensus pattern (534 bp):
AGTAGTTACTACCTACAGAGTCCCTCTGTATAACGTGGTGGACGAGCATGGAATCTCCTGCGGGG
CCTGCAAATCTGCCGGTGAGTTATCTTGTTTTTTTGGTTTTTTTGTTGGCGCAGAGTTTTCTCGT
TATCTAGGGTTTTTTCAGAAAACAAAATTATTTCAAGAAACTGACAATCCCTGTTCAAAAAACAA
AAGATTTACCGAGATGTTGGGTAGTAAGTTGAACTCTTAAATCAGGAGAGTGGAACCCCTTAATA
TGCAAAGACAAAACCAAAGCGGAAAATCAGAAATGGAGTATAAAGTAAGAAAGAAACAGAAAACT
GACTGCATTAGTCAAAACCCAAAAACCAAGAAAAATAGACACAGAGCTAAAGCAAAAAAAGACAA
AGAAAACCTAGGACGAAAAAAAAAAACTAGAAAGATGTCGAAGAATCTGAGTAGACGTCAACCCT
TTAAAGAGAACATTAAAACCTTCTTGAAGAAAAGCAAAAGTGTAAAAGTCGGTAGAAATGCAGTA
AAGATTTGGAAGAG
Found at i:25452 original size:16 final size:16
Alignment explanation
Indices: 25411--25455 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
25401 TCGGATTTTG
**
25411 TCGGTTTCGGGTTATC
1 TCGGTTTCGGGTTAAA
*
25427 TC-GATTCGGGTTAAA
1 TCGGTTTCGGGTTAAA
25442 TCGGTTTCGGGTTA
1 TCGGTTTCGGGTTA
25456 TAGTACTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.13, C:0.16, G:0.31, T:0.40
Consensus pattern (16 bp):
TCGGTTTCGGGTTAAA
Found at i:38978 original size:77 final size:79
Alignment explanation
Indices: 38887--39040 Score: 267
Period size: 77 Copynumber: 2.0 Consensus size: 79
38877 TTGCTTTTGT
38887 TTTTTTATTATGCAAAAATTCATGAATTCTCCATTAATGCTTT-CAAGTTTTAATTCTCCATA-T
1 TTTTTTATTATGCAAAAATTCATGAATTCTCCATTAATGCTTTACAAGTTTTAATTCTCCATATT
38950 TTCTACCCATGCTG
66 TTCTACCCATGCTG
* * *
38964 TTTTTTATTGTGCAAAAATTCATGATTTTTCCATTAATGCTTTACAAGTTTTAATTCTCCATATT
1 TTTTTTATTATGCAAAAATTCATGAATTCTCCATTAATGCTTTACAAGTTTTAATTCTCCATATT
39029 TTCTACCCATGC
66 TTCTACCCATGC
39041 AATTTAATTA
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
77 40 0.56
78 19 0.26
79 13 0.18
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.47
Consensus pattern (79 bp):
TTTTTTATTATGCAAAAATTCATGAATTCTCCATTAATGCTTTACAAGTTTTAATTCTCCATATT
TTCTACCCATGCTG
Done.