Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007241.1 Corchorus capsularis cultivar CVL-1 contig07262, 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: 29256
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1456 original size:25 final size:25
Alignment explanation
Indices: 1422--1476 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
1412 AAAGAGTCAG
*
1422 AAGTTGAAGAAGATAATGCTCTGCA
1 AAGTTGAAGAAAATAATGCTCTGCA
1447 AAGTTGAAGAAAATAATGCTCTGCA
1 AAGTTGAAGAAAATAATGCTCTGCA
1472 AAGTT
1 AAGTT
1477 ATCCTCATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.25
Consensus pattern (25 bp):
AAGTTGAAGAAAATAATGCTCTGCA
Found at i:1515 original size:55 final size:55
Alignment explanation
Indices: 1452--1561 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
1442 CTGCAAAGTT
1452 GAAGAAAATAATGCTCTGCAAAGTTATCCTCATCATGGAGGGAATCTCTGCAAAA
1 GAAGAAAATAATGCTCTGCAAAGTTATCCTCATCATGGAGGGAATCTCTGCAAAA
*
1507 GAAGAAAATAATGCTCTGCAAAGTTATCCTCATCATGGAGGGAATGTCTGCAAAA
1 GAAGAAAATAATGCTCTGCAAAGTTATCCTCATCATGGAGGGAATCTCTGCAAAA
1562 TGTTTTCAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (55 bp):
GAAGAAAATAATGCTCTGCAAAGTTATCCTCATCATGGAGGGAATCTCTGCAAAA
Found at i:1832 original size:2 final size:2
Alignment explanation
Indices: 1825--1853 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1815 CTGGTATCAG
1825 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1854 CACACACGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5557 original size:2 final size:2
Alignment explanation
Indices: 5545--5574 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5535 TCAACATTGT
5545 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5575 CTAAGCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5700 original size:9 final size:9
Alignment explanation
Indices: 5686--5712 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
5676 ATATATTATC
5686 ATCTTTGAA
1 ATCTTTGAA
5695 ATCTTTGAA
1 ATCTTTGAA
5704 ATCTTTGAA
1 ATCTTTGAA
5713 GAGATATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (9 bp):
ATCTTTGAA
Found at i:8434 original size:18 final size:17
Alignment explanation
Indices: 8411--8446 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
8401 CTCAACCTAA
8411 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAA-TAG
8429 AACTAGAAGAAAAATAG
1 AACTAGAAGAAAAATAG
8446 A
1 A
8447 TGAAGAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11
Consensus pattern (17 bp):
AACTAGAAGAAAAATAG
Found at i:12330 original size:30 final size:30
Alignment explanation
Indices: 12294--12361 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
12284 CGGCCACTTG
*
12294 ACCGGCCATCGCATGGGGC-TACCG-GCCACA
1 ACCGGCCATCGCATGGGCCAT-CCGCG-CACA
12324 ACCGGCCATCGCATGGGCCATCCGCGCACA
1 ACCGGCCATCGCATGGGCCATCCGCGCACA
12354 ACCGGCCA
1 ACCGGCCA
12362 ATGGACCCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
30 33 0.94
31 2 0.06
ACGTcount: A:0.21, C:0.43, G:0.28, T:0.09
Consensus pattern (30 bp):
ACCGGCCATCGCATGGGCCATCCGCGCACA
Found at i:14881 original size:37 final size:40
Alignment explanation
Indices: 14831--14912 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 40
14821 TTTTGTTTTT
* *
14831 TTTTTCCGTTTTTTCT-AATAAAAAA-AAGT-TTTTTCCG
1 TTTTTCCGATTTTTCTAAAAAAAAAATAAGTATTTTTCCG
*
14868 TTTTTCCGATTTTTCTAAAAAAAAAATAATTATTTTTCCG
1 TTTTTCCGATTTTTCTAAAAAAAAAATAAGTATTTTTCCG
14908 TTTTT
1 TTTTT
14913 AATTTTAGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
37 15 0.38
38 8 0.21
39 3 0.08
40 13 0.33
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (40 bp):
TTTTTCCGATTTTTCTAAAAAAAAAATAAGTATTTTTCCG
Found at i:18635 original size:9 final size:9
Alignment explanation
Indices: 18623--18656 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
18613 TTTTCCATAC
18623 CAAAGGAGA
1 CAAAGGAGA
*
18632 CAAAGGA-C
1 CAAAGGAGA
18640 CAAAGGAGA
1 CAAAGGAGA
18649 CAAAGGAG
1 CAAAGGAG
18657 GTTTTCATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.53, C:0.15, G:0.32, T:0.00
Consensus pattern (9 bp):
CAAAGGAGA
Found at i:18641 original size:17 final size:17
Alignment explanation
Indices: 18621--18655 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
18611 GATTTTCCAT
18621 ACCAAAGGAGACAAAGG
1 ACCAAAGGAGACAAAGG
18638 ACCAAAGGAGACAAAGG
1 ACCAAAGGAGACAAAGG
18655 A
1 A
18656 GGTTTTCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.17, G:0.29, T:0.00
Consensus pattern (17 bp):
ACCAAAGGAGACAAAGG
Done.