Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009648.1 Corchorus capsularis cultivar CVL-1 contig09669, 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: 63063
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:488 original size:2 final size:2
Alignment explanation
Indices: 481--525 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
471 AGAAACAGGA
* *
481 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
523 AT A
1 AT A
526 AACAACTAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:8411 original size:60 final size:60
Alignment explanation
Indices: 8343--8502 Score: 212
Period size: 60 Copynumber: 2.6 Consensus size: 60
8333 CTAATTGCTT
** * * * ** *
8343 AAATAAGGGTTTAATGTTTGTCAAAATGCTCAAAAAAGGGTCTGATCTTTTAATTTGACC
1 AAATAAGGGCCTAACGTTTGCCAAAATGCTCAAAAAAGGATCCCATCTTTGAATTTGACC
* *
8403 AAATAAGGGCCTAACGTTTGCCAAAATGTTCAAATAAGGATCCCATCTTTGAATTTGACC
1 AAATAAGGGCCTAACGTTTGCCAAAATGCTCAAAAAAGGATCCCATCTTTGAATTTGACC
*
8463 AAATAAGAGCCTAACGTTTGCCAAAATGCTCAAATAAAGG
1 AAATAAGGGCCTAACGTTTGCCAAAATGCTCAAA-AAAGG
8503 CTTGTTTCAT
Statistics
Matches: 86, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
60 82 0.95
61 4 0.05
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (60 bp):
AAATAAGGGCCTAACGTTTGCCAAAATGCTCAAAAAAGGATCCCATCTTTGAATTTGACC
Found at i:8437 original size:31 final size:31
Alignment explanation
Indices: 8402--8499 Score: 85
Period size: 31 Copynumber: 3.2 Consensus size: 31
8392 TTAATTTGAC
*
8402 CAAATAAGGGCCTAACGTTTGCCAAAATGTT
1 CAAATAAGGGCCTAACGTTTGCCAAAATGAT
* * * ** *
8433 CAAATAAGGATCCCATC-TTTG--AATTTGAC
1 CAAATAAGG-GCCTAACGTTTGCCAAAATGAT
* *
8462 CAAATAAGAGCCTAACGTTTGCCAAAATGCT
1 CAAATAAGGGCCTAACGTTTGCCAAAATGAT
8493 CAAATAA
1 CAAATAA
8500 AGGCTTGTTT
Statistics
Matches: 48, Mismatches: 15, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
28 4 0.08
29 16 0.33
31 24 0.50
32 4 0.08
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGAT
Found at i:8577 original size:31 final size:31
Alignment explanation
Indices: 8539--8636 Score: 85
Period size: 31 Copynumber: 3.2 Consensus size: 31
8529 CATCAGTTCA
8539 TTATTTGAGCATTTTCAATAACGTTAGACCC
1 TTATTTGAGCATTTTCAATAACGTTAGACCC
* ** **
8570 TTATTTGACCAAATT-AA-AA-GATCGGACCC
1 TTATTTGAGCATTTTCAATAACG-TTAGACCC
* * * *
8599 TTGTTTGAGCATTTTCGATAACGTTAGGCTC
1 TTATTTGAGCATTTTCAATAACGTTAGACCC
8630 TTATTTG
1 TTATTTG
8637 GCCAAATTAA
Statistics
Matches: 48, Mismatches: 15, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
28 1 0.02
29 19 0.40
30 3 0.06
31 24 0.50
32 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (31 bp):
TTATTTGAGCATTTTCAATAACGTTAGACCC
Found at i:8685 original size:60 final size:60
Alignment explanation
Indices: 8539--8697 Score: 216
Period size: 60 Copynumber: 2.6 Consensus size: 60
8529 CATCAGTTCA
*
8539 TTATTTGAGCATTTT-CAATAACGTTAGACCCTTATTTGACCAAATTAAAAGATCGGACCC
1 TTATTTGAGCATTTTGC-ATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCGGACCC
* * * *
8599 TTGTTTGAGCATTTT-CGATAACGTTAGGCTCTTATTTGGCCAAATTAAAAGATCGGGCCC
1 TTATTTGAGCATTTTGC-ATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCGGACCC
*
8659 TTATTTGAGCATTTTGGCA-AATGTTAGGCCCTTATTTGA
1 TTATTTGAGCATTTT-GCATAACGTTAGGCCCTTATTTGA
8698 GCAATTAGCC
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
60 85 0.98
61 1 0.01
62 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (60 bp):
TTATTTGAGCATTTTGCATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCGGACCC
Found at i:10695 original size:2 final size:2
Alignment explanation
Indices: 10688--10757 Score: 67
Period size: 2 Copynumber: 36.0 Consensus size: 2
10678 TACATACATG
10688 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T CAT -T AT -T ACT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT A-T AT
* * *
10728 AA AA AG AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10758 TCATATAAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
1 4 0.07
2 53 0.88
3 3 0.05
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (2 bp):
AT
Found at i:14626 original size:5 final size:5
Alignment explanation
Indices: 14616--14643 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
14606 TACGGTTTTC
14616 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
14644 TGTTTTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:19866 original size:15 final size:15
Alignment explanation
Indices: 19846--19877 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
19836 AAGAAAAGAT
19846 ATTATTAATATAGAA
1 ATTATTAATATAGAA
19861 ATTATTAATATAGAA
1 ATTATTAATATAGAA
19876 AT
1 AT
19878 GCATGAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (15 bp):
ATTATTAATATAGAA
Found at i:23189 original size:109 final size:109
Alignment explanation
Indices: 22993--23284 Score: 464
Period size: 109 Copynumber: 2.7 Consensus size: 109
22983 ACTATTATAG
* *
22993 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
23058 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
23107 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
*
23172 TTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
* *
23216 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATAT-TTTAT-ATAACTTTTTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTTTATAATTACTTTATT
23278 TTTACCA
65 TTTACCA
23285 TTTTAATTTA
Statistics
Matches: 172, Mismatches: 5, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
107 16 0.09
108 6 0.03
109 124 0.72
110 3 0.02
111 2 0.01
114 21 0.12
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.49
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:25384 original size:25 final size:27
Alignment explanation
Indices: 25332--25384 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
25322 TTACTCAACT
*
25332 AAAAACTCTATTTTTATTTTTATGTAA
1 AAAAACTCTATTTTTATTTTAATGTAA
25359 AAAAACTCTATTTTTA-TTTAAT-TAA
1 AAAAACTCTATTTTTATTTTAATGTAA
25384 A
1 A
25385 TCTAATATCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 4 0.16
26 5 0.20
27 16 0.64
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.49
Consensus pattern (27 bp):
AAAAACTCTATTTTTATTTTAATGTAA
Found at i:56478 original size:2 final size:2
Alignment explanation
Indices: 56471--56497 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
56461 CGATAATTAG
56471 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 A
56498 AGAAAAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:62145 original size:85 final size:81
Alignment explanation
Indices: 62000--62173 Score: 249
Period size: 85 Copynumber: 2.1 Consensus size: 81
61990 CCGATCCTAT
*
62000 ACAATTAATGATTGAAAGGGAATATATACTAGTAGTAATAAAACAAAGAAAAATATATAATGTGT
1 ACAATGAATGATTGAAAGGGAATATATACTAGTAGTAATAAAACAAAGAAAAATATATAATGTGT
*
62065 TTTTGATATTATAAAG
66 TTTTGATATAATAAAG
* * *
62081 ACGATGAATGATTGAAAGGGAATACTAGCTAGCTATTAGTAATAAAACAAAGAAAAGTATATAAT
1 ACAATGAATGATTGAAAGGGAATA-TA--TA-CTAGTAGTAATAAAACAAAGAAAAATATATAAT
* *
62146 GTGTTTTTTATATAATTAAG
62 GTGTTTTTGATATAATAAAG
62166 ACAATGAA
1 ACAATGAA
62174 GATAACGATG
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
81 22 0.27
82 2 0.02
84 2 0.02
85 55 0.68
ACGTcount: A:0.48, C:0.05, G:0.16, T:0.31
Consensus pattern (81 bp):
ACAATGAATGATTGAAAGGGAATATATACTAGTAGTAATAAAACAAAGAAAAATATATAATGTGT
TTTTGATATAATAAAG
Done.