Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01002929.1 Corchorus capsularis cultivar CVL-1 contig02937, 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: 8416
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Found at i:407 original size:71 final size:73
Alignment explanation
Indices: 307--450 Score: 256
Period size: 71 Copynumber: 2.0 Consensus size: 73
297 AAATCATAGA
307 AATATAATAAATAATAATAATTTGGGGTCTTGCCAATTTGTGGGAGACTAAAGAAAAAAGATATG
1 AATATAATAAATAATAATAATTTGGGGTCTTGCCAATTTGTGGGAGACTAAAGAAAAAAGATATG
*
372 ATCAAAAT
66 ACCAAAAT
*
380 AATA-AAT-AATAATAATAATTTGGGGTCTTGCCAATTTGTGGGAGACTAAATAAAAAAGATATG
1 AATATAATAAATAATAATAATTTGGGGTCTTGCCAATTTGTGGGAGACTAAAGAAAAAAGATATG
443 ACCAAAAT
66 ACCAAAAT
451 TCAAAAATTG
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
71 62 0.90
72 3 0.04
73 4 0.06
ACGTcount: A:0.47, C:0.08, G:0.17, T:0.28
Consensus pattern (73 bp):
AATATAATAAATAATAATAATTTGGGGTCTTGCCAATTTGTGGGAGACTAAAGAAAAAAGATATG
ACCAAAAT
Found at i:5635 original size:47 final size:47
Alignment explanation
Indices: 5582--5678 Score: 176
Period size: 47 Copynumber: 2.1 Consensus size: 47
5572 TTGACATGTT
*
5582 CTATTTGATAGTTTAATATATTATTATGATTAAAATTTATTATTTCC
1 CTATTTGATAGTTTAATATAATATTATGATTAAAATTTATTATTTCC
*
5629 CTATTTGATAGTTTAATGTAATATTATGATTAAAATTTATTATTTCC
1 CTATTTGATAGTTTAATATAATATTATGATTAAAATTTATTATTTCC
5676 CTA
1 CTA
5679 ACGTGCAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (47 bp):
CTATTTGATAGTTTAATATAATATTATGATTAAAATTTATTATTTCC
Found at i:6319 original size:67 final size:65
Alignment explanation
Indices: 6213--6338 Score: 191
Period size: 67 Copynumber: 1.9 Consensus size: 65
6203 AAAAAAATCT
* *
6213 ATAGATTCTACTTTCTTTTAGTTGGGATTCAACTCTCATATTTTCCTATGTTAAAAGAAAATTAC
1 ATAGATTCTACATTCTTTTAGTTAGGATTCAACTCTCATATTTTCCTATGTTAAAAGAAAATTAC
*
6278 ATAGATT-TACATTCTTTTAGTTATTAGGATTCAACTCTCATATTTTCCTTTGTTAAAAGAA
1 ATAGATTCTACATTCTTTTAG---TTAGGATTCAACTCTCATATTTTCCTATGTTAAAAGAA
6339 GGAAGATGTT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
64 12 0.22
65 7 0.13
67 36 0.65
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.44
Consensus pattern (65 bp):
ATAGATTCTACATTCTTTTAGTTAGGATTCAACTCTCATATTTTCCTATGTTAAAAGAAAATTAC
Found at i:7288 original size:6 final size:6
Alignment explanation
Indices: 7277--7315 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
7267 CCGAAGCCGT
* *
7277 CCGAAC CCGAAC CCGAAA CCGAAC CCG-AC CCGAGC CCGA
1 CCGAAC CCGAAC CCGAAC CCGAAC CCGAAC CCGAAC CCGA
7316 GATCAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.31, C:0.49, G:0.21, T:0.00
Consensus pattern (6 bp):
CCGAAC
Found at i:7529 original size:31 final size:31
Alignment explanation
Indices: 7458--7529 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
7448 GTCCATTAGC
*
7458 TTTTAATTTGTTTAATCTAAGACTTGCATTT
1 TTTTAATTTGTTTAATCTAAGACTTGAATTT
** * * *
7489 TGATGATTTGTTTAATTTAATACTT-AATTT
1 TTTTAATTTGTTTAATCTAAGACTTGAATTT
7519 GTTTTAATTTG
1 -TTTTAATTTG
7530 CTACAATTTA
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.26, C:0.06, G:0.11, T:0.57
Consensus pattern (31 bp):
TTTTAATTTGTTTAATCTAAGACTTGAATTT
Found at i:8063 original size:23 final size:23
Alignment explanation
Indices: 8033--8087 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
8023 TATCGAAAAT
*
8033 GAACCCGAACCCGA-CCAGGGCCC
1 GAACCCGAACCCGATCC-GAGCCC
8056 GAACCCGAACCCGATCCGAGCCC
1 GAACCCGAACCCGATCCGAGCCC
*
8079 GAACACGAA
1 GAACCCGAA
8088 AATACCCGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 27 0.93
24 2 0.07
ACGTcount: A:0.31, C:0.44, G:0.24, T:0.02
Consensus pattern (23 bp):
GAACCCGAACCCGATCCGAGCCC
Found at i:8097 original size:16 final size:16
Alignment explanation
Indices: 8076--8149 Score: 107
Period size: 15 Copynumber: 4.8 Consensus size: 16
8066 CCGATCCGAG
*
8076 CCCGAACACGAAAATA
1 CCCGAACCCGAAAATA
8092 CCCGAACCCG-AAATA
1 CCCGAACCCGAAAATA
*
8107 TCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
*
8123 CCCGAACCCG-AAGTA
1 CCCGAACCCGAAAATA
8138 CCCGAACCCGAA
1 CCCGAACCCGAA
8150 CCTGCCCAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
15 28 0.54
16 24 0.46
ACGTcount: A:0.41, C:0.38, G:0.15, T:0.07
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:8119 original size:31 final size:31
Alignment explanation
Indices: 8076--8149 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
8066 CCGATCCGAG
*
8076 CCCGAACACGAAAATACCCGAACCCGAAATA
1 CCCGAACCCGAAAATACCCGAACCCGAAATA
* *
8107 TCCGAACCCGAAAATACCCGAACCCGAAGTA
1 CCCGAACCCGAAAATACCCGAACCCGAAATA
8138 CCCGAACCCGAA
1 CCCGAACCCGAA
8150 CCTGCCCAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.41, C:0.38, G:0.15, T:0.07
Consensus pattern (31 bp):
CCCGAACCCGAAAATACCCGAACCCGAAATA
Done.