Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011073.1 Corchorus capsularis cultivar CVL-1 contig11094, 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: 76385
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:32550 original size:4 final size:4
Alignment explanation
Indices: 32541--32566 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
32531 AATTTAGGGA
32541 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
32567 TTATATAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:32736 original size:2 final size:2
Alignment explanation
Indices: 32724--32758 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
32714 TTCTTTGGCT
* *
32724 TA TA CA TA TA TA TA TA GA 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 TA TA T
32759 CAATCGAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:41169 original size:53 final size:52
Alignment explanation
Indices: 41106--41211 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 52
41096 ATCATGGTGG
41106 ATATATGCTTAGTATATTAAAGACACCAATTTAGTTTAACCAAAAGCAACTTA
1 ATATATGCTTAGTATATTAAAGACACCAATTTAGTTTAACCAAAAGCAA-TTA
*
41159 ATATATGCTTAGTGTATTAAAGACACCAATTTAGTTTAACCAAAAGCAATTA
1 ATATATGCTTAGTATATTAAAGACACCAATTTAGTTTAACCAAAAGCAATTA
41211 A
1 A
41212 GTTGATGGAC
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 4 0.08
53 48 0.92
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.32
Consensus pattern (52 bp):
ATATATGCTTAGTATATTAAAGACACCAATTTAGTTTAACCAAAAGCAATTA
Found at i:44298 original size:78 final size:80
Alignment explanation
Indices: 44152--44298 Score: 244
Period size: 78 Copynumber: 1.9 Consensus size: 80
44142 TTGACTTATA
*
44152 ATAATGCATAAATAATTTTAGATCAAACAAAAAAACATAGCAGATCTTCATCCCTTTCTTTTTTT
1 ATAATGCATAAATAATTTTAGATCAAACAAAAAAACATAGCAGATCTTCATCCCTTTCTTTTTAT
44217 CTACCCCTTTGGTTT
66 CTACCCCTTTGGTTT
* * *
44232 ATAATGCATAAATTATTTTGGATCAAAC-AAAAAA-ATAGCATATCTTCATCCCTTTCTTTTTAT
1 ATAATGCATAAATAATTTTAGATCAAACAAAAAAACATAGCAGATCTTCATCCCTTTCTTTTTAT
44295 CTAC
66 CTAC
44299 ATTGATCTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
78 31 0.49
79 6 0.10
80 26 0.41
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.39
Consensus pattern (80 bp):
ATAATGCATAAATAATTTTAGATCAAACAAAAAAACATAGCAGATCTTCATCCCTTTCTTTTTAT
CTACCCCTTTGGTTT
Found at i:45583 original size:191 final size:192
Alignment explanation
Indices: 45258--45615 Score: 610
Period size: 191 Copynumber: 1.9 Consensus size: 192
45248 GGGCCATGAT
* * *
45258 ATACCTTATGACAACCAAATTTATTGGCACATCACGAGAAAACACCCTCTCTAGCAAGAAAGTGG
1 ATACCTTATGACAACAAAAGTTATAGGCACATCACGAGAAAACACCCTCTCTAGCAAGAAAGTGG
* * *
45323 ATATGCCCAAACAAAGTAGTGAGAAGAAGGCACTCACATCAACAACGGAGTAAGAGCCTAATGGG
66 ATATGCCCAAACAAAGTAGTGAGAAGAAGGCACTCACATCAACAACAGAGCAAGAGCCCAATGGG
*
45388 TGAAAAAAGTAGGGTAAAATACCACCGAAGCATAAAAAGTAAGGTAAAACAAAAATAGCATG
131 TGAAAAAAGTAGAGTAAAATACCACCGAAGCATAAAAAGTAAGGTAAAACAAAAATAGCATG
45450 ATACCTTATGACAACAAAAGTTATAGGCACATCACGAGAAAACACCCTCT-TAGCAAGAAAGTGG
1 ATACCTTATGACAACAAAAGTTATAGGCACATCACGAGAAAACACCCTCTCTAGCAAGAAAGTGG
* * *
45514 ATTTGCCCAAACAAAGTAGTGAGAAGAAGGCACTCACATCAACAATAGAGCAAGAGCCCGATGGG
66 ATATGCCCAAACAAAGTAGTGAGAAGAAGGCACTCACATCAACAACAGAGCAAGAGCCCAATGGG
*
45579 TGAAAAACGTAGAGTAAAATACCACCGAAGCATAAAA
131 TGAAAAAAGTAGAGTAAAATACCACCGAAGCATAAAA
45616 CAAAGATAGC
Statistics
Matches: 155, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
191 108 0.70
192 47 0.30
ACGTcount: A:0.44, C:0.20, G:0.20, T:0.16
Consensus pattern (192 bp):
ATACCTTATGACAACAAAAGTTATAGGCACATCACGAGAAAACACCCTCTCTAGCAAGAAAGTGG
ATATGCCCAAACAAAGTAGTGAGAAGAAGGCACTCACATCAACAACAGAGCAAGAGCCCAATGGG
TGAAAAAAGTAGAGTAAAATACCACCGAAGCATAAAAAGTAAGGTAAAACAAAAATAGCATG
Found at i:47233 original size:9 final size:9
Alignment explanation
Indices: 47213--47241 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
47203 TCTTATTACA
47213 ATTCAA-TT
1 ATTCAATTT
47221 ATTCAATTT
1 ATTCAATTT
47230 ATTCAATTT
1 ATTCAATTT
47239 ATT
1 ATT
47242 ATTCTTAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.55
Consensus pattern (9 bp):
ATTCAATTT
Found at i:48966 original size:2 final size:2
Alignment explanation
Indices: 48959--48994 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
48949 AACATCTAAT
48959 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TCA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
48995 AATTTATGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.94
3 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:50416 original size:14 final size:14
Alignment explanation
Indices: 50397--50425 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
50387 TAGTGACAGT
50397 TTTAGTTACTTATA
1 TTTAGTTACTTATA
50411 TTTAGTTACTTATA
1 TTTAGTTACTTATA
50425 T
1 T
50426 CCTTTCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.59
Consensus pattern (14 bp):
TTTAGTTACTTATA
Found at i:55391 original size:2 final size:2
Alignment explanation
Indices: 55384--55411 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
55374 TTACTACCAC
55384 AT AT 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
55412 CATCTCATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55706 original size:2 final size:2
Alignment explanation
Indices: 55669--55694 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
55659 TTGAGTTTAA
55669 AT 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
55695 GTTTTTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62413 original size:6 final size:6
Alignment explanation
Indices: 62402--62428 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
62392 CTGATGGAAA
62402 AAAAAC AAAAAC AAAAAC AAAAAC AAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAA
62429 CAAACAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:71381 original size:36 final size:36
Alignment explanation
Indices: 71334--71404 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
71324 TTACAATCCA
*
71334 AAACTCAAAATCGGAAACATGAAAACTCCAAAACCG
1 AAACTCAAAATCGAAAACATGAAAACTCCAAAACCG
* *
71370 AAACTCAAAATCGAAAACATGAATACTCCGAAACC
1 AAACTCAAAATCGAAAACATGAAAACTCCAAAACC
71405 CATCTCTTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.52, C:0.25, G:0.10, T:0.13
Consensus pattern (36 bp):
AAACTCAAAATCGAAAACATGAAAACTCCAAAACCG
Done.