Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013010.1 Corchorus capsularis cultivar CVL-1 contig13031, 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: 9041
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Found at i:557 original size:11 final size:11
Alignment explanation
Indices: 541--571 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
531 TATCACGTTT
541 AAATTAAATAA
1 AAATTAAATAA
552 AAATTAAATAA
1 AAATTAAATAA
563 ATAATTAAA
1 A-AATTAAA
572 ATTAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.63
12 7 0.37
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AAATTAAATAA
Found at i:5339 original size:85 final size:85
Alignment explanation
Indices: 5244--5400 Score: 253
Period size: 85 Copynumber: 1.8 Consensus size: 85
5234 GTTTTTTAAT
* * *
5244 TAAAATAGTAAAATGGTAAAATAGAATAGTTAT-AAGGATATTAGATTTAATTAAATAAAAATAT
1 TAAAATAGTAAAATGGTAAAATAAAATAATTATGAA-GATATTAGATTTAATTAAATAAAAATAG
5308 AATTTTTAATTTTTAGTTGAG
65 AATTTTTAATTTTTAGTTGAG
*
5329 TAAAATAGTAAAATGGTAAAGTAAAATAATTATGAAGATATTAGATTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATAAAATAATTATGAAGATATTAGATTTAATTAAATAAAAATAGA
*
5394 GTTTTTA
66 ATTTTTA
5401 GTTAAGTAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
85 64 0.97
86 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (85 bp):
TAAAATAGTAAAATGGTAAAATAAAATAATTATGAAGATATTAGATTTAATTAAATAAAAATAGA
ATTTTTAATTTTTAGTTGAG
Found at i:5718 original size:22 final size:22
Alignment explanation
Indices: 5650--5909 Score: 74
Period size: 22 Copynumber: 11.8 Consensus size: 22
5640 TTATTGTGTG
* * *
5650 GTTATTAAAATTTTATAAGGAA
1 GTTATCAAAATTTCATAAGGAT
* * * *
5672 ATTATCAAAA-ATCAT-AGAAAA
1 GTTATCAAAATTTCATAAG-GAT
5693 GTTATCAAAATTTCATAAGGAT
1 GTTATCAAAATTTCATAAGGAT
* * **
5715 GTTA-CTAAAACTTCATACGGGG
1 GTTATC-AAAATTTCATAAGGAT
*
5737 GTTATCAAAAATGTCATAAGCG-T
1 GTTATC-AAAATTTCATAAG-GAT
* ** *
5760 GGTTATCAAACTTTCATTGGGAG
1 -GTTATCAAAATTTCATAAGGAT
*
5783 GTTATCACAATTTCAT-AGTG-T
1 GTTATCAAAATTTCATAAG-GAT
* * **
5804 GATCAACAAAATTTCAT-AGTTT
1 G-TTATCAAAATTTCATAAGGAT
* * *
5826 GGTTA-CTAACATTTCAT-AGAAAG
1 -GTTATC-AAAATTTCATAAG-GAT
* *
5849 GTTATCAAAATTTC-TTAGTAT
1 GTTATCAAAATTTCATAAGGAT
* *
5870 GGTTATCAAAATTTCA-AACGAA
1 -GTTATCAAAATTTCATAAGGAT
*
5892 GATTATCAAATTTTCATA
1 G-TTATCAAAATTTCATA
5910 GGAGATTATC
Statistics
Matches: 174, Mismatches: 44, Indels: 39
0.68 0.17 0.15
Matches are distributed among these distances:
20 2 0.01
21 21 0.12
22 119 0.68
23 25 0.14
24 7 0.04
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (22 bp):
GTTATCAAAATTTCATAAGGAT
Found at i:5799 original size:45 final size:44
Alignment explanation
Indices: 5693--5799 Score: 112
Period size: 45 Copynumber: 2.4 Consensus size: 44
5683 TCATAGAAAA
5693 GTTATCAAAATTTCATAAGGATGTTACTAAAACTTCATACGGGG
1 GTTATCAAAATTTCATAAGGATGTTACTAAAACTTCATACGGGG
* * *
5737 GTTATCAAAAATGTCATAAGCG-TGGTTA-TCAAACTTTCAT-TGGGAG
1 GTTATC-AAAATTTCATAAG-GAT-GTTACTAAAAC-TTCATACGGG-G
*
5783 GTTATCACAATTTCATA
1 GTTATCAAAATTTCATA
5800 GTGTGATCAA
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
44 6 0.11
45 30 0.57
46 17 0.32
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.34
Consensus pattern (44 bp):
GTTATCAAAATTTCATAAGGATGTTACTAAAACTTCATACGGGG
Found at i:5830 original size:44 final size:44
Alignment explanation
Indices: 5782--5885 Score: 102
Period size: 44 Copynumber: 2.4 Consensus size: 44
5772 TTCATTGGGA
*** *
5782 GGTTATCACAATTTCATAGTGTGATCAACAAAATTTCATAGTTT
1 GGTTATCACAATTTCATAGAAAGATCAACAAAATTTCATAGTAT
* * * * *
5826 GGTTACTAAC-ATTTCATAGAAAGGTTATCAAAATTTCTTAGTAT
1 GGTTA-TCACAATTTCATAGAAAGATCAACAAAATTTCATAGTAT
*
5870 GGTTATCAAAATTTCA
1 GGTTATCACAATTTCA
5886 AACGAAGATT
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
43 2 0.04
44 42 0.89
45 3 0.06
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.38
Consensus pattern (44 bp):
GGTTATCACAATTTCATAGAAAGATCAACAAAATTTCATAGTAT
Found at i:5898 original size:44 final size:44
Alignment explanation
Indices: 5810--5910 Score: 116
Period size: 44 Copynumber: 2.3 Consensus size: 44
5800 GTGTGATCAA
* * * *
5810 CAAAATTTCATAGTTTGGTTACTAACATTTCATAGAAAGGTTAT
1 CAAAATTTCATAGTATGGTTACTAAAATTTCAAAGAAAGATTAT
*
5854 CAAAATTTCTTAGTATGGTTA-TCAAAATTTCAAACG-AAGATTAT
1 CAAAATTTCATAGTATGGTTACT-AAAATTTCAAA-GAAAGATTAT
*
5898 CAAATTTTCATAG
1 CAAAATTTCATAG
5911 GAGATTATCG
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
43 1 0.02
44 46 0.96
45 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.38
Consensus pattern (44 bp):
CAAAATTTCATAGTATGGTTACTAAAATTTCAAAGAAAGATTAT
Found at i:7106 original size:71 final size:69
Alignment explanation
Indices: 6988--7128 Score: 203
Period size: 71 Copynumber: 2.0 Consensus size: 69
6978 AAAACTAACA
* *
6988 ACTAAGGAAAAAATGGTGGGAGCACCATTAATTACATCTCAACGCTAAAATTACATATAAAGACA
1 ACTAAGGAAAAAATGGTAGGAACACCATTAATTACATCTCAACGCTAAAATTACATATAAAGACA
7053 ATGC
66 ATGC
* * *
7057 ACTAAGGAAAAAAAATGGTAGGAACACCATTAATTACATC-CAAATGCTAAAATTGCATATTAAG
1 ACTAAGG--AAAAAATGGTAGGAACACCATTAATTACATCTC-AACGCTAAAATTACATATAAAG
7121 ACAATGC
63 ACAATGC
7128 A
1 A
7129 TTTCAAGCAA
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
69 7 0.11
70 1 0.02
71 56 0.88
ACGTcount: A:0.47, C:0.16, G:0.15, T:0.22
Consensus pattern (69 bp):
ACTAAGGAAAAAATGGTAGGAACACCATTAATTACATCTCAACGCTAAAATTACATATAAAGACA
ATGC
Done.