Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006060.1 Corchorus capsularis cultivar CVL-1 contig06078, 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: 36143
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:7565 original size:28 final size:28
Alignment explanation
Indices: 7495--7566 Score: 94
Period size: 28 Copynumber: 2.5 Consensus size: 28
7485 TAACCTGAAC
7495 GGGCAAAAAGTCTCAAAATTGAAGTTTAA
1 GGGCAAAAAGTC-CAAAATTGAAGTTTAA
7524 GGGCAAAATA-TCCAAAATTGAAG-TTAA
1 GGGCAAAA-AGTCCAAAATTGAAGTTTAA
*
7551 GGGACAAAACGTCCAA
1 GGG-CAAAAAGTCCAA
7567 CCCCTAAAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
27 7 0.18
28 21 0.54
29 10 0.26
30 1 0.03
ACGTcount: A:0.46, C:0.14, G:0.21, T:0.19
Consensus pattern (28 bp):
GGGCAAAAAGTCCAAAATTGAAGTTTAA
Found at i:13593 original size:12 final size:12
Alignment explanation
Indices: 13576--13618 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
13566 CATAATACTC
*
13576 ATCTATCTATAT
1 ATCTATATATAT
13588 ATCTATATATAT
1 ATCTATATATAT
*
13600 ATATATATATAT
1 ATCTATATATAT
13612 A-CTATAT
1 ATCTATAT
13619 TAAAAAGTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 5 0.18
12 23 0.82
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (12 bp):
ATCTATATATAT
Found at i:13596 original size:2 final size:2
Alignment explanation
Indices: 13583--13618 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
13573 CTCATCTATC
*
13583 TA TA TA TC TA TA TA TA TA TA TA TA TA TA TA CTA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T
13619 TAAAAAGTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13788 original size:70 final size:69
Alignment explanation
Indices: 13713--13938 Score: 308
Period size: 70 Copynumber: 3.1 Consensus size: 69
13703 GGTTTTTATA
* *
13713 ATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAACTATTTTATT
1 ATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATC-TTATAACTATTTTATT
13778 TTACT
65 TTACT
13783 ATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATACTTATAACTATTATATT
1 ATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATAT-CTTATAAC-----TATT
13848 TTACCATTTTACT
60 TT---ATTTTACT
* *
13861 ATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATTACTATTATATT
1 ATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATAT-CTTATAACTATTTTATT
*
13926 TTACC
65 TTACT
13931 ATTTTACT
1 ATTTTACT
13939 ATTTTAATTA
Statistics
Matches: 141, Mismatches: 6, Indels: 18
0.85 0.04 0.11
Matches are distributed among these distances:
70 67 0.48
71 1 0.01
73 5 0.04
75 6 0.04
78 62 0.44
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (69 bp):
ATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTATAACTATTTTATTT
TACT
Found at i:13788 original size:78 final size:77
Alignment explanation
Indices: 13713--13944 Score: 354
Period size: 78 Copynumber: 3.1 Consensus size: 77
13703 GGTTTTTATA
* *
13713 ATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTT-T-A-TA--ACTATT
1 ATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTATAACTATTA-TATT
13773 TT---ATTTTACT
65 TTACCATTTTACT
13783 ATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATACTTATAACTATTATATT
1 ATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATAT-CTTATAACTATTATATT
13848 TTACCATTTTACT
65 TTACCATTTTACT
*
13861 ATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATTACTATTATATT
1 ATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATAT-CTTATAACTATTATATT
13926 TTACCATTTTACT
65 TTACCATTTTACT
13939 ATTTTA
1 ATTTTA
13945 ATTAAAAAAC
Statistics
Matches: 149, Mismatches: 4, Indels: 10
0.91 0.02 0.06
Matches are distributed among these distances:
70 45 0.30
71 3 0.02
72 1 0.01
73 1 0.01
74 2 0.01
75 6 0.04
76 1 0.01
78 90 0.60
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (77 bp):
ATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTATAACTATTATATTT
TACCATTTTACT
Found at i:15526 original size:31 final size:31
Alignment explanation
Indices: 15491--15551 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
15481 AACTGAACAA
15491 ACTCAAACATCCAAGATCTAAAGATCTGGAG
1 ACTCAAACATCCAAGATCTAAAGATCTGGAG
15522 ACTCAAACATCCAAGATCTAAAGATCTGGA
1 ACTCAAACATCCAAGATCTAAAGATCTGGA
15552 AACTGATAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.43, C:0.23, G:0.15, T:0.20
Consensus pattern (31 bp):
ACTCAAACATCCAAGATCTAAAGATCTGGAG
Found at i:20729 original size:31 final size:30
Alignment explanation
Indices: 20694--20795 Score: 84
Period size: 31 Copynumber: 3.4 Consensus size: 30
20684 ATGAGATAGG
20694 CCCTTATTTGAGCATTTTGGCAAACGTTAGA
1 CCCTTATTTGAGCATTTT-GCAAACGTTAGA
* ** *** *
20725 CCCTTGTTTG-GTCAAATT-CAAA-GACCGGG
1 CCCTTATTTGAG-CATTTTGCAAACG-TTAGA
20754 CCCTTATTTGAGCATTTTGACAAACGTTAGA
1 CCCTTATTTGAGCATTTTG-CAAACGTTAGA
20785 CCCTTATTTGA
1 CCCTTATTTGA
20796 ACAATTAACC
Statistics
Matches: 51, Mismatches: 14, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
28 1 0.02
29 18 0.35
30 2 0.04
31 29 0.57
32 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (30 bp):
CCCTTATTTGAGCATTTTGCAAACGTTAGA
Found at i:21920 original size:27 final size:26
Alignment explanation
Indices: 21869--21923 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
21859 ATGGAAAACA
*
21869 TTTTGAACCACAATTCGAGTATTTTT
1 TTTTGAACCACAATTCCAGTATTTTT
*
21895 TTTTGAACATACAATTCCA-TATTTTT
1 TTTTGAAC-CACAATTCCAGTATTTTT
21921 TTT
1 TTT
21924 ATTGTCTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.51
Consensus pattern (26 bp):
TTTTGAACCACAATTCCAGTATTTTT
Found at i:35909 original size:48 final size:48
Alignment explanation
Indices: 35854--35948 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 48
35844 GAGGATAAGA
35854 TATAAATATAGTTTAAATATAAGAAAATGTGAAAATAACCAA-ATTTTT
1 TATAAATATAGTTTAAATATAA-AAAATGTGAAAATAACCAATATTTTT
* * *
35902 TATAAATATAGTTTAAATATCAAATATGTGAAAATAGCCAATATTTT
1 TATAAATATAGTTTAAATATAAAAAATGTGAAAATAACCAATATTTT
35949 ATGGGGTCAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
47 17 0.40
48 26 0.60
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.37
Consensus pattern (48 bp):
TATAAATATAGTTTAAATATAAAAAATGTGAAAATAACCAATATTTTT
Done.