Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005022.1 Corchorus capsularis cultivar CVL-1 contig05040, 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: 9468
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:2505 original size:15 final size:15
Alignment explanation
Indices: 2485--2514 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2475 TGGGCGAATT
2485 TGAGACATACTTAAA
1 TGAGACATACTTAAA
*
2500 TGAGACATGCTTAAA
1 TGAGACATACTTAAA
2515 CTTTGAACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (15 bp):
TGAGACATACTTAAA
Found at i:2673 original size:24 final size:24
Alignment explanation
Indices: 2646--2696 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
2636 AATACTTTCA
2646 ACTCCTCATTGGTGAAATTTGAAT
1 ACTCCTCATTGGTGAAATTTGAAT
*
2670 ACTCCTCATTGGTGAAATTTGCAT
1 ACTCCTCATTGGTGAAATTTGAAT
2694 ACT
1 ACT
2697 GCTGAAAGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (24 bp):
ACTCCTCATTGGTGAAATTTGAAT
Found at i:2753 original size:34 final size:34
Alignment explanation
Indices: 2710--2775 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
2700 GAAAGCATTG
2710 ATGCAAGCTTAATTATTAACCCAATATTTGAACA
1 ATGCAAGCTTAATTATTAACCCAATATTTGAACA
2744 ATGCAAGCTTAATTATTAACCCAATATTTGAA
1 ATGCAAGCTTAATTATTAACCCAATATTTGAA
2776 ATGTCAAACG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (34 bp):
ATGCAAGCTTAATTATTAACCCAATATTTGAACA
Found at i:5709 original size:78 final size:77
Alignment explanation
Indices: 5621--5859 Score: 350
Period size: 78 Copynumber: 3.2 Consensus size: 77
5611 TTTTTTTAAC
*
5621 TAAAATAGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGA
1 TAAAATAGTAAAA-TGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
5686 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
*
5699 TAAAATAGTAAAATGGTAAAATATAATAGCTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAAT-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
5764 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
* * *
5777 TAAAATAGTAAAA--T-AAA-AT-A-A-TTATAAAGATATTATATTTAATTAAATAAAAATAGAG
1 TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
5835 TTTTTAGTTGAG
66 TTTTTAGTTGAG
5847 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
5860 ACCTAAACAA
Statistics
Matches: 153, Mismatches: 6, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
70 55 0.36
71 3 0.02
72 1 0.01
73 2 0.01
74 3 0.02
75 1 0.01
77 1 0.01
78 87 0.57
ACGTcount: A:0.50, C:0.01, G:0.13, T:0.37
Consensus pattern (77 bp):
TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
TTTTTAGTTGAG
Found at i:5710 original size:70 final size:71
Alignment explanation
Indices: 5627--5859 Score: 301
Period size: 70 Copynumber: 3.2 Consensus size: 71
5617 TAACTAAAAT
* *
5627 AGTAAAA-TTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTT
1 AGTAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTT
5691 TAGTTG
66 TAGTTG
* *
5697 AGTAAAATAGTAAAATGGTAAAATATAATAGCTATAAGGATATTAGATTTAATTATATAAAAATA
1 AGT-AAA-ACT---A--GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
5762 GAGTTTTTAGTTG
59 GAGTTTTTAGTTG
* * * * *
5775 AGTAAAA-TAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTT
1 AGTAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTT
5839 TAGTTG
66 TAGTTG
5845 AGTAAAACTA-TAAAA
1 AGTAAAACTAGTAAAA
5860 ACCTAAACAA
Statistics
Matches: 145, Mismatches: 9, Indels: 18
0.84 0.05 0.10
Matches are distributed among these distances:
70 70 0.48
71 5 0.03
72 2 0.01
73 1 0.01
75 1 0.01
76 1 0.01
77 3 0.02
78 62 0.43
ACGTcount: A:0.49, C:0.01, G:0.13, T:0.37
Consensus pattern (71 bp):
AGTAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTT
TAGTTG
Found at i:9010 original size:31 final size:30
Alignment explanation
Indices: 8972--9045 Score: 96
Period size: 31 Copynumber: 2.5 Consensus size: 30
8962 AAAAAATGAG
*
8972 TCAGGGACCCAATTGCTCAATTAACTCCACT
1 TCAGGGACCCAATTGCTC-ACTAACTCCACT
* * *
9003 TCAGGGACTCAATTGCTCACTAAGTTCACT
1 TCAGGGACCCAATTGCTCACTAACTCCACT
9033 TCAGGGA-CCAATT
1 TCAGGGACCCAATT
9046 TACACATTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 5 0.13
30 16 0.42
31 17 0.45
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.27
Consensus pattern (30 bp):
TCAGGGACCCAATTGCTCACTAACTCCACT
Found at i:9035 original size:30 final size:30
Alignment explanation
Indices: 8972--9045 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 30
8962 AAAAAATGAG
*
8972 TCAGGGACCCAATTGCTCAATTAACTCCACT
1 TCAGGGA-CCAATTGCTCAACTAACTCCACT
* *
9003 TCAGGGACTCAATTGCTC-ACTAAGTTCACT
1 TCAGGGAC-CAATTGCTCAACTAACTCCACT
9033 TCAGGGACCAATT
1 TCAGGGACCAATT
9046 TACACATTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 5 0.13
30 18 0.46
31 16 0.41
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.27
Consensus pattern (30 bp):
TCAGGGACCAATTGCTCAACTAACTCCACT
Done.