Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015338.1 Corchorus capsularis cultivar CVL-1 contig15359, 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: 19184
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Found at i:9670 original size:78 final size:77
Alignment explanation
Indices: 9582--9820 Score: 359
Period size: 78 Copynumber: 3.2 Consensus size: 77
9572 TTTTTTTAAC
*
9582 TAAAATAGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGA
1 TAAAATAGTAAAA-TGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
9647 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
9660 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAAT-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
9725 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
* * *
9738 TAAAATAGTAAAA--T-AAA-AT-A-A-TTATAAAGATATTATATTTAATTAAATAAAAATAGAG
1 TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
9796 TTTTTAGTTGAG
66 TTTTTAGTTGAG
9808 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
9821 ACCTAAACAA
Statistics
Matches: 155, Mismatches: 4, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
70 56 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 88 0.57
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (77 bp):
TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
TTTTTAGTTGAG
Found at i:9671 original size:70 final size:71
Alignment explanation
Indices: 9588--9820 Score: 310
Period size: 70 Copynumber: 3.2 Consensus size: 71
9578 TAACTAAAAT
* *
9588 AGTAAAA-TTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTT
1 AGTAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTT
9652 TAGTTG
66 TAGTTG
*
9658 AGTAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
1 AGT-AAA-ACT---A--GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
9723 GAGTTTTTAGTTG
59 GAGTTTTTAGTTG
* * * * *
9736 AGTAAAA-TAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTT
1 AGTAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTT
9800 TAGTTG
66 TAGTTG
9806 AGTAAAACTA-TAAAA
1 AGTAAAACTAGTAAAA
9821 ACCTAAACAA
Statistics
Matches: 147, Mismatches: 7, Indels: 18
0.85 0.04 0.10
Matches are distributed among these distances:
70 71 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 63 0.43
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.37
Consensus pattern (71 bp):
AGTAAAACTAGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTT
TAGTTG
Found at i:13242 original size:271 final size:271
Alignment explanation
Indices: 12759--13302 Score: 1088
Period size: 271 Copynumber: 2.0 Consensus size: 271
12749 TTTACCCATC
12759 AATTTCAACACAATAAAAGAAATTCAAAAAAATTATATAATTTGATGATACAAATTTAAGTTTCG
1 AATTTCAACACAATAAAAGAAATTCAAAAAAATTATATAATTTGATGATACAAATTTAAGTTTCG
12824 ATGATTAGAATTACGAGTTCAGCACTATCTATTTATAGAGTCACGCCATTGTTAATATATCTTAA
66 ATGATTAGAATTACGAGTTCAGCACTATCTATTTATAGAGTCACGCCATTGTTAATATATCTTAA
12889 AGTCAAATGGTTTTGAATGATTTGAAATCATAAATGAGTTTAGCTTCCTTGTTGAATAGATAGTC
131 AGTCAAATGGTTTTGAATGATTTGAAATCATAAATGAGTTTAGCTTCCTTGTTGAATAGATAGTC
12954 CTTGTTTGATCATAATTATAACATGCTAAGATGAATAAAAGGGTGAACAAGAAAATATAATCAAT
196 CTTGTTTGATCATAATTATAACATGCTAAGATGAATAAAAGGGTGAACAAGAAAATATAATCAAT
13019 TAATTGTACAA
261 TAATTGTACAA
13030 AATTTCAACACAATAAAAGAAATTCAAAAAAATTATATAATTTGATGATACAAATTTAAGTTTCG
1 AATTTCAACACAATAAAAGAAATTCAAAAAAATTATATAATTTGATGATACAAATTTAAGTTTCG
13095 ATGATTAGAATTACGAGTTCAGCACTATCTATTTATAGAGTCACGCCATTGTTAATATATCTTAA
66 ATGATTAGAATTACGAGTTCAGCACTATCTATTTATAGAGTCACGCCATTGTTAATATATCTTAA
13160 AGTCAAATGGTTTTGAATGATTTGAAATCATAAATGAGTTTAGCTTCCTTGTTGAATAGATAGTC
131 AGTCAAATGGTTTTGAATGATTTGAAATCATAAATGAGTTTAGCTTCCTTGTTGAATAGATAGTC
13225 CTTGTTTGATCATAATTATAACATGCTAAGATGAATAAAAGGGTGAACAAGAAAATATAATCAAT
196 CTTGTTTGATCATAATTATAACATGCTAAGATGAATAAAAGGGTGAACAAGAAAATATAATCAAT
13290 TAATTGTACAA
261 TAATTGTACAA
13301 AA
1 AA
13303 GGGTACAAAT
Statistics
Matches: 273, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
271 273 1.00
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (271 bp):
AATTTCAACACAATAAAAGAAATTCAAAAAAATTATATAATTTGATGATACAAATTTAAGTTTCG
ATGATTAGAATTACGAGTTCAGCACTATCTATTTATAGAGTCACGCCATTGTTAATATATCTTAA
AGTCAAATGGTTTTGAATGATTTGAAATCATAAATGAGTTTAGCTTCCTTGTTGAATAGATAGTC
CTTGTTTGATCATAATTATAACATGCTAAGATGAATAAAAGGGTGAACAAGAAAATATAATCAAT
TAATTGTACAA
Found at i:13792 original size:2 final size:2
Alignment explanation
Indices: 13785--13818 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
13775 ATTTATGATC
*
13785 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13819 TCATATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:14443 original size:30 final size:30
Alignment explanation
Indices: 14399--14457 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
14389 GTTGAATTTG
14399 TTTTTAAGGTAGTGATTGCAAACTATTTTC
1 TTTTTAAGGTAGTGATTGCAAACTATTTTC
14429 TTTTTGAAGG-AGTGATTGCAAACTATTTT
1 TTTTT-AAGGTAGTGATTGCAAACTATTTT
14458 ATTTCGGTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.46
Consensus pattern (30 bp):
TTTTTAAGGTAGTGATTGCAAACTATTTTC
Found at i:16728 original size:22 final size:22
Alignment explanation
Indices: 16690--16732 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
16680 TTTATTTAAC
16690 TTTATAAATAAAGAAATTAAATA
1 TTTATAAATAAAGAAA-TAAATA
*
16713 TTTAT-AATAAATAAATAAAT
1 TTTATAAATAAAGAAATAAAT
16733 CTATGCACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 9 0.47
23 5 0.26
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
TTTATAAATAAAGAAATAAATA
Done.