Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003015.1 Corchorus capsularis cultivar CVL-1 contig03023, 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: 8073
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:3256 original size:70 final size:70
Alignment explanation
Indices: 3180--3404 Score: 315
Period size: 70 Copynumber: 3.1 Consensus size: 70
3170 TAACTAAAAT
*
3180 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGAGTTTTT
1 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
3245 AGTTG
66 AGTTG
3250 AGTAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
1 AGT-AAA-A-T----T-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATA
3315 GAGTTTTTAGTTG
58 GAGTTTTTAGTTG
* * * * * *
3328 AGTAAAATAGTAAAATAAAATAATTATAAAGATATTATATTTAATTAAATAAAAATAGAGTTTTT
1 AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
3393 AGTTG
66 AGTTG
3398 AGTAAAA
1 AGTAAAA
3405 CTATAAGAAG
Statistics
Matches: 140, Mismatches: 7, Indels: 16
0.86 0.04 0.10
Matches are distributed among these distances:
70 66 0.47
71 3 0.02
72 1 0.01
73 1 0.01
75 1 0.01
76 1 0.01
77 4 0.03
78 63 0.45
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (70 bp):
AGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
AGTTG
Found at i:3257 original size:78 final size:77
Alignment explanation
Indices: 3174--3404 Score: 359
Period size: 78 Copynumber: 3.1 Consensus size: 77
3164 TTTTTTTAAC
*
3174 TAAAATAGTAAAATTGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATTGA
1 TAAAATAGTAAAA-TGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
3239 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
3252 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAAT-GTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
3317 GTTTTTAGTTGAG
65 GTTTTTAGTTGAG
* * *
3330 TAAAATAGTAAAA--T-AAA-AT-A-A-TTATAAAGATATTATATTTAATTAAATAAAAATAGAG
1 TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
3388 TTTTTAGTTGAG
66 TTTTTAGTTGAG
3400 TAAAA
1 TAAAA
3405 CTATAAGAAG
Statistics
Matches: 148, Mismatches: 4, Indels: 10
0.91 0.02 0.06
Matches are distributed among these distances:
70 51 0.34
71 1 0.01
72 1 0.01
73 2 0.01
74 3 0.02
75 1 0.01
77 1 0.01
78 88 0.59
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (77 bp):
TAAAATAGTAAAATGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
TTTTTAGTTGAG
Found at i:3557 original size:11 final size:11
Alignment explanation
Indices: 3514--3551 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3504 AGTATAGATA
*
3514 AAATAAATTAT
1 AAATTAATTAT
3525 CAAA-TAATTAT
1 -AAATTAATTAT
3536 AAATTAATTAT
1 AAATTAATTAT
3547 AAATT
1 AAATT
3552 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:3731 original size:14 final size:14
Alignment explanation
Indices: 3712--3739 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3702 CTTACTTTGT
3712 TATGTAATAAGATG
1 TATGTAATAAGATG
3726 TATGTAATAAGATG
1 TATGTAATAAGATG
3740 AATGAGAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (14 bp):
TATGTAATAAGATG
Found at i:3909 original size:41 final size:42
Alignment explanation
Indices: 3847--3925 Score: 151
Period size: 41 Copynumber: 1.9 Consensus size: 42
3837 TCATTTCTAA
3847 TTAACTGAATCTTTCTTAAAAGAATTTATAAAATAAAATTTC
1 TTAACTGAATCTTTCTTAAAAGAATTTATAAAATAAAATTTC
3889 TTAACTGAAT-TTTCTTAAAAGAATTTATAAAATAAAA
1 TTAACTGAATCTTTCTTAAAAGAATTTATAAAATAAAA
3926 CAGCGTCACG
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
41 27 0.73
42 10 0.27
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.39
Consensus pattern (42 bp):
TTAACTGAATCTTTCTTAAAAGAATTTATAAAATAAAATTTC
Found at i:5816 original size:2 final size:2
Alignment explanation
Indices: 5809--5841 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5799 ATTTTCCCTC
5809 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5842 AAATTGCCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.