Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01002801.1 Corchorus capsularis cultivar CVL-1 contig02809, 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: 7406
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:3744 original size:2 final size:2
Alignment explanation
Indices: 3725--3830 Score: 65
Period size: 2 Copynumber: 59.0 Consensus size: 2
3715 TATATTTTTG
* * * *
3725 AT AT AT -T AT A- AT AT -T AT AT AT AT AA AC AA AT -T AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
3763 A- AT AT A- AA AT AT AA AT AT A- AT AT AT AT AT A- AC AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3800 AT AT AT AT AT AT A- AT AT AT AT A- AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3831 TTCGTCGGTT
Statistics
Matches: 82, Mismatches: 10, Indels: 24
0.71 0.09 0.21
Matches are distributed among these distances:
1 12 0.15
2 70 0.85
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:3779 original size:18 final size:17
Alignment explanation
Indices: 3725--3822 Score: 85
Period size: 18 Copynumber: 5.6 Consensus size: 17
3715 TATATTTTTG
* *
3725 ATATATTATAATATTATAT
1 ATATAATATAA-A-TATAA
*
3744 ATATAA-ACAAAT-TAA
1 ATATAATATAAATATAA
3759 ATATAATATAAAATATAA
1 ATATAATAT-AAATATAA
*
3777 ATATAATATATATATAA
1 ATATAATATAAATATAA
*
3794 CATATAATATATATATATA
1 -ATATAATATAAATATA-A
3813 ATAT-ATATAA
1 ATATAATATAA
3823 TAATATATTT
Statistics
Matches: 68, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
15 8 0.12
16 2 0.03
17 17 0.25
18 35 0.51
19 6 0.09
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAATATAAATATAA
Found at i:3791 original size:29 final size:30
Alignment explanation
Indices: 3731--3830 Score: 74
Period size: 29 Copynumber: 3.5 Consensus size: 30
3721 TTTGATATAT
*
3731 TATAATAT--TATATATATAA-ACA-AAT-
1 TATAATATAATATATATATAATATATAATA
*
3756 TA-AATATAATATAAAATATAA-ATATAATA
1 TATAATATAATAT-ATATATAATATATAATA
*
3785 TAT-ATATAACATATAATATATATATATAATA
1 TATAATATAATATAT-ATATA-ATATATAATA
3816 TAT-ATAATAATATAT
1 TATAAT-ATAATATAT
3831 TTCGTCGGTT
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
24 5 0.08
25 2 0.03
26 3 0.05
27 9 0.15
28 4 0.07
29 15 0.25
30 1 0.02
31 13 0.22
32 8 0.13
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (30 bp):
TATAATATAATATATATATAATATATAATA
Found at i:3799 original size:31 final size:32
Alignment explanation
Indices: 3764--3830 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
3754 ATTAAATATA
3764 ATATAAAATATAAATATAATATATAT-ATAAC
1 ATATAAAATATAAATATAATATATATAATAAC
* * *
3795 ATATAATATATATATATAATATATATAATAAT
1 ATATAAAATATAAATATAATATATATAATAAC
3827 ATAT
1 ATAT
3831 TTCGTCGGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 24 0.75
32 8 0.25
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (32 bp):
ATATAAAATATAAATATAATATATATAATAAC
Found at i:4166 original size:20 final size:20
Alignment explanation
Indices: 4140--4195 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
4130 TAGGAGATTT
*
4140 ATCAAAATTTCATAGTGTGG
1 ATCAAAATTTCATAGTGTAG
*
4160 TTCAAAATTTTCAGT-GTGTAG
1 ATCAAAA-TTTCA-TAGTGTAG
4181 ATCAAAATTTCATAG
1 ATCAAAATTTCATAG
4196 GGAGGTTAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 1 0.03
20 12 0.40
21 16 0.53
22 1 0.03
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.38
Consensus pattern (20 bp):
ATCAAAATTTCATAGTGTAG
Found at i:4296 original size:22 final size:22
Alignment explanation
Indices: 4260--4318 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
4250 AAAATTTGTG
*
4260 GTTT-TCAAAATTTTTTAGGGAA
1 GTTTATCAAAATTTTATAGGG-A
4282 GTTTATCAAAATTTTATAGGGA
1 GTTTATCAAAATTTTATAGGGA
*
4304 GAATTATCAAAATTT
1 G-TTTATCAAAATTT
4319 CATAACGAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 6 0.18
23 27 0.82
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.42
Consensus pattern (22 bp):
GTTTATCAAAATTTTATAGGGA
Found at i:4525 original size:23 final size:22
Alignment explanation
Indices: 4483--4525 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
4473 TCTCATATGG
**
4483 AGGTTAACAAAATTTTATAAAA
1 AGGTTAACAAAATTCCATAAAA
4505 AGGTTAACTAAAATTCCATAA
1 AGGTTAAC-AAAATTCCATAA
4526 TAGATTCTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.30
Consensus pattern (22 bp):
AGGTTAACAAAATTCCATAAAA
Found at i:4580 original size:22 final size:22
Alignment explanation
Indices: 4552--4613 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
4542 CATAGTGTCG
*
4552 TTATCAAAAGTTCTTAG-GAAGA
1 TTATCAAAAGTTCATAGAG-AGA
* *
4574 TTATCAAAATTTCATAGAGAGT
1 TTATCAAAAGTTCATAGAGAGA
*
4596 TTATCAAAATGTTAATAG
1 TTATCAAAA-GTTCATAG
4614 GGTAATTATC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
22 26 0.79
23 7 0.21
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (22 bp):
TTATCAAAAGTTCATAGAGAGA
Found at i:5086 original size:8 final size:8
Alignment explanation
Indices: 5053--5094 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
5043 TGTATTTAAA
5053 ATATATTT
1 ATATATTT
5061 AT-TATTT
1 ATATATTT
*
5068 ATTTATTT
1 ATATATTT
*
5076 ATATATAT
1 ATATATTT
5084 ATATA-TT
1 ATATATTT
5091 ATAT
1 ATAT
5095 CTAAAATAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
7 12 0.40
8 18 0.60
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATATATTT
Done.