Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015619.1 Corchorus capsularis cultivar CVL-1 contig15640, 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: 114909
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:12748 original size:16 final size:16
Alignment explanation
Indices: 12727--12758 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12717 TGAGTTTCTG
12727 TTTTTATATATGTTCC
1 TTTTTATATATGTTCC
12743 TTTTTATATATGTTCC
1 TTTTTATATATGTTCC
12759 ACCAGGGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.06, T:0.62
Consensus pattern (16 bp):
TTTTTATATATGTTCC
Found at i:15892 original size:19 final size:19
Alignment explanation
Indices: 15865--15934 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
15855 AAAAAGGAAA
15865 TATTATAACTATTTCAATC
1 TATTATAACTATTTCAATC
* *
15884 TATTCTAACTATAAGTC-A-C
1 TATTATAACTAT--TTCAATC
*
15903 ATATTATAACTATTTTAATC
1 -TATTATAACTATTTCAATC
* *
15923 TGTTCTAACTAT
1 TATTATAACTAT
15935 AAGTCAGAAG
Statistics
Matches: 39, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
18 1 0.03
19 23 0.59
20 13 0.33
21 2 0.05
ACGTcount: A:0.36, C:0.16, G:0.03, T:0.46
Consensus pattern (19 bp):
TATTATAACTATTTCAATC
Found at i:15923 original size:39 final size:39
Alignment explanation
Indices: 15864--15940 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
15854 TAAAAAGGAA
15864 ATATTATAACTATTTCAATCTATTCTAACTATAAGTCAC
1 ATATTATAACTATTTCAATCTATTCTAACTATAAGTCAC
* *
15903 ATATTATAACTATTTTAATCTGTTCTAACTATAAGTCA
1 ATATTATAACTATTTCAATCTATTCTAACTATAAGTCA
15941 GAAGGACTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (39 bp):
ATATTATAACTATTTCAATCTATTCTAACTATAAGTCAC
Found at i:26580 original size:18 final size:20
Alignment explanation
Indices: 26557--26594 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
26547 AGCATTTAGG
26557 CTGTC-AATCCCT-CTAATT
1 CTGTCAAATCCCTACTAATT
26575 CTGTCAAATCCCTACTAATT
1 CTGTCAAATCCCTACTAATT
26595 AGTCTGTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 7 0.39
20 6 0.33
ACGTcount: A:0.26, C:0.32, G:0.05, T:0.37
Consensus pattern (20 bp):
CTGTCAAATCCCTACTAATT
Found at i:37772 original size:14 final size:12
Alignment explanation
Indices: 37754--37800 Score: 55
Period size: 11 Copynumber: 4.1 Consensus size: 12
37744 AGAGGAATAT
*
37754 TATATTATAT-A
1 TATAATATATAA
37765 TATAATATATAA
1 TATAATATATAA
37777 TA-AATATATAA
1 TATAATATATAA
37788 TAATAATA-ATAA
1 T-ATAATATATAA
37800 T
1 T
37801 CTAAACAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
11 19 0.59
12 9 0.28
13 4 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TATAATATATAA
Found at i:37785 original size:20 final size:20
Alignment explanation
Indices: 37759--37799 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 20
37749 AATATTATAT
37759 TATATATATAATATATAATAAA
1 TATATA-ATAATA-ATAATAAA
37781 TATATAATAATAATAATAA
1 TATATAATAATAATAATAA
37800 TCTAAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
21 6 0.32
22 6 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TATATAATAATAATAATAAA
Found at i:38871 original size:32 final size:32
Alignment explanation
Indices: 38826--38917 Score: 102
Period size: 28 Copynumber: 3.0 Consensus size: 32
38816 GTAAGTGGTC
38826 TGTTCCAACTTAAACAGGTCTCAGGTTCGAGA
1 TGTTCCAACTTAAACAGGTCTCAGGTTCGAGA
* * * ** *
38858 TGTTCCAATTTAAATAAGTCTC--GAAC--CA
1 TGTTCCAACTTAAACAGGTCTCAGGTTCGAGA
38886 TGTTCCAACTTAAACAGGTCTCAGGTTCGAGA
1 TGTTCCAACTTAAACAGGTCTCAGGTTCGAGA
38918 CCTTGCGTAC
Statistics
Matches: 44, Mismatches: 12, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
28 20 0.45
30 4 0.09
32 20 0.45
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.29
Consensus pattern (32 bp):
TGTTCCAACTTAAACAGGTCTCAGGTTCGAGA
Found at i:41237 original size:25 final size:25
Alignment explanation
Indices: 41192--41249 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
41182 CGCTCATGTT
41192 CTTGCGTTTGGCAAACGAGCCTATG
1 CTTGCGTTTGGCAAACGAGCCTATG
*
41217 CTTGCGTTTGGCAAACGAGCCTGTG
1 CTTGCGTTTGGCAAACGAGCCTATG
*
41242 CTCGCGTT
1 CTTGCGTT
41250 GAAAAACACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.29
Consensus pattern (25 bp):
CTTGCGTTTGGCAAACGAGCCTATG
Found at i:47783 original size:10 final size:10
Alignment explanation
Indices: 47768--47793 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
47758 AGTTGCTGCC
47768 AAATTCCAGA
1 AAATTCCAGA
47778 AAATTCCAGA
1 AAATTCCAGA
47788 AAATTC
1 AAATTC
47794 TAGAGTCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (10 bp):
AAATTCCAGA
Found at i:49955 original size:20 final size:20
Alignment explanation
Indices: 49930--49969 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
49920 TTCACTATAC
49930 CCAATAAACGTTTGTGAGAT
1 CCAATAAACGTTTGTGAGAT
*
49950 CCAATAAACGTTTGTTAGAT
1 CCAATAAACGTTTGTGAGAT
49970 TACGGAGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (20 bp):
CCAATAAACGTTTGTGAGAT
Found at i:57226 original size:31 final size:29
Alignment explanation
Indices: 57187--57314 Score: 117
Period size: 31 Copynumber: 4.4 Consensus size: 29
57177 GTCCGACGTG
*
57187 GCACGCCACGTGTACCAAAAAGTGACATGT
1 GCACGCCACATGTACCAAAAAGTGACA-GT
57217 GACACGCCACATGTACCAAAAA--GAC-GT
1 G-CACGCCACATGTACCAAAAAGTGACAGT
*
57244 ----GCCACATGTACCAAAAAGTGACACAT
1 GCACGCCACATGTACCAAAAAGTGACA-GT
*
57270 GTCACGCCACGTGTACCAAAAAGTGACACGT
1 G-CACGCCACATGTACCAAAAAGTGACA-GT
*
57301 GGCATGCCACATGT
1 -GCACGCCACATGT
57315 TTCAAAAAAT
Statistics
Matches: 81, Mismatches: 6, Indels: 21
0.75 0.06 0.19
Matches are distributed among these distances:
22 17 0.21
24 3 0.04
26 1 0.01
27 2 0.02
29 3 0.04
30 1 0.01
31 53 0.65
32 1 0.01
ACGTcount: A:0.35, C:0.28, G:0.21, T:0.16
Consensus pattern (29 bp):
GCACGCCACATGTACCAAAAAGTGACAGT
Found at i:57266 original size:53 final size:53
Alignment explanation
Indices: 57191--57292 Score: 159
Period size: 53 Copynumber: 1.9 Consensus size: 53
57181 GACGTGGCAC
* **
57191 GCCACGTGTACCAAAAAGTGACATGTGACACGCCACATGTACCAAAAAGACGT
1 GCCACATGTACCAAAAAGTGACACATGACACGCCACATGTACCAAAAAGACGT
* *
57244 GCCACATGTACCAAAAAGTGACACATGTCACGCCACGTGTACCAAAAAG
1 GCCACATGTACCAAAAAGTGACACATGACACGCCACATGTACCAAAAAG
57293 TGACACGTGG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.38, C:0.27, G:0.20, T:0.15
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGACACGCCACATGTACCAAAAAGACGT
Found at i:57321 original size:31 final size:31
Alignment explanation
Indices: 57243--57332 Score: 108
Period size: 31 Copynumber: 2.9 Consensus size: 31
57233 CAAAAAGACG
*
57243 TGCCACATGTACCAAAAAGTGACACATGTCA
1 TGCCACATGTACCAAAAAGTGACACATGGCA
* * *
57274 CGCCACGTGTACCAAAAAGTGACACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACATGGCA
** * *
57305 TGCCACATGTTTCAAAAAATGGCACATG
1 TGCCACATGTACCAAAAAGTGACACATG
57333 CACAAAAGGA
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (31 bp):
TGCCACATGTACCAAAAAGTGACACATGGCA
Found at i:58535 original size:25 final size:25
Alignment explanation
Indices: 58474--58535 Score: 58
Period size: 25 Copynumber: 2.4 Consensus size: 25
58464 AGTGAAGACT
58474 AGTTTATAGAAAAAATATTTAAAATTAAA
1 AGTTTAT--AAAAAATATTT--AATTAAA
58503 A-TTT-TAAAAAATATTT-ATTAGAA
1 AGTTTATAAAAAATATTTAATTA-AA
58526 AGTTTATAAA
1 AGTTTATAAA
58536 TCAAAGTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
22 4 0.13
23 3 0.10
24 3 0.10
25 15 0.50
27 1 0.03
28 3 0.10
29 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (25 bp):
AGTTTATAAAAAATATTTAATTAAA
Found at i:63769 original size:21 final size:23
Alignment explanation
Indices: 63741--63788 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
63731 GATAAGGGTG
* *
63741 AATATATAATTTGATCCATATAT
1 AATATAGATTTTGATCCATATAT
* *
63764 AATATAGATTTTTATCTATATAT
1 AATATAGATTTTGATCCATATAT
63787 AA
1 AA
63789 ATTTTTCTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (23 bp):
AATATAGATTTTGATCCATATAT
Found at i:64946 original size:24 final size:24
Alignment explanation
Indices: 64914--64964 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
64904 TTAGTTGAAC
64914 ATGGAAATGCATGAACAAGCAATT
1 ATGGAAATGCATGAACAAGCAATT
*
64938 ATGGAAATGCATGAATAAGCAATT
1 ATGGAAATGCATGAACAAGCAATT
64962 ATG
1 ATG
64965 AGCCACTGAC
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:0.45, C:0.10, G:0.22, T:0.24
Consensus pattern (24 bp):
ATGGAAATGCATGAACAAGCAATT
Found at i:73814 original size:14 final size:14
Alignment explanation
Indices: 73795--73825 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
73785 ACGACGACGC
73795 AGTTGACAGTGCGG
1 AGTTGACAGTGCGG
73809 AGTTGACAGTGCGG
1 AGTTGACAGTGCGG
73823 AGT
1 AGT
73826 GGGTGGAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.23, C:0.13, G:0.42, T:0.23
Consensus pattern (14 bp):
AGTTGACAGTGCGG
Found at i:82686 original size:5 final size:5
Alignment explanation
Indices: 82676--82709 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
82666 CTACTCTTAA
* *
82676 TTTTC TTTTC TTTTC TTTTC TTTTT TTTTG TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
82710 TGTTTATTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (5 bp):
TTTTC
Found at i:97928 original size:2 final size:2
Alignment explanation
Indices: 97921--97947 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
97911 TGAATATAGA
97921 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 A
97948 CTTTTATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:113576 original size:2 final size:2
Alignment explanation
Indices: 113569--113597 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
113559 TACAATACAC
113569 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
113598 TCTGTCATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.