Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009794.1 Corchorus capsularis cultivar CVL-1 contig09815, 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: 21689
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:461 original size:2 final size:2
Alignment explanation
Indices: 449--477 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
439 TAGCTAGTTC
449 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
478 TGTAATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5330 original size:21 final size:21
Alignment explanation
Indices: 5304--5352 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
5294 GCACTGGAGG
* * *
5304 ACATGGGTCGCGAGGCAAACC
1 ACATGGGGCGCCAAGCAAACC
*
5325 ACATGGGGCGCCAAGCATACC
1 ACATGGGGCGCCAAGCAAACC
5346 ACATGGG
1 ACATGGG
5353 CCCCTAGCTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.33, T:0.10
Consensus pattern (21 bp):
ACATGGGGCGCCAAGCAAACC
Found at i:13205 original size:30 final size:30
Alignment explanation
Indices: 13164--13246 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 30
13154 ACAAACAAAC
* *
13164 ATTCTATCAATCAATTAACAA-ATATTTGCA
1 ATTCAATCAATCAATTAACAAGATA-TAGCA
*
13194 ATTCAATCAATCAA-TAGCAAGATATAGCA
1 ATTCAATCAATCAATTAACAAGATATAGCA
*
13223 ATTCAAATCAA-CAATTGA-AAGATA
1 ATTC-AATCAATCAATTAACAAGATA
13247 GAATTAACAA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
29 22 0.49
30 23 0.51
ACGTcount: A:0.48, C:0.16, G:0.07, T:0.29
Consensus pattern (30 bp):
ATTCAATCAATCAATTAACAAGATATAGCA
Found at i:13237 original size:29 final size:29
Alignment explanation
Indices: 13191--13246 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
13181 ACAAATATTT
*
13191 GCAATTCAATCAATCAATAGCAAGATATA
1 GCAATTCAATCAATCAATAGAAAGATATA
*
13220 GCAATTCAAATCAA-CAATTGAAAGATA
1 GCAATTC-AATCAATCAATAGAAAGATA
13247 GAATTAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.50, C:0.16, G:0.11, T:0.23
Consensus pattern (29 bp):
GCAATTCAATCAATCAATAGAAAGATATA
Found at i:18309 original size:21 final size:22
Alignment explanation
Indices: 18264--18310 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
18254 AAGCACAATT
18264 GAAATCGAAAATTACAAGCAAA
1 GAAATCGAAAATTACAAGCAAA
18286 GAAATCGAAAAATTA-AAG-AAA
1 GAAATCG-AAAATTACAAGCAAA
18307 GAAA
1 GAAA
18311 AGGAGAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 7 0.29
22 10 0.42
23 7 0.29
ACGTcount: A:0.64, C:0.09, G:0.15, T:0.13
Consensus pattern (22 bp):
GAAATCGAAAATTACAAGCAAA
Found at i:18491 original size:19 final size:20
Alignment explanation
Indices: 18453--18493 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
18443 AGGGGAATCG
18453 GGAAAAGAAAGAAAAGAAAA
1 GGAAAAGAAAGAAAAGAAAA
*
18473 GGAAAAGAAA-AAAATAAAA
1 GGAAAAGAAAGAAAAGAAAA
18492 GG
1 GG
18494 TTTGTGCGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.02
Consensus pattern (20 bp):
GGAAAAGAAAGAAAAGAAAA
Found at i:20305 original size:21 final size:19
Alignment explanation
Indices: 20260--20358 Score: 56
Period size: 21 Copynumber: 4.7 Consensus size: 19
20250 ACTCTTTGAA
* *
20260 TTACTGATCACCTTTTACTC
1 TTACTGATTA-CTTTGACTC
20280 TTTACTGATTACTAATTGACTC
1 -TTACTGATTACT--TTGACTC
*
20302 TTACTAATCATCACTTTG-CTC
1 TTACTGAT--T-ACTTTGACTC
* *
20323 TTACTGGTTACTGTTTTACTC
1 TTACTGATTAC--TTTGACTC
20344 TTACTGATTATCTTT
1 TTACTGATTA-CTTT
20359 TATCGATTAC
Statistics
Matches: 62, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
18 2 0.03
19 1 0.02
20 8 0.13
21 37 0.60
22 10 0.16
23 1 0.02
24 3 0.05
ACGTcount: A:0.21, C:0.22, G:0.08, T:0.48
Consensus pattern (19 bp):
TTACTGATTACTTTGACTC
Found at i:20392 original size:16 final size:16
Alignment explanation
Indices: 20371--20404 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
20361 TCGATTACTT
*
20371 TTTTACTCTTTGCTGA
1 TTTTACTCTTTACTGA
20387 TTTTACTCTTTACTGA
1 TTTTACTCTTTACTGA
20403 TT
1 TT
20405 ACCTTCTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.18, G:0.09, T:0.59
Consensus pattern (16 bp):
TTTTACTCTTTACTGA
Found at i:20491 original size:35 final size:34
Alignment explanation
Indices: 20448--20529 Score: 92
Period size: 35 Copynumber: 2.4 Consensus size: 34
20438 GGTTACTATT
** *
20448 TTACTCTTTACTCTTTACTTTTTTTTCTTTACTGA
1 TTACTCTTTACTCTTTAC-CATTTTACTTTACTGA
* * *
20483 TTATTCTTTTACTTTTTACCATTTTACTTTGCTGA
1 TTACTC-TTTACTCTTTACCATTTTACTTTACTGA
20518 TTACTCTTTACT
1 TTACTCTTTACT
20530 TTACTCTCTA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
34 6 0.15
35 22 0.56
36 11 0.28
ACGTcount: A:0.16, C:0.20, G:0.04, T:0.61
Consensus pattern (34 bp):
TTACTCTTTACTCTTTACCATTTTACTTTACTGA
Found at i:20615 original size:82 final size:77
Alignment explanation
Indices: 20393--20666 Score: 189
Period size: 82 Copynumber: 3.4 Consensus size: 77
20383 CTGATTTTAC
* * * *
20393 TCTTTACTGATTAC-CTTCTTACTTTTTA--ATGATTACCATTTTGCTGGTTACTATTTTACTCT
1 TCTTTACTGATTACTCTT-TTACTTTTTACCAT-TTTA-C--TTTACTGATTACTCTTTTACTCT
**
20455 TTACTCTTTACTTTTTTT
61 TTACTCTTTAC-CATTTT
* * *
20473 TCTTTACTGATTATTCTTTTACTTTTTACCATTTTACTTTGCTGATTACTCTTTACTTTACTCTC
1 TCTTTACTGATTACTCTTTTACTTTTTACCATTTTACTTTACTGATTACTC--T--TTTACTCTT
20538 TACTCTTTACCATTTT
62 TACTCTTTACCATTTT
*
20554 TCTTTACTGATTACTCTTGTATGAATACTCTTTTA-C-TTTTTCTTTACTGATTACTCTTTTACT
1 TCTTTACTGATTACTC-T-T-T---TACT-TTTTACCATTTTACTTTACTGATTACTCTTTTACT
* **
20617 TTTTACTGATTACCATTTT
59 CTTTACTCTTTACCATTTT
* * * *
20636 ACTCTTTTCTAATTACTATTTTACCTTTTAC
1 --TCTTTACTGATTACTCTTTTACTTTTTAC
20667 TGATTACCTT
Statistics
Matches: 159, Mismatches: 18, Indels: 36
0.75 0.08 0.17
Matches are distributed among these distances:
77 5 0.03
78 15 0.09
80 25 0.16
81 26 0.16
82 43 0.27
83 2 0.01
84 15 0.09
86 18 0.11
87 5 0.03
88 5 0.03
ACGTcount: A:0.19, C:0.20, G:0.05, T:0.57
Consensus pattern (77 bp):
TCTTTACTGATTACTCTTTTACTTTTTACCATTTTACTTTACTGATTACTCTTTTACTCTTTACT
CTTTACCATTTT
Found at i:20624 original size:22 final size:22
Alignment explanation
Indices: 20596--20688 Score: 118
Period size: 22 Copynumber: 4.2 Consensus size: 22
20586 TTACTTTTTC
20596 TTTACTGATTACTC-TTTTACTT
1 TTTACTGATTAC-CATTTTACTT
20618 TTTACTGATTACCATTTTACTCT
1 TTTACTGATTACCATTTTACT-T
* * *
20641 TTT-CTAATTACTATTTTACCT
1 TTTACTGATTACCATTTTACTT
*
20662 TTTACTGATTACCTTTTTACTT
1 TTTACTGATTACCATTTTACTT
20684 TTTAC
1 TTTAC
20689 CATTTCACCT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
21 5 0.08
22 52 0.85
23 4 0.07
ACGTcount: A:0.20, C:0.19, G:0.03, T:0.57
Consensus pattern (22 bp):
TTTACTGATTACCATTTTACTT
Found at i:20658 original size:44 final size:44
Alignment explanation
Indices: 20594--20686 Score: 134
Period size: 44 Copynumber: 2.1 Consensus size: 44
20584 TTTTACTTTT
* * * *
20594 TCTTTACTGATTACTCTTTTACTTTTTACTGATTACCATTTTAC
1 TCTTTTCTAATTACTATTTTACCTTTTACTGATTACCATTTTAC
*
20638 TCTTTTCTAATTACTATTTTACCTTTTACTGATTACCTTTTTAC
1 TCTTTTCTAATTACTATTTTACCTTTTACTGATTACCATTTTAC
20682 T-TTTT
1 TCTTTT
20687 ACCATTTCAC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 4 0.09
44 40 0.91
ACGTcount: A:0.19, C:0.19, G:0.03, T:0.58
Consensus pattern (44 bp):
TCTTTTCTAATTACTATTTTACCTTTTACTGATTACCATTTTAC
Found at i:20821 original size:22 final size:21
Alignment explanation
Indices: 20796--20923 Score: 118
Period size: 22 Copynumber: 6.0 Consensus size: 21
20786 CCCTTTCAGA
20796 TACCTTTTCACTTTTTACTGAT
1 TACCTTTT-ACTTTTTACTGAT
20818 TACCTTTTACTTTTTACTG-T
1 TACCTTTTACTTTTTACTGAT
* *
20838 T-CACTATTACTTCTTACTGAT
1 TAC-CTTTTACTTTTTACTGAT
* * *
20859 T-TCTATTACTCTTTACTGAT
1 TACCTTTTACTTTTTACTGAT
*
20879 TACCATTTTACTCTTTACTGAT
1 TACC-TTTTACTTTTTACTGAT
* * *
20901 TGCCATTATACCTTTTACTGAT
1 TACC-TTTTACTTTTTACTGAT
20923 T
1 T
20924 GCATCTTTCT
Statistics
Matches: 91, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.01
20 33 0.36
21 14 0.15
22 43 0.47
ACGTcount: A:0.20, C:0.22, G:0.05, T:0.52
Consensus pattern (21 bp):
TACCTTTTACTTTTTACTGAT
Found at i:20847 original size:20 final size:20
Alignment explanation
Indices: 20805--20901 Score: 97
Period size: 20 Copynumber: 4.7 Consensus size: 20
20795 ATACCTTTTC
*
20805 ACTTTTTACTGATTACCTTTT
1 ACTTTTTACTGATTA-CTATT
20826 ACTTTTTACTG-TTCACTATT
1 ACTTTTTACTGATT-ACTATT
* *
20846 ACTTCTTACTGATTTCTATT
1 ACTTTTTACTGATTACTATT
* *
20866 ACTCTTTACTGATTACCATTTT
1 ACTTTTTACTGATTA-C-TATT
*
20888 ACTCTTTACTGATT
1 ACTTTTTACTGATT
20902 GCCATTATAC
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
20 33 0.51
21 15 0.23
22 17 0.26
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.54
Consensus pattern (20 bp):
ACTTTTTACTGATTACTATT
Done.