Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014454.1 Corchorus capsularis cultivar CVL-1 contig14475, 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: 64349
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:376 original size:109 final size:109
Alignment explanation
Indices: 242--516 Score: 428
Period size: 109 Copynumber: 2.5 Consensus size: 109
232 AAAATATATA
242 TATAAA-ATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
1 TATAAAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
*
305 AAAAAATTTTAATATATCCAATTTTTTTGGTAAAAATAAAGTAAT
65 AAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
*
350 TATAACGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
1 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
* *
415 AAAAATTTTAGTATATCCAAATTTTTTGGTTAAAATAAAGTAAT
66 AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
* *
459 TATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTAGTAGAATAAAA
1 TATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTAGTAGAATAAAA
517 CTATAATAGT
Statistics
Matches: 153, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
108 5 0.03
109 116 0.76
110 3 0.02
111 1 0.01
114 28 0.18
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (109 bp):
TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
Found at i:1976 original size:2 final size:2
Alignment explanation
Indices: 1964--1997 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1954 TCACTACTGT
1964 TA TA TA T- 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 TA TA TA T
1998 TACCTTGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:6122 original size:2 final size:2
Alignment explanation
Indices: 6110--6141 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
6100 TTAGTAATCC
*
6110 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6142 ATTTGGCCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:7148 original size:15 final size:15
Alignment explanation
Indices: 7128--7194 Score: 71
Period size: 15 Copynumber: 4.5 Consensus size: 15
7118 GCCTTTCTTT
* *
7128 GATGATGTTGTTGAG
1 GATGATGATGATGAG
7143 GATGATGATGATGAG
1 GATGATGATGATGAG
* * * *
7158 GATGGTGACGAGGAT
1 GATGATGATGATGAG
*
7173 GATGATGAGGATGAG
1 GATGATGATGATGAG
7188 GATGATG
1 GATGATG
7195 CTTCCTCGCT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.28, C:0.01, G:0.43, T:0.27
Consensus pattern (15 bp):
GATGATGATGATGAG
Found at i:7149 original size:3 final size:3
Alignment explanation
Indices: 7127--7194 Score: 55
Period size: 3 Copynumber: 22.7 Consensus size: 3
7117 TGCCTTTCTT
* * * * * * *
7127 TGA TGA TGT TGT TGA GGA TGA TGA TGA TGA GGA TGG TGA CGA GGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
* *
7175 TGA TGA GGA TGA GGA TGA TG
1 TGA TGA TGA TGA TGA TGA TG
7195 CTTCCTCGCT
Statistics
Matches: 50, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.28, C:0.01, G:0.43, T:0.28
Consensus pattern (3 bp):
TGA
Found at i:7161 original size:12 final size:12
Alignment explanation
Indices: 7146--7192 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
7136 TGTTGAGGAT
7146 GATGATGATGAG
1 GATGATGATGAG
* *
7158 GATGGTGACGAG
1 GATGATGATGAG
7170 GATGATGATGAG
1 GATGATGATGAG
*
7182 GATGAGGATGA
1 GATGATGATGA
7193 TGCTTCCTCG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.32, C:0.02, G:0.45, T:0.21
Consensus pattern (12 bp):
GATGATGATGAG
Found at i:9458 original size:42 final size:42
Alignment explanation
Indices: 9373--9467 Score: 118
Period size: 42 Copynumber: 2.3 Consensus size: 42
9363 GGCATAATGA
* * * * *
9373 TCATCCTCATCTACATGCGCTTTAGCATATTTGTCTTCTTCC
1 TCATCCTCCTCTACATGCGCTTTAGCATATCTATCATCCTCC
*
9415 TCATCCTCCTCTACATGTGCTTTAGCATATCTATCATCCTCC
1 TCATCCTCCTCTACATGCGCTTTAGCATATCTATCATCCTCC
* *
9457 TCTTCCCCCTC
1 TCATCCTCCTC
9468 CAGATGACCT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.16, C:0.37, G:0.07, T:0.40
Consensus pattern (42 bp):
TCATCCTCCTCTACATGCGCTTTAGCATATCTATCATCCTCC
Found at i:24864 original size:13 final size:13
Alignment explanation
Indices: 24841--24880 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
24831 TACATTTAAT
24841 TATTAGGAGGGTCA
1 TATT-GGAGGGTCA
*
24855 TATTGGAGGGTTA
1 TATTGGAGGGTCA
*
24868 AATTGGAGGGTCA
1 TATTGGAGGGTCA
24881 AAAAGAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.28, C:0.05, G:0.38, T:0.30
Consensus pattern (13 bp):
TATTGGAGGGTCA
Found at i:25462 original size:16 final size:16
Alignment explanation
Indices: 25408--25523 Score: 74
Period size: 16 Copynumber: 7.1 Consensus size: 16
25398 CTCAGCCATG
25408 GCGGAGCCTCCCCACT
1 GCGGAGCCTCCCCACT
* *
25424 AG-GGAGGCC-CAACCACG
1 -GCGGA-GCCTC-CCCACT
25441 GCGGAGCCTCCCCACT
1 GCGGAGCCTCCCCACT
* * * *
25457 GTGGAGGCTCAACCACG
1 GCGGAGCCTC-CCCACT
25474 GCGGAGCCTCCCCACT
1 GCGGAGCCTCCCCACT
* * * *
25490 GTGGAGGCTCAACCACG
1 GCGGAGCCTC-CCCACT
*
25507 GCGGAACCTCCCCACT
1 GCGGAGCCTCCCCACT
25523 G
1 G
25524 GGGCGGCTTC
Statistics
Matches: 72, Mismatches: 21, Indels: 13
0.68 0.20 0.12
Matches are distributed among these distances:
16 37 0.51
17 35 0.49
ACGTcount: A:0.19, C:0.41, G:0.29, T:0.10
Consensus pattern (16 bp):
GCGGAGCCTCCCCACT
Found at i:25523 original size:33 final size:33
Alignment explanation
Indices: 25382--25523 Score: 207
Period size: 33 Copynumber: 4.3 Consensus size: 33
25372 TACACTGGGT
* * *
25382 CTCCCCACT-AGGACGGCTCAGCCATGGCGGAGC
1 CTCCCCACTGTGGA-GGCTCAACCACGGCGGAGC
*
25415 CTCCCCACTAG-GGAGGCCCAACCACGGCGGAGC
1 CTCCCCACT-GTGGAGGCTCAACCACGGCGGAGC
25448 CTCCCCACTGTGGAGGCTCAACCACGGCGGAGC
1 CTCCCCACTGTGGAGGCTCAACCACGGCGGAGC
*
25481 CTCCCCACTGTGGAGGCTCAACCACGGCGGAAC
1 CTCCCCACTGTGGAGGCTCAACCACGGCGGAGC
25514 CTCCCCACTG
1 CTCCCCACTG
25524 GGGCGGCTTC
Statistics
Matches: 101, Mismatches: 5, Indels: 6
0.90 0.04 0.05
Matches are distributed among these distances:
32 1 0.01
33 97 0.96
34 3 0.03
ACGTcount: A:0.19, C:0.42, G:0.28, T:0.11
Consensus pattern (33 bp):
CTCCCCACTGTGGAGGCTCAACCACGGCGGAGC
Found at i:25539 original size:66 final size:66
Alignment explanation
Indices: 25382--25540 Score: 214
Period size: 66 Copynumber: 2.4 Consensus size: 66
25372 TACACTGGGT
* * * *
25382 CTCCCCACTAGGACGGCTCAGCCATGGCGGAGCCTCCCCACTAGGGAGGCCCAACCACGGCGGAG
1 CTCCCCACTGGGGCGGCTCAGCCACGGCGGAGCCTCCCCACTAGGGAGGCCCAACCACGGCGGAA
25447 C
66 C
* * * *
25448 CTCCCCACTGTGGAGGCTCAACCACGGCGGAGCCTCCCCACT-GTGGAGGCTCAACCACGGCGGA
1 CTCCCCACTGGGGCGGCTCAGCCACGGCGGAGCCTCCCCACTAG-GGAGGCCCAACCACGGCGGA
25512 AC
65 AC
25514 CTCCCCACTGGGGCGGCTTC-GCCACGG
1 CTCCCCACTGGGGCGGC-TCAGCCACGG
25541 TAAGCCGCCC
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
65 1 0.01
66 77 0.96
67 2 0.03
ACGTcount: A:0.18, C:0.41, G:0.30, T:0.11
Consensus pattern (66 bp):
CTCCCCACTGGGGCGGCTCAGCCACGGCGGAGCCTCCCCACTAGGGAGGCCCAACCACGGCGGAA
C
Found at i:26352 original size:33 final size:33
Alignment explanation
Indices: 26310--26397 Score: 115
Period size: 33 Copynumber: 2.7 Consensus size: 33
26300 CCCATGGTGA
* * *
26310 AGCCGCCCCAGTGGGGAGGTTCCGCCGTGGTTG
1 AGCCTCCCCAGTGGGGAGGCTCCGCCGTGGCTG
*
26343 AGCCTCCCCACTGGGGAGGCTCCGCCGTGGCTG
1 AGCCTCCCCAGTGGGGAGGCTCCGCCGTGGCTG
*
26376 AGCCGT-CCTAGTGGGGAGGCTC
1 AGCC-TCCCCAGTGGGGAGGCTC
26398 AGTGTAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
33 47 0.98
34 1 0.02
ACGTcount: A:0.10, C:0.33, G:0.40, T:0.17
Consensus pattern (33 bp):
AGCCTCCCCAGTGGGGAGGCTCCGCCGTGGCTG
Found at i:28778 original size:22 final size:22
Alignment explanation
Indices: 28734--28778 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
28724 TGACACGATT
* *
28734 AAACACAAAACACGTTAAGCCC
1 AAACACAAAACACGTAAAACCC
28756 AAACAC-AAACACGGTAAAACCC
1 AAACACAAAACAC-GTAAAACCC
28778 A
1 A
28779 TATCGTTCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.53, C:0.31, G:0.09, T:0.07
Consensus pattern (22 bp):
AAACACAAAACACGTAAAACCC
Found at i:33652 original size:4 final size:4
Alignment explanation
Indices: 33643--33670 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
33633 TCCTATTCAT
33643 ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC
33671 TTATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:39743 original size:10 final size:10
Alignment explanation
Indices: 39724--39764 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
39714 AGGCATGTAA
39724 TCTC-TTTTC
1 TCTCTTTTTC
39733 TCTCTTTTTC
1 TCTCTTTTTC
39743 TC-CTTTTTC
1 TCTCTTTTTC
*
39752 TCTCTCTTTC
1 TCTCTTTTTC
39762 TCT
1 TCT
39765 TCCCCTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 13 0.45
10 16 0.55
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (10 bp):
TCTCTTTTTC
Found at i:45468 original size:5 final size:5
Alignment explanation
Indices: 45458--45486 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
45448 TGCCAAAGAC
45458 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
45487 AGGAGATGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:46063 original size:2 final size:2
Alignment explanation
Indices: 46056--46087 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
46046 TTAAAATCAT
46056 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46088 AAGCCGCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53649 original size:12 final size:11
Alignment explanation
Indices: 53632--53669 Score: 58
Period size: 12 Copynumber: 3.3 Consensus size: 11
53622 TTCTTTATTC
53632 TAATATAATATA
1 TAATAT-ATATA
53644 TAATATATATA
1 TAATATATATA
53655 TACATATATATA
1 TA-ATATATATA
53667 TAA
1 TAA
53670 ATAAATAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 8 0.32
12 17 0.68
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (11 bp):
TAATATATATA
Done.