Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016197.1 Corchorus olitorius cultivar O-4 contig16230, 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: 20406
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2043 original size:31 final size:31
Alignment explanation
Indices: 2008--2071 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
1998 CAAATTTGTC
2008 TGTCAATAGGAGAAGATACGGGGAATTAATA
1 TGTCAATAGGAGAAGATACGGGGAATTAATA
2039 TGTCAATAGGAGAAGATACGGGGAATTAATA
1 TGTCAATAGGAGAAGATACGGGGAATTAATA
2070 TG
1 TG
2072 CTTGACAGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.41, C:0.06, G:0.30, T:0.23
Consensus pattern (31 bp):
TGTCAATAGGAGAAGATACGGGGAATTAATA
Found at i:2356 original size:55 final size:55
Alignment explanation
Indices: 2263--2464 Score: 278
Period size: 55 Copynumber: 3.7 Consensus size: 55
2253 GATACCGGAC
* * * * * *
2263 AACTGTGTACAAATTATCTGTTATAGAAAAGAAGATTCGAGGGAATATACATGAT
1 AACTGTGTACAAATTATCTATCATAAAAAAGAAGATTCGAGGGAATATGCCTGAA
* * ** *
2318 AACTATGTACAAATTATCTATCATAAAAAAGAAAATTCGAGAAAATATGCCTGAC
1 AACTGTGTACAAATTATCTATCATAAAAAAGAAGATTCGAGGGAATATGCCTGAA
* * *
2373 AACTGTATACAAATTATCTGTTATAAAAAAGAAGATTCGAGGGAATATGCCTGAA
1 AACTGTGTACAAATTATCTATCATAAAAAAGAAGATTCGAGGGAATATGCCTGAA
2428 AACTGTGTACAAATTATCTATCATAAAAAAGAAGATT
1 AACTGTGTACAAATTATCTATCATAAAAAAGAAGATT
2465 GTACGTATCT
Statistics
Matches: 126, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 126 1.00
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.28
Consensus pattern (55 bp):
AACTGTGTACAAATTATCTATCATAAAAAAGAAGATTCGAGGGAATATGCCTGAA
Found at i:2403 original size:110 final size:110
Alignment explanation
Indices: 2260--2460 Score: 348
Period size: 110 Copynumber: 1.8 Consensus size: 110
2250 CCTGATACCG
* * *
2260 GACAACTGTGTACAAATTATCTGTTATAGAAAAGAAGATTCGAGGGAATATACATGATAACTATG
1 GACAACTGTATACAAATTATCTGTTATAAAAAAGAAGATTCGAGGGAATATACATGAAAACTATG
2325 TACAAATTATCTATCATAAAAAAGAAAATTCGAGAAAATATGCCT
66 TACAAATTATCTATCATAAAAAAGAAAATTCGAGAAAATATGCCT
* * *
2370 GACAACTGTATACAAATTATCTGTTATAAAAAAGAAGATTCGAGGGAATATGCCTGAAAACTGTG
1 GACAACTGTATACAAATTATCTGTTATAAAAAAGAAGATTCGAGGGAATATACATGAAAACTATG
2435 TACAAATTATCTATCATAAAAAAGAA
66 TACAAATTATCTATCATAAAAAAGAA
2461 GATTGTACGT
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
110 85 1.00
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27
Consensus pattern (110 bp):
GACAACTGTATACAAATTATCTGTTATAAAAAAGAAGATTCGAGGGAATATACATGAAAACTATG
TACAAATTATCTATCATAAAAAAGAAAATTCGAGAAAATATGCCT
Found at i:3230 original size:54 final size:55
Alignment explanation
Indices: 3084--3594 Score: 681
Period size: 55 Copynumber: 9.5 Consensus size: 55
3074 CAAGAGGGAC
* * * *
3084 TAAAAAAGAAGATTCGACGGAATATGCCTGACAACTGTGTACAAATAATTTGTCA
1 TAAAAAAGAAGATTCGAGGGAATATGCCTGTCAACTGTGTACAAATTATCTGTCA
*
3139 TAAAAAAGAAGATTCGAGGGAATATGCCTGTCAACTGTGTACAAATAATCTGTCA
1 TAAAAAAGAAGATTCGAGGGAATATGCCTGTCAACTGTGTACAAATTATCTGTCA
* *
3194 TAAAAAAGAAGATTCGACGGAATATG-CTGTCAACTGTGTACAAATAATCTGTCA
1 TAAAAAAGAAGATTCGAGGGAATATGCCTGTCAACTGTGTACAAATTATCTGTCA
* *
3248 TAAAAAAGAAGATTCGAGGGAATATGCCTGTCAACTATGTACAAATTATATGTCA
1 TAAAAAAGAAGATTCGAGGGAATATGCCTGTCAACTGTGTACAAATTATCTGTCA
*
3303 TAAAAAAGAAGATTCGAGGGAATATGCCTGTCAACTATGTACAAATTATCTGTCA
1 TAAAAAAGAAGATTCGAGGGAATATGCCTGTCAACTGTGTACAAATTATCTGTCA
* ** *
3358 TAGAAAA-AAGATTCGAGGGAATATGCCTAACAACTATGTACAAATTATCTGTCA
1 TAAAAAAGAAGATTCGAGGGAATATGCCTGTCAACTGTGTACAAATTATCTGTCA
* * * *
3412 TAGAAAA-AAGATTCGAGGGAATATGCCTGACAACTGTGTAAAAATTATCTGTTA
1 TAAAAAAGAAGATTCGAGGGAATATGCCTGTCAACTGTGTACAAATTATCTGTCA
* * * * * *
3466 TAGAAAAGAAGATTCGAAGGAATATACC--T-AACAGTATATAAATTATCTGTCA
1 TAAAAAAGAAGATTCGAGGGAATATGCCTGTCAACTGTGTACAAATTATCTGTCA
* *
3518 TAAAAAAGAAGATTCGAAGGAATATACCTG-----T-T-TACAAATTATCTGTCA
1 TAAAAAAGAAGATTCGAGGGAATATGCCTGTCAACTGTGTACAAATTATCTGTCA
*
3566 TAAAAAAGAAGATTTGA-GGAATATGCCTG
1 TAAAAAAGAAGATTCGAGGGAATATGCCTG
3595 ACTACTGTTA
Statistics
Matches: 424, Mismatches: 28, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
47 11 0.03
48 31 0.07
49 1 0.00
52 46 0.11
54 155 0.37
55 180 0.42
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (55 bp):
TAAAAAAGAAGATTCGAGGGAATATGCCTGTCAACTGTGTACAAATTATCTGTCA
Found at i:3276 original size:109 final size:110
Alignment explanation
Indices: 3084--3594 Score: 683
Period size: 109 Copynumber: 4.8 Consensus size: 110
3074 CAAGAGGGAC
* * *
3084 TAAAAAAGAAGATTCGACGGAATATGCCTGACAACTGTGTACAAATAATTTGTCATAAAAAAGAA
1 TAAAAAAGAAGATTCGACGGAATATGCCTGTCAACTGTGTACAAATTATCTGTCATAAAAAAGAA
* *
3149 GATTCGAGGGAATATGCCTGTCAACTGTGTACAAATAATCTGTCA
66 GATTCGAGGGAATATGCCTGTCAACTATGTACAAATTATCTGTCA
*
3194 TAAAAAAGAAGATTCGACGGAATATG-CTGTCAACTGTGTACAAATAATCTGTCATAAAAAAGAA
1 TAAAAAAGAAGATTCGACGGAATATGCCTGTCAACTGTGTACAAATTATCTGTCATAAAAAAGAA
*
3258 GATTCGAGGGAATATGCCTGTCAACTATGTACAAATTATATGTCA
66 GATTCGAGGGAATATGCCTGTCAACTATGTACAAATTATCTGTCA
* * *
3303 TAAAAAAGAAGATTCGAGGGAATATGCCTGTCAACTATGTACAAATTATCTGTCATAGAAAA-AA
1 TAAAAAAGAAGATTCGACGGAATATGCCTGTCAACTGTGTACAAATTATCTGTCATAAAAAAGAA
**
3367 GATTCGAGGGAATATGCCTAACAACTATGTACAAATTATCTGTCA
66 GATTCGAGGGAATATGCCTGTCAACTATGTACAAATTATCTGTCA
* * * * * *
3412 TAGAAAA-AAGATTCGAGGGAATATGCCTGACAACTGTGTAAAAATTATCTGTTATAGAAAAGAA
1 TAAAAAAGAAGATTCGACGGAATATGCCTGTCAACTGTGTACAAATTATCTGTCATAAAAAAGAA
* * * *
3476 GATTCGAAGGAATATACC--T-AAC-AGTATATAAATTATCTGTCA
66 GATTCGAGGGAATATGCCTGTCAACTA-TGTACAAATTATCTGTCA
* *
3518 TAAAAAAGAAGATTCGAAGGAATATACCTG-----T-T-TACAAATTATCTGTCATAAAAAAGAA
1 TAAAAAAGAAGATTCGACGGAATATGCCTGTCAACTGTGTACAAATTATCTGTCATAAAAAAGAA
*
3576 GATTTGA-GGAATATGCCTG
66 GATTCGAGGGAATATGCCTG
3595 ACTACTGTTA
Statistics
Matches: 365, Mismatches: 30, Indels: 21
0.88 0.07 0.05
Matches are distributed among these distances:
99 9 0.02
100 29 0.08
101 1 0.00
102 1 0.00
105 1 0.00
106 25 0.07
107 20 0.05
108 50 0.14
109 171 0.47
110 58 0.16
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (110 bp):
TAAAAAAGAAGATTCGACGGAATATGCCTGTCAACTGTGTACAAATTATCTGTCATAAAAAAGAA
GATTCGAGGGAATATGCCTGTCAACTATGTACAAATTATCTGTCA
Found at i:3576 original size:48 final size:48
Alignment explanation
Indices: 3453--3594 Score: 187
Period size: 52 Copynumber: 2.9 Consensus size: 48
3443 AACTGTGTAA
* * *
3453 AAATTATCTGTTATAGAAAAGAAGATTCGAAGGAATATACCTAACAGTATAT
1 AAATTATCTGTCATAAAAAAGAAGATTCGAAGGAATATACCT----GTATAC
*
3505 AAATTATCTGTCATAAAAAAGAAGATTCGAAGGAATATACCTGTTTAC
1 AAATTATCTGTCATAAAAAAGAAGATTCGAAGGAATATACCTGTATAC
* *
3553 AAATTATCTGTCATAAAAAAGAAGATTTG-AGGAATATGCCTG
1 AAATTATCTGTCATAAAAAAGAAGATTCGAAGGAATATACCTG
3595 ACTACTGTTA
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
47 12 0.14
48 32 0.38
52 40 0.48
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (48 bp):
AAATTATCTGTCATAAAAAAGAAGATTCGAAGGAATATACCTGTATAC
Found at i:10438 original size:37 final size:37
Alignment explanation
Indices: 10388--10461 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
10378 GGTAAAGTTT
10388 TTAGATTTTTTGACACCAATAGCGAGTTAAAATGTTG
1 TTAGATTTTTTGACACCAATAGCGAGTTAAAATGTTG
10425 TTAGATTTTTTGACACCAATAGCGAGTTAAAATGTTG
1 TTAGATTTTTTGACACCAATAGCGAGTTAAAATGTTG
10462 ACACGTACCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (37 bp):
TTAGATTTTTTGACACCAATAGCGAGTTAAAATGTTG
Found at i:13298 original size:29 final size:29
Alignment explanation
Indices: 13264--13321 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
13254 TTAACAATCT
13264 CAAACGGCCCAATATTTTCCCATTAACCA
1 CAAACGGCCCAATATTTTCCCATTAACCA
*
13293 CAAACGGTCCAATATTTTCCCATTAACCA
1 CAAACGGCCCAATATTTTCCCATTAACCA
13322 GGCTCCGAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.34, C:0.33, G:0.07, T:0.26
Consensus pattern (29 bp):
CAAACGGCCCAATATTTTCCCATTAACCA
Found at i:18012 original size:6 final size:6
Alignment explanation
Indices: 18003--18037 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
17993 AAAAAAAAAA
18003 AAAACC AAAAACC AAAACC AAAACC AAAAACC AAA
1 AAAACC -AAAACC AAAACC AAAACC -AAAACC AAA
18038 CTAAAAATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 15 0.56
7 12 0.44
ACGTcount: A:0.71, C:0.29, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACC
Found at i:18012 original size:7 final size:7
Alignment explanation
Indices: 18002--18037 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
17992 AAAAAAAAAA
18002 AAAAACC
1 AAAAACC
18009 AAAAACC
1 AAAAACC
18016 -AAAACC
1 AAAAACC
18022 -AAAACC
1 AAAAACC
18028 AAAAACC
1 AAAAACC
18035 AAA
1 AAA
18038 CTAAAAATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.43
7 16 0.57
ACGTcount: A:0.72, C:0.28, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAACC
Found at i:18012 original size:13 final size:13
Alignment explanation
Indices: 17970--18037 Score: 64
Period size: 13 Copynumber: 5.2 Consensus size: 13
17960 TCTGATTTAT
**
17970 AAAAAAAAAAAAA
1 AAAAAAAAAAACC
**
17983 AAAAAAAAAAAAA
1 AAAAAAAAAAACC
17996 AAAAAAAAAAACC
1 AAAAAAAAAAACC
**
18009 AAAAACCAAAACC
1 AAAAAAAAAAACC
**
18022 AAAACCAAAAACC
1 AAAAAAAAAAACC
18035 AAA
1 AAA
18038 CTAAAAATCT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 49 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAACC
Found at i:18013 original size:1 final size:1
Alignment explanation
Indices: 17970--18006 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
17960 TCTGATTTAT
17970 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
18007 CCAAAAACCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:18484 original size:10 final size:10
Alignment explanation
Indices: 18469--18494 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
18459 ATACCTCGAT
18469 ATATCCGTAA
1 ATATCCGTAA
18479 ATATCCGTAA
1 ATATCCGTAA
18489 ATATCC
1 ATATCC
18495 ATATTGAATT
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:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:19356 original size:12 final size:12
Alignment explanation
Indices: 19339--19382 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
19329 TCGATACCTC
19339 GATATATCCCTT
1 GATATATCCCTT
* *
19351 GATATATCCGTC
1 GATATATCCCTT
*
19363 GATATATTCCTT
1 GATATATCCCTT
19375 CGATATAT
1 -GATATAT
19383 TTGTGGAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 19 0.73
13 7 0.27
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (12 bp):
GATATATCCCTT
Found at i:19379 original size:13 final size:13
Alignment explanation
Indices: 19337--19383 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
19327 CATCGATACC
*
19337 TCGATATATCCCT
1 TCGATATATTCCT
*
19350 T-GATATA-TCCG
1 TCGATATATTCCT
19361 TCGATATATTCCT
1 TCGATATATTCCT
19374 TCGATATATT
1 TCGATATATT
19384 TGTGGAAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 3 0.10
12 12 0.41
13 14 0.48
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.43
Consensus pattern (13 bp):
TCGATATATTCCT
Done.