Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001133.1 Corchorus capsularis cultivar CVL-1 contig01133, 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: 11961
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Found at i:181 original size:33 final size:31
Alignment explanation
Indices: 131--248 Score: 100
Period size: 33 Copynumber: 3.6 Consensus size: 31
121 CCCCACCGGT
131 GCCGTCCC-CCTGGGGCGGCTGAGCCATGGCCAA
1 GCCG-CCCTCCTGGGGCGGCT-A-CCATGGCCAA
*
164 GCCGCCCTCCTGGGGCGGCACTACCATGGCCAG
1 GCCGCCCTCCTGGGGCGG--CTACCATGGCCAA
197 GCCG-CCTCCCTGGGGCGGCCCTACCATGG--ATA
1 GCCGCCCT-CCTGGGGCGG--CTACCATGGCCA-A
*
229 GACCGCCCCCCTGGGGCGGC
1 G-CCGCCCTCCTGGGGCGGC
249 ACCGGTACTA
Statistics
Matches: 74, Mismatches: 4, Indels: 16
0.79 0.04 0.17
Matches are distributed among these distances:
31 2 0.03
32 7 0.09
33 60 0.81
34 3 0.04
35 2 0.03
ACGTcount: A:0.11, C:0.42, G:0.35, T:0.12
Consensus pattern (31 bp):
GCCGCCCTCCTGGGGCGGCTACCATGGCCAA
Found at i:407 original size:33 final size:32
Alignment explanation
Indices: 287--403 Score: 198
Period size: 32 Copynumber: 3.6 Consensus size: 32
277 AAAAAGCCTT
*
287 GCCGTCCTAGTGGGGCGGCTAGCCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCTAGCCGTGGCAGA
*
319 GCCGTCCTAGTGGGGCGGCTAGCCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCTAGCCGTGGCAGA
*
351 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCT-AGCCGTGGCAGA
384 GCCGTCCTAGTGGGGAGGCT
1 GCCGTCCTAGTGGGGAGGCT
404 CCGCGTGGCT
Statistics
Matches: 82, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
32 51 0.62
33 31 0.38
ACGTcount: A:0.12, C:0.28, G:0.44, T:0.16
Consensus pattern (32 bp):
GCCGTCCTAGTGGGGAGGCTAGCCGTGGCAGA
Found at i:1666 original size:17 final size:17
Alignment explanation
Indices: 1640--1681 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1630 TTATTTAAGA
*
1640 TATTAATTAATTATT-AT
1 TATTATTTAA-TATTAAT
1657 TATTATTTAATATTAAT
1 TATTATTTAATATTAAT
*
1674 TAATATTT
1 TATTATTT
1682 TTTAAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTATTTAATATTAAT
Found at i:3068 original size:2 final size:2
Alignment explanation
Indices: 3061--3091 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3051 TTTATTTATT
3061 TA TA TA TA -A 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
3092 GAAAATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3497 original size:29 final size:30
Alignment explanation
Indices: 3432--3498 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
3422 AGAACACAAA
* * *
3432 AAGAGGAAAGAGAGAGAAGGAGGGGGAGAAG
1 AAGA-GAAAGAAAGAGAAGGAGGGAGAGAAC
*
3463 AA-AGAAAGAAAGAGAGGGAGGGAGA-AAC
1 AAGAGAAAGAAAGAGAAGGAGGGAGAGAAC
3491 AAGAGAAA
1 AAGAGAAA
3499 AGCTAAGATC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 4 0.13
29 24 0.77
30 1 0.03
31 2 0.06
ACGTcount: A:0.55, C:0.01, G:0.43, T:0.00
Consensus pattern (30 bp):
AAGAGAAAGAAAGAGAAGGAGGGAGAGAAC
Found at i:4022 original size:12 final size:12
Alignment explanation
Indices: 4007--4052 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
3997 GAACGGGAAA
*
4007 GAGATAGAGAGC
1 GAGATAGAGAAC
4019 GAGATAGAGAAC
1 GAGATAGAGAAC
* *
4031 GAGATAGGGAAA
1 GAGATAGAGAAC
*
4043 GAGAAAGAGA
1 GAGATAGAGA
4053 TCGCTTGAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.50, C:0.04, G:0.39, T:0.07
Consensus pattern (12 bp):
GAGATAGAGAAC
Found at i:4053 original size:18 final size:18
Alignment explanation
Indices: 4001--4053 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
3991 GAACGAGAAC
* **
4001 GGGAAAGAGATAGAGAGC
1 GGGAAAGAGAAAGAGATA
* * *
4019 GAGATAGAGAACGAGATA
1 GGGAAAGAGAAAGAGATA
4037 GGGAAAGAGAAAGAGAT
1 GGGAAAGAGAAAGAGAT
4054 CGCTTGAGTA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.49, C:0.04, G:0.40, T:0.08
Consensus pattern (18 bp):
GGGAAAGAGAAAGAGATA
Found at i:7745 original size:9 final size:9
Alignment explanation
Indices: 7727--7761 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
7717 TTCACAACTT
*
7727 CAGCAGCAG
1 CAGCAACAG
7736 CAGCAACAG
1 CAGCAACAG
*
7745 CAACAACAG
1 CAGCAACAG
7754 CAGCAACA
1 CAGCAACA
7762 ACCATCCTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.46, C:0.34, G:0.20, T:0.00
Consensus pattern (9 bp):
CAGCAACAG
Found at i:11437 original size:13 final size:14
Alignment explanation
Indices: 11421--11478 Score: 59
Period size: 13 Copynumber: 4.3 Consensus size: 14
11411 TAAAGAAGAA
11421 AAAAACAGAAAA-T
1 AAAAACAGAAAAGT
*
11434 -AAAACAAGAAAAAT
1 AAAAAC-AGAAAAGT
* *
11448 AAAAAAAGAAAAGG
1 AAAAACAGAAAAGT
11462 AAAAA-AGAAAAGT
1 AAAAACAGAAAAGT
11475 AAAA
1 AAAA
11479 GAAGTAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
12 5 0.13
13 17 0.45
14 12 0.32
15 4 0.11
ACGTcount: A:0.79, C:0.03, G:0.12, T:0.05
Consensus pattern (14 bp):
AAAAACAGAAAAGT
Found at i:11446 original size:14 final size:14
Alignment explanation
Indices: 11413--11478 Score: 59
Period size: 14 Copynumber: 4.9 Consensus size: 14
11403 TTTCACCATA
11413 AAGAAGAAA-AAAAC
1 AAGAA-AAATAAAAC
11427 -AG-AAAATAAAAC
1 AAGAAAAATAAAAC
*
11439 AAGAAAAATAAAAA
1 AAGAAAAATAAAAC
**
11453 AAGAAAAGGAAAA-
1 AAGAAAAATAAAAC
*
11466 AAGAAAAGTAAAA
1 AAGAAAAATAAAA
11479 GAAGTAAGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
11 3 0.07
12 6 0.13
13 16 0.36
14 20 0.44
ACGTcount: A:0.79, C:0.03, G:0.14, T:0.05
Consensus pattern (14 bp):
AAGAAAAATAAAAC
Found at i:11457 original size:27 final size:28
Alignment explanation
Indices: 11420--11478 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
11410 ATAAAGAAGA
*
11420 AAAAAACAGAAAA-TAAAACAAGAAAAAT
1 AAAAAACAGAAAAGGAAAA-AAGAAAAAT
*
11448 AAAAAA-AGAAAAGGAAAAAAGAAAAGT
1 AAAAAACAGAAAAGGAAAAAAGAAAAAT
11475 AAAA
1 AAAA
11479 GAAGTAAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 18 0.64
28 10 0.36
ACGTcount: A:0.80, C:0.03, G:0.12, T:0.05
Consensus pattern (28 bp):
AAAAAACAGAAAAGGAAAAAAGAAAAAT
Done.