Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015524.1 Corchorus capsularis cultivar CVL-1 contig15545, 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: 30382
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:276 original size:16 final size:16
Alignment explanation
Indices: 248--340 Score: 134
Period size: 16 Copynumber: 5.9 Consensus size: 16
238 TCGAAGTCTA
248 AACCCGA-ACCCGAAT
1 AACCCGAGACCCGAAT
*
263 AACCCGAGACCCGATT
1 AACCCGAGACCCGAAT
*
279 AACCCGAGAACCGAAT
1 AACCCGAGACCCGAAT
* * *
295 GACCCGAAACCCGATT
1 AACCCGAGACCCGAAT
311 AACCCGAGACCCGAAT
1 AACCCGAGACCCGAAT
327 AACCCGAGACCCGA
1 AACCCGAGACCCGA
341 TAGAGCTTTC
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
15 7 0.10
16 60 0.90
ACGTcount: A:0.37, C:0.38, G:0.18, T:0.08
Consensus pattern (16 bp):
AACCCGAGACCCGAAT
Found at i:300 original size:32 final size:32
Alignment explanation
Indices: 248--341 Score: 154
Period size: 32 Copynumber: 3.0 Consensus size: 32
238 TCGAAGTCTA
248 AACCCGA-ACCCGAATAACCCGAGACCCGATT
1 AACCCGAGACCCGAATAACCCGAGACCCGATT
* * *
279 AACCCGAGAACCGAATGACCCGAAACCCGATT
1 AACCCGAGACCCGAATAACCCGAGACCCGATT
311 AACCCGAGACCCGAATAACCCGAGACCCGAT
1 AACCCGAGACCCGAATAACCCGAGACCCGAT
342 AGAGCTTTCA
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
31 7 0.12
32 49 0.88
ACGTcount: A:0.36, C:0.37, G:0.18, T:0.09
Consensus pattern (32 bp):
AACCCGAGACCCGAATAACCCGAGACCCGATT
Found at i:315 original size:48 final size:47
Alignment explanation
Indices: 249--340 Score: 148
Period size: 48 Copynumber: 1.9 Consensus size: 47
239 CGAAGTCTAA
*
249 ACCCGAACCCGAATAACCCGAGACCCGATTAACCCGAGAACCGAATG
1 ACCCGAACCCGAATAACCCGAGACCCGAATAACCCGAGAACCGAATG
* *
296 ACCCGAAACCCGATTAACCCGAGACCCGAATAACCCGAGACCCGA
1 ACCCG-AACCCGAATAACCCGAGACCCGAATAACCCGAGAACCGA
341 TAGAGCTTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 5 0.12
48 36 0.88
ACGTcount: A:0.36, C:0.38, G:0.18, T:0.08
Consensus pattern (47 bp):
ACCCGAACCCGAATAACCCGAGACCCGAATAACCCGAGAACCGAATG
Found at i:1256 original size:22 final size:22
Alignment explanation
Indices: 1238--1279 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1228 TTTTTATTAG
1238 AAAGGCAAAAC-ATTATTATATA
1 AAAGG-AAAACTATTATTATATA
*
1260 AAAGGAATACTATTATTATA
1 AAAGGAAAACTATTATTATA
1280 GAGTGGATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (22 bp):
AAAGGAAAACTATTATTATATA
Found at i:3948 original size:2 final size:2
Alignment explanation
Indices: 3943--3971 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3933 CTTTTTTGTT
3943 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
3972 GAATGAATCT
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
Found at i:4436 original size:26 final size:27
Alignment explanation
Indices: 4384--4447 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
4374 CTACGTATAC
***
4384 ACGATTTCTTTTTATATTTTTTCAAAA
1 ACGATTTCTTTTTATATTTGGACAAAA
*
4411 A-GATTTCTTTTTATATTTGGAGAAAA
1 ACGATTTCTTTTTATATTTGGACAAAA
4437 ACGATTT-TTTT
1 ACGATTTCTTTT
4448 CTACGTACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 26 0.81
27 6 0.19
ACGTcount: A:0.30, C:0.08, G:0.09, T:0.53
Consensus pattern (27 bp):
ACGATTTCTTTTTATATTTGGACAAAA
Found at i:9576 original size:1 final size:1
Alignment explanation
Indices: 9570--9595 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
9560 TCATTCAGAC
9570 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
9596 AAAAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:18116 original size:25 final size:25
Alignment explanation
Indices: 18082--18132 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
18072 GACTGCTACT
18082 TTTTCAAAACTTAAAACATGCGGAG
1 TTTTCAAAACTTAAAACATGCGGAG
18107 TTTTCAAAACTTAAAACATGCGGAG
1 TTTTCAAAACTTAAAACATGCGGAG
18132 T
1 T
18133 ATAATATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (25 bp):
TTTTCAAAACTTAAAACATGCGGAG
Found at i:23628 original size:36 final size:36
Alignment explanation
Indices: 23563--23635 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
23553 TTCAAATCTT
* * *
23563 TCTTTTCAATAACTATTCATTGATGACTCATGATTG
1 TCTTTTCAATAACTACTCATGGATAACTCATGATTG
* *
23599 TCTTTTCAATAACTACTCATGGCTAACTCATGTTTG
1 TCTTTTCAATAACTACTCATGGATAACTCATGATTG
23635 T
1 T
23636 TCATCAACAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.44
Consensus pattern (36 bp):
TCTTTTCAATAACTACTCATGGATAACTCATGATTG
Found at i:29689 original size:11 final size:12
Alignment explanation
Indices: 29647--29687 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
29637 CCCTTTCCTA
*
29647 TATAAAATAAAT
1 TATAAAATTAAT
*
29659 TATCAAA-TAAT
1 TATAAAATTAAT
29670 TATAAAATTAAT
1 TATAAAATTAAT
29682 TATAAA
1 TATAAA
29688 TTTGTTATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (12 bp):
TATAAAATTAAT
Found at i:29908 original size:17 final size:17
Alignment explanation
Indices: 29886--29920 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
29876 CAATTTCTCC
* *
29886 TCTTCTTCATATTTTAT
1 TCTTCTCCATATTCTAT
29903 TCTTCTCCATATTCTAT
1 TCTTCTCCATATTCTAT
29920 T
1 T
29921 GTCTCTGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.00, T:0.60
Consensus pattern (17 bp):
TCTTCTCCATATTCTAT
Found at i:30074 original size:41 final size:42
Alignment explanation
Indices: 30006--30089 Score: 143
Period size: 41 Copynumber: 2.0 Consensus size: 42
29996 ACAAAATTTC
*
30006 ATTTCTTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTATTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
*
30048 ATTTATTAATTGAA-TTTTCTTAAAAGAATTTATAAAATAAA
1 ATTTATTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
30089 A
1 A
30090 CAGCCGCACG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 28 0.70
42 12 0.30
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (42 bp):
ATTTATTAACTGAATTTTTCTTAAAAGAATTTATAAAATAAA
Done.