Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006068.1 Corchorus capsularis cultivar CVL-1 contig06086, 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: 44452
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:127 original size:31 final size:31
Alignment explanation
Indices: 66--227 Score: 200
Period size: 31 Copynumber: 5.3 Consensus size: 31
56 TTTGAAATAT
** * *
66 TGGCATGCCGCGTATCAC-TTTTGGTACACG
1 TGGCATGCCATGTGTCACTTTTTCGTACACG
* *
96 TGGCGTGACATGTGTCACTTTTTCGTACACG
1 TGGCATGCCATGTGTCACTTTTTCGTACACG
127 TGGCATGCCATGTGTCACTTTTTCGTACACG
1 TGGCATGCCATGTGTCACTTTTTCGTACACG
*
158 TGGCATGCCATGTGTCACTTTTTCGTACACA
1 TGGCATGCCATGTGTCACTTTTTCGTACACG
** ** * *
189 TGGTGTGCCACATGTCACTTTTTTGTATACG
1 TGGCATGCCATGTGTCACTTTTTCGTACACG
220 TGGCATGC
1 TGGCATGC
228 TACGTCGGAC
Statistics
Matches: 113, Mismatches: 18, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
30 13 0.12
31 100 0.88
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (31 bp):
TGGCATGCCATGTGTCACTTTTTCGTACACG
Found at i:171 original size:62 final size:62
Alignment explanation
Indices: 33--227 Score: 216
Period size: 62 Copynumber: 3.2 Consensus size: 62
23 AATTTTGTGT
** * * * * *
33 ACGTGGCATGCCACATGTCACTTTTT-G-AAATATTGGCATGCCGCGTATCAC-TTTTGGTAC
1 ACGTGGCATGCCATGTGTCACTTTTTCGTACACA-TGGCATGCCACGTGTCACTTTTTCGTAC
* * * *
93 ACGTGGCGTGACATGTGTCACTTTTTCGTACACGTGGCATGCCATGTGTCACTTTTTCGTAC
1 ACGTGGCATGCCATGTGTCACTTTTTCGTACACATGGCATGCCACGTGTCACTTTTTCGTAC
** * * *
155 ACGTGGCATGCCATGTGTCACTTTTTCGTACACATGGTGTGCCACATGTCACTTTTTTGTAT
1 ACGTGGCATGCCATGTGTCACTTTTTCGTACACATGGCATGCCACGTGTCACTTTTTCGTAC
217 ACGTGGCATGC
1 ACGTGGCATGC
228 TACGTCGGAC
Statistics
Matches: 112, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
60 22 0.20
61 16 0.14
62 74 0.66
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (62 bp):
ACGTGGCATGCCATGTGTCACTTTTTCGTACACATGGCATGCCACGTGTCACTTTTTCGTAC
Found at i:223 original size:93 final size:91
Alignment explanation
Indices: 25--227 Score: 219
Period size: 93 Copynumber: 2.2 Consensus size: 91
15 GCACATATAA
* * * *
25 TTTTGTGTACGTGGCATGCCACATGTCACTTTTTGAAATATTGGCATGCCGCGTATCACTTTTGG
1 TTTTGTATACGTGGCATGCCACATGTCACTTTTTGAAATAGTGGCATGCCACGTATCACTTTTCG
* **
90 TACACGTGGCGTGACATGTGTCACTT
66 TACACATGGCGTGACACATGTCACTT
* * ** * * * *
116 TTTCGTACACGTGGCATGCCATGTGTCACTTTTTCGTACA-CGTGGCATGCCATGTGTCACTTTT
1 TTTTGTATACGTGGCATGCCACATGTCACTTTTT-G-AAATAGTGGCATGCCACGTATCAC-TTT
* *
180 TCGTACACATGGTGTGCCACATGTCACTT
63 TCGTACACATGGCGTGACACATGTCACTT
209 TTTTGTATACGTGGCATGC
1 TTTTGTATACGTGGCATGC
228 TACGTCGGAC
Statistics
Matches: 90, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
91 29 0.32
92 16 0.18
93 45 0.50
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (91 bp):
TTTTGTATACGTGGCATGCCACATGTCACTTTTTGAAATAGTGGCATGCCACGTATCACTTTTCG
TACACATGGCGTGACACATGTCACTT
Found at i:3613 original size:1 final size:1
Alignment explanation
Indices: 3609--3633 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
3599 TTTTAACGTC
3609 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
3634 ACTATGTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:8804 original size:1 final size:1
Alignment explanation
Indices: 8798--8831 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
8788 TATTTGACGC
*
8798 TTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
8832 ACCTAGTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:9936 original size:1 final size:1
Alignment explanation
Indices: 9926--9960 Score: 61
Period size: 1 Copynumber: 35.0 Consensus size: 1
9916 TATGTAGACC
*
9926 TTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
9961 ACAAACACCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:16931 original size:20 final size:22
Alignment explanation
Indices: 16891--16932 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
16881 CTACTCGGAC
16891 TCGACTCGAGAAAAAATCGAGT
1 TCGACTCGAGAAAAAATCGAGT
16913 TCGACTCG-GAAAAAA-CGAGT
1 TCGACTCGAGAAAAAATCGAGT
16933 CGAGCTTGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.25
21 7 0.35
22 8 0.40
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.17
Consensus pattern (22 bp):
TCGACTCGAGAAAAAATCGAGT
Found at i:42374 original size:12 final size:12
Alignment explanation
Indices: 42357--42384 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
42347 ACCTGACAAT
42357 TCGTGTTTCGTG
1 TCGTGTTTCGTG
42369 TCGTGTTTCGTG
1 TCGTGTTTCGTG
42381 TCGT
1 TCGT
42385 ATAAACATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.18, G:0.32, T:0.50
Consensus pattern (12 bp):
TCGTGTTTCGTG
Found at i:43569 original size:37 final size:37
Alignment explanation
Indices: 43489--43585 Score: 124
Period size: 37 Copynumber: 2.6 Consensus size: 37
43479 TCAATTTACC
* *
43489 TTTTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTG
1 TTTTTGTTTCCAACATCCTATTTAATTTTGCCTTTAG
* **
43526 TCTTTGTTTCCAATCATTGTATTTAATTTTG-CTTTAG
1 TTTTTGTTTCCAA-CATCCTATTTAATTTTGCCTTTAG
*
43563 TTTTTGTCTCCAACATCCTATTT
1 TTTTTGTTTCCAACATCCTATTT
43586 GGGCTTAGAT
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
36 8 0.16
37 28 0.56
38 14 0.28
ACGTcount: A:0.16, C:0.19, G:0.09, T:0.56
Consensus pattern (37 bp):
TTTTTGTTTCCAACATCCTATTTAATTTTGCCTTTAG
Done.