Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015280.1 Corchorus capsularis cultivar CVL-1 contig15301, 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: 21126
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:4241 original size:18 final size:18
Alignment explanation
Indices: 4218--4268 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 18
4208 AAAGCTGAAG
*
4218 TTATAACCTTAATTTTTT
1 TTATAACCTTAATTATTT
4236 TTATAACCTCTATAATTATTT
1 TTATAA-C-CT-TAATTATTT
4257 TTAGTAACCTTA
1 TTA-TAACCTTA
4269 TTAGATGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 3 0.11
20 4 0.14
21 12 0.43
22 3 0.11
ACGTcount: A:0.31, C:0.14, G:0.02, T:0.53
Consensus pattern (18 bp):
TTATAACCTTAATTATTT
Found at i:4856 original size:28 final size:28
Alignment explanation
Indices: 4816--4872 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
4806 TCAATCTCTC
*
4816 TTTCGTTTTATTTTACAATGGGGGGAGG
1 TTTCGTTTTATTTCACAATGGGGGGAGG
4844 TTTCGTTTTATTTCACAATGGGGGGAGG
1 TTTCGTTTTATTTCACAATGGGGGGAGG
4872 T
1 T
4873 GGGATGGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.18, C:0.09, G:0.32, T:0.42
Consensus pattern (28 bp):
TTTCGTTTTATTTCACAATGGGGGGAGG
Found at i:5889 original size:17 final size:19
Alignment explanation
Indices: 5867--5909 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
5857 AGAATGAGAG
5867 TTATTAT-TATAT-TATAT
1 TTATTATATATATATATAT
5884 TTATTATATATATATATAT
1 TTATTATATATATATATAT
*
5903 ATATTAT
1 TTATTAT
5910 CTTAATTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 5 0.22
19 11 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTATTATATATATATATAT
Found at i:10503 original size:12 final size:13
Alignment explanation
Indices: 10472--10505 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
10462 ATGAAAATGA
10472 CACGTGGCATGCT
1 CACGTGGCATGCT
*
10485 AACGTGGCATGC-
1 CACGTGGCATGCT
10497 CACGTGGCA
1 CACGTGGCA
10506 ATTTTTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.21, C:0.29, G:0.32, T:0.18
Consensus pattern (13 bp):
CACGTGGCATGCT
Found at i:12810 original size:32 final size:32
Alignment explanation
Indices: 12774--12835 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
12764 TGTAGCTAAA
12774 ATGTATTAGACT-CAGAATGAAGATCAATTGGT
1 ATGTATTA-ACTACAGAATGAAGATCAATTGGT
* * *
12806 ATGTATTAACTACGGGATGAAGGTCAATTG
1 ATGTATTAACTACAGAATGAAGATCAATTG
12836 TTACGGACGC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 3 0.12
32 23 0.88
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (32 bp):
ATGTATTAACTACAGAATGAAGATCAATTGGT
Found at i:13963 original size:14 final size:14
Alignment explanation
Indices: 13944--13971 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13934 AATTTGAAGG
13944 CAATTGAAATATTT
1 CAATTGAAATATTT
13958 CAATTGAAATATTT
1 CAATTGAAATATTT
13972 GTTTTTGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
CAATTGAAATATTT
Found at i:16360 original size:14 final size:14
Alignment explanation
Indices: 16327--16367 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
16317 GCCACGTCAG
16327 CGTTGACTTTTG-C
1 CGTTGACTTTTGAC
* *
16340 AGTTGACTATTGAC
1 CGTTGACTTTTGAC
16354 CGTTGACTTTTGAC
1 CGTTGACTTTTGAC
16368 TTTGACCTCC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (14 bp):
CGTTGACTTTTGAC
Done.