Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023021.1 Corchorus olitorius cultivar O-4 contig23054, 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: 11434
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Found at i:81 original size:22 final size:22
Alignment explanation
Indices: 32--130 Score: 103
Period size: 21 Copynumber: 4.6 Consensus size: 22
22 TATTTTTATG
*
32 AAATTTTGATAACTACCCTA-A
1 AAATTTTGATAACTACCATATA
* *
53 AAATTTTGATAAGTACCATATG
1 AAATTTTGATAACTACCATATA
*
75 AAATTTTGATAATTACC-TATA
1 AAATTTTGATAACTACCATATA
* * * *
96 AAATTGTGATAAATTCCATAAA
1 AAATTTTGATAACTACCATATA
*
118 AAACTTTGATAAC
1 AAATTTTGATAAC
131 CTAACAATGA
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
21 35 0.55
22 29 0.45
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.35
Consensus pattern (22 bp):
AAATTTTGATAACTACCATATA
Found at i:115 original size:43 final size:43
Alignment explanation
Indices: 28--130 Score: 127
Period size: 43 Copynumber: 2.4 Consensus size: 43
18 TGAATATTTT
* *
28 TATGAAATTTTGATAACTACCCTAAAAATTTTGATAAGTACCA
1 TATGAAATTTTGATAACTACCCTAAAAATTGTGATAAATACCA
* *
71 TATGAAATTTTGATAATTA-CCTATAAAATTGTGATAAATTCCA
1 TATGAAATTTTGATAACTACCCTA-AAAATTGTGATAAATACCA
** *
114 TAAAAAACTTTGATAAC
1 TATGAAATTTTGATAAC
131 CTAACAATGA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 4 0.08
43 47 0.92
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.36
Consensus pattern (43 bp):
TATGAAATTTTGATAACTACCCTAAAAATTGTGATAAATACCA
Found at i:2732 original size:27 final size:26
Alignment explanation
Indices: 2678--2738 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
2668 CTAAATTTTC
2678 ATTATTTTAATAATGGAATAATTAAAAT
1 ATTA-TTTAATAATGGAAT-ATTAAAAT
2706 ATTATTTAATAATGGCAAT-TTAGAAAT
1 ATTATTTAATAATGG-AATATTA-AAAT
2733 A-TATTT
1 ATTATTT
2739 GAAAAAAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 8 0.26
27 16 0.52
28 7 0.23
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (26 bp):
ATTATTTAATAATGGAATATTAAAAT
Found at i:3748 original size:2 final size:2
Alignment explanation
Indices: 3741--3779 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3731 GTTAGTGTAG
3741 TA TA TA TA TA 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 TA TA TA TA TA T
3780 GAAATGACCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5448 original size:2 final size:2
Alignment explanation
Indices: 5441--5468 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5431 GATATTTGTC
5441 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5469 CCATATTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6404 original size:19 final size:19
Alignment explanation
Indices: 6376--6418 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
6366 TTGGGTTTAG
6376 TCAG-TTTTTTGAGTCAGT
1 TCAGTTTTTTTGAGTCAGT
*
6394 TCAGTTTTTTTTAGTCAGT
1 TCAGTTTTTTTGAGTCAGT
6413 T-AGTTT
1 TCAGTTT
6419 GAATCTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.16, C:0.09, G:0.19, T:0.56
Consensus pattern (19 bp):
TCAGTTTTTTTGAGTCAGT
Found at i:7054 original size:33 final size:33
Alignment explanation
Indices: 6995--7082 Score: 149
Period size: 33 Copynumber: 2.6 Consensus size: 33
6985 GTAGAAAACC
6995 AATTATCTTCACCTTACCCTTTTTTTTTGGTGAA
1 AATTATCTTCACCTTA-CCTTTTTTTTTGGTGAA
**
7029 AATTATCTTCACCTTACCTTTTTTTTTTTTGAA
1 AATTATCTTCACCTTACCTTTTTTTTTGGTGAA
7062 AATTATCTTCACCTTACCTTT
1 AATTATCTTCACCTTACCTTT
7083 ACTTGAAGGA
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
33 36 0.69
34 16 0.31
ACGTcount: A:0.22, C:0.22, G:0.05, T:0.52
Consensus pattern (33 bp):
AATTATCTTCACCTTACCTTTTTTTTTGGTGAA
Found at i:7088 original size:28 final size:29
Alignment explanation
Indices: 7025--7089 Score: 69
Period size: 33 Copynumber: 2.1 Consensus size: 29
7015 TTTTTTTTGG
**
7025 TGAAAATTATCTTCACCTTACCTTTTTTTTTTT
1 TGAAAATTATCTTCACCTTACC----TTTTACT
7058 TGAAAATTATCTTCACCTTACC-TTTACT
1 TGAAAATTATCTTCACCTTACCTTTTACT
7086 TGAA
1 TGAA
7090 GGAATTGGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 8 0.27
33 22 0.73
ACGTcount: A:0.26, C:0.20, G:0.05, T:0.49
Consensus pattern (29 bp):
TGAAAATTATCTTCACCTTACCTTTTACT
Done.