Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022845.1 Corchorus olitorius cultivar O-4 contig22878, 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: 15614
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:6639 original size:137 final size:137
Alignment explanation
Indices: 6423--6705 Score: 557
Period size: 137 Copynumber: 2.1 Consensus size: 137
6413 CCATGACCCG
6423 GCCATGCCGAGGCCAAGCACCAGCCACACCAGGCCCTAGCCCGGACGTGTCCGAGCTAAAGGCCG
1 GCCATGCCGAGGCCAAGCACCAGCCACACCAGGCCCTAGCCCGGACGTGTCCGAGCTAAAGGCCG
6488 AGCACGCCAGGCACCTCAGCCAAGCCACGCAGAAACAAAGGCCATGTCGCGCATCAGCACCAGGC
66 AGCACGCCAGGCACCTCAGCCAAGCCACGCAGAAACAAAGGCCATGTCGCGCATCAGCACCAGGC
6553 ATGTCGA
131 ATGTCGA
6560 GCCATGCCGAGGCCAAGCACCAGCCACACCAGGCCCTAGCCCGGACGTGTCCGAGCTAAAGGCCG
1 GCCATGCCGAGGCCAAGCACCAGCCACACCAGGCCCTAGCCCGGACGTGTCCGAGCTAAAGGCCG
*
6625 AGCACGCCAGGCACCTCAGCCAAGCCACGCAGAGACAAAGGCCATGTCGCGCATCAGCACCAGGC
66 AGCACGCCAGGCACCTCAGCCAAGCCACGCAGAAACAAAGGCCATGTCGCGCATCAGCACCAGGC
6690 ATGTCGA
131 ATGTCGA
6697 GCCATGCCG
1 GCCATGCCG
6706 CGCACCAGCA
Statistics
Matches: 145, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 145 1.00
ACGTcount: A:0.26, C:0.38, G:0.28, T:0.08
Consensus pattern (137 bp):
GCCATGCCGAGGCCAAGCACCAGCCACACCAGGCCCTAGCCCGGACGTGTCCGAGCTAAAGGCCG
AGCACGCCAGGCACCTCAGCCAAGCCACGCAGAAACAAAGGCCATGTCGCGCATCAGCACCAGGC
ATGTCGA
Found at i:9940 original size:32 final size:32
Alignment explanation
Indices: 9902--9965 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
9892 GTGAGTAATT
9902 CTTTTCTTTACTCCAATGTAGAATTTAATTGA
1 CTTTTCTTTACTCCAATGTAGAATTTAATTGA
9934 CTTTTCTTTACTCCAATGTAGAATTTAATTGA
1 CTTTTCTTTACTCCAATGTAGAATTTAATTGA
9966 TCTCTTGACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.47
Consensus pattern (32 bp):
CTTTTCTTTACTCCAATGTAGAATTTAATTGA
Found at i:9958 original size:27 final size:28
Alignment explanation
Indices: 9895--9958 Score: 71
Period size: 32 Copynumber: 2.2 Consensus size: 28
9885 TTTATGAGTG
9895 AGTAATT--CTTTTCTTTACTCCAATGT
1 AGTAATTGACTTTTCTTTACTCCAATGT
9921 AGAATTTAATTGACTTTTCTTTACTCCAATGT
1 AG----TAATTGACTTTTCTTTACTCCAATGT
9953 AG-AATT
1 AGTAATT
9959 TAATTGATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
26 2 0.06
27 4 0.12
30 5 0.16
32 21 0.66
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.47
Consensus pattern (28 bp):
AGTAATTGACTTTTCTTTACTCCAATGT
Found at i:11473 original size:2 final size:2
Alignment explanation
Indices: 11466--11494 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11456 TTTAGTTGGG
11466 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
11495 GTTATTTGAA
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:14271 original size:4 final size:4
Alignment explanation
Indices: 14258--14292 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
14248 TCCTTTCTAT
14258 TTTA -TTA TTTA TTTA TTTA TTTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTT
14293 TTTTTAAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.10
4 22 0.76
5 4 0.14
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:14283 original size:13 final size:13
Alignment explanation
Indices: 14265--14298 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
14255 TATTTTATTA
14265 TTTATTTATTTAT
1 TTTATTTATTTAT
14278 TTTATTTATTTAT
1 TTTATTTATTTAT
*
14291 TTTTTTTA
1 TTTATTTA
14299 AACTTTGGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTATTTATTTAT
Found at i:14284 original size:17 final size:17
Alignment explanation
Indices: 14262--14298 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
14252 TTCTATTTTA
14262 TTATTTATTTATTTATT
1 TTATTTATTTATTTATT
*
14279 TTATTTATTTATTTTTT
1 TTATTTATTTATTTATT
14296 TTA
1 TTA
14299 AACTTTGGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
TTATTTATTTATTTATT
Found at i:14401 original size:24 final size:24
Alignment explanation
Indices: 14350--14402 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
14340 CTGGGCCGTG
*
14350 CTGGCTGGCACGCTGGCCCGCGTG
1 CTGGCTGGCACGCTGGCCCGCGTC
* *
14374 CTGGCTGGCAGGCTGGGCCTGCG-C
1 CTGGCTGGCACGCT-GGCCCGCGTC
14398 CTGGC
1 CTGGC
14403 CAGCCCATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.04, C:0.36, G:0.43, T:0.17
Consensus pattern (24 bp):
CTGGCTGGCACGCTGGCCCGCGTC
Done.