Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014980.1 Corchorus olitorius cultivar O-4 contig15013, 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: 70729
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:4294 original size:27 final size:26
Alignment explanation
Indices: 4253--4303 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
4243 AACTCACCAT
4253 TTTGCTCTTCCTTTTTCTCTCTTTTTGG
1 TTTGCTCTTCCTTTTT-T-TCTTTTTGG
*
4281 TTTGC-CTTTCTTTTTTTCTTTTT
1 TTTGCTCTTCCTTTTTTTCTTTTT
4304 CTTTTCTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 1 0.05
27 9 0.41
28 5 0.23
ACGTcount: A:0.00, C:0.22, G:0.08, T:0.71
Consensus pattern (26 bp):
TTTGCTCTTCCTTTTTTTCTTTTTGG
Found at i:17607 original size:72 final size:73
Alignment explanation
Indices: 17519--17670 Score: 279
Period size: 72 Copynumber: 2.1 Consensus size: 73
17509 GTGCCATGTG
*
17519 TCTTGTTTGTTAAATGAAAGGAGTAATATAATGATATGAATATTCAATTCCATAAATTAGGCTTA
1 TCTTGTTTGTTAAATGAAAGGAGTAATATAATGATACGAATATTCAATTCCATAAATTAGGCTTA
17584 TACATACA
66 TACATACA
*
17592 T-TTGTTTGTTAAATGAAAGGTGTAATATAATGATACGAATATTCAATTCCATAAATTAGGCTTA
1 TCTTGTTTGTTAAATGAAAGGAGTAATATAATGATACGAATATTCAATTCCATAAATTAGGCTTA
17656 TACATACA
66 TACATACA
17664 TCTTGTT
1 TCTTGTT
17671 ATAAATGAAA
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
72 70 0.92
73 6 0.08
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.39
Consensus pattern (73 bp):
TCTTGTTTGTTAAATGAAAGGAGTAATATAATGATACGAATATTCAATTCCATAAATTAGGCTTA
TACATACA
Found at i:25191 original size:16 final size:16
Alignment explanation
Indices: 25170--25201 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
25160 GTTTGGTTCC
*
25170 AAGTTTGAGGACTGGT
1 AAGTTTGAAGACTGGT
25186 AAGTTTGAAGACTGGT
1 AAGTTTGAAGACTGGT
25202 GGTGGTGGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.06, G:0.34, T:0.31
Consensus pattern (16 bp):
AAGTTTGAAGACTGGT
Found at i:26191 original size:2 final size:2
Alignment explanation
Indices: 26184--26209 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
26174 ATACGTTGTT
26184 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
26210 ATAGTTCCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33883 original size:17 final size:16
Alignment explanation
Indices: 33843--33893 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
33833 CATGTAATCT
*
33843 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
33859 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
33876 TTAGATCACTAGTGATC
1 TT-GATCACTGGTGATC
33893 T
1 T
33894 GGGGGTGATC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:41865 original size:24 final size:24
Alignment explanation
Indices: 41838--41884 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
41828 TGGGGAAAGG
41838 AGCCTGTAATTTCATAATTTGTTA
1 AGCCTGTAATTTCATAATTTGTTA
41862 AGCCTGTAATTTCATAATTTGTT
1 AGCCTGTAATTTCATAATTTGTT
41885 GGTTGTCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.47
Consensus pattern (24 bp):
AGCCTGTAATTTCATAATTTGTTA
Found at i:58373 original size:47 final size:47
Alignment explanation
Indices: 58299--58392 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 47
58289 AGCTAAAAAC
*
58299 TTCTTTAATTTACTGCACTTCCCAAAGAAGAAATTACGTCAATTGGG
1 TTCTTTAATTTACTGCACTTACCAAAGAAGAAATTACGTCAATTGGG
* * *
58346 TTCTTTAGTTTACTGCACTTACTAAAGAAGAAATTACGTTAATTGGG
1 TTCTTTAATTTACTGCACTTACCAAAGAAGAAATTACGTCAATTGGG
58393 AGCATGTACA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (47 bp):
TTCTTTAATTTACTGCACTTACCAAAGAAGAAATTACGTCAATTGGG
Found at i:64438 original size:14 final size:14
Alignment explanation
Indices: 64419--64445 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
64409 GCCTGTAGTG
64419 AAAAAAGGGAAAAA
1 AAAAAAGGGAAAAA
64433 AAAAAAGGGAAAA
1 AAAAAAGGGAAAA
64446 TATCACAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (14 bp):
AAAAAAGGGAAAAA
Found at i:66732 original size:1 final size:1
Alignment explanation
Indices: 66726--66761 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
66716 CTCCAAATAT
66726 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
66762 CTAGTCTAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:67292 original size:5 final size:5
Alignment explanation
Indices: 67273--67305 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
67263 TTTCAGTTTC
*
67273 AATTT -ATTT AATTT AGTTT AATTT AATTT AATT
1 AATTT AATTT AATTT AATTT AATTT AATTT AATT
67306 GCTTTTACTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (5 bp):
AATTT
Found at i:67294 original size:10 final size:10
Alignment explanation
Indices: 67267--67305 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
67257 TGTGCTTTTC
67267 AGTTTCAATTT
1 AGTTT-AATTT
67278 A-TTTAATTT
1 AGTTTAATTT
67287 AGTTTAATTT
1 AGTTTAATTT
*
67297 AATTTAATT
1 AGTTTAATT
67306 GCTTTTACTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 6 0.23
10 19 0.73
11 1 0.04
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (10 bp):
AGTTTAATTT
Done.