Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024191.1 Corchorus olitorius cultivar O-4 contig24224, 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: 17986
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:453 original size:13 final size:13
Alignment explanation
Indices: 435--461 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
425 TGAACTATTG
435 AACCTATTAAATA
1 AACCTATTAAATA
448 AACCTATTAAATA
1 AACCTATTAAATA
461 A
1 A
462 GCACACATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (13 bp):
AACCTATTAAATA
Found at i:506 original size:53 final size:53
Alignment explanation
Indices: 448--553 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
438 CTATTAAATA
448 AACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACTATTG
1 AACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACTATTG
501 AACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACTATTG
1 AACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACTATTG
554 GATTTAAAGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.51, C:0.19, G:0.08, T:0.23
Consensus pattern (53 bp):
AACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACTATTG
Found at i:2368 original size:14 final size:14
Alignment explanation
Indices: 2349--2383 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
2339 GTTTATCTCT
2349 TTTTTTTTTCTTTG
1 TTTTTTTTTCTTTG
2363 TTTTTTTTTCTTTG
1 TTTTTTTTTCTTTG
2377 TTTTTTT
1 TTTTTTT
2384 GAAAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.89
Consensus pattern (14 bp):
TTTTTTTTTCTTTG
Found at i:5445 original size:2 final size:2
Alignment explanation
Indices: 5440--5486 Score: 76
Period size: 2 Copynumber: 23.0 Consensus size: 2
5430 ATAACTGAGA
*
5440 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
5483 AT AT
1 AT AT
5487 GTGTTTCTAC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 41 0.98
3 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10980 original size:21 final size:21
Alignment explanation
Indices: 10945--10986 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
10935 TGTGTGTGTG
*
10945 TGTGATTGTTTGGTTTGGTAGA
1 TGTGATTGATTGGTTT-GTAGA
10967 TGTGA-TGATTGGTTTGTAGA
1 TGTGATTGATTGGTTTGTAGA
10987 GACCGAGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.48
Consensus pattern (21 bp):
TGTGATTGATTGGTTTGTAGA
Found at i:11017 original size:25 final size:25
Alignment explanation
Indices: 10983--11031 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
10973 GATTGGTTTG
10983 TAGAGACCGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
11008 TAGAGACCGAGCGAGAGTGCTCAA
1 TAGAGACCGAGCGAGAGTGCTCAA
11032 GATTGTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.33, T:0.12
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAA
Found at i:16452 original size:13 final size:13
Alignment explanation
Indices: 16434--16458 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16424 GAAGACCAAC
16434 ACAAAACCACAAG
1 ACAAAACCACAAG
16447 ACAAAACCACAA
1 ACAAAACCACAA
16459 TTCTGCTATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.32, G:0.04, T:0.00
Consensus pattern (13 bp):
ACAAAACCACAAG
Found at i:17182 original size:29 final size:28
Alignment explanation
Indices: 17126--17182 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
17116 TATGTTTTGC
* *
17126 TTTTGGGACAAAATAATTCATTATGTTT
1 TTTTGGGACAAAATAATCCATTACGTTT
* *
17154 TTTTCGGGACAAATTAATCCCTTACGTTT
1 TTTT-GGGACAAAATAATCCATTACGTTT
17183 CAAAAATGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (28 bp):
TTTTGGGACAAAATAATCCATTACGTTT
Found at i:17341 original size:31 final size:31
Alignment explanation
Indices: 17306--17402 Score: 167
Period size: 31 Copynumber: 3.1 Consensus size: 31
17296 AAGGGAATGA
17306 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
17337 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
* *
17368 TTTGTCCCAAAAGAAAAATATAAGAGAATTTT
1 TTTGTCCCAAAAGAAAAACATAAG-GGATTTT
17400 TTT
1 TTT
17403 AGTATTTAGT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
31 54 0.86
32 9 0.14
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.32
Consensus pattern (31 bp):
TTTGTCCCAAAAGAAAAACATAAGGGATTTT
Done.