Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016657.1 Corchorus olitorius cultivar O-4 contig16690, 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: 20012
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30
Found at i:345 original size:15 final size:15
Alignment explanation
Indices: 312--354 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
302 TACATACCAC
*
312 TAATAATAATTATTA
1 TAATAATAATAATTA
327 TAATAATAATAAGTT-
1 TAATAATAATAA-TTA
*
342 TAATAATTATAAT
1 TAATAATAATAAT
355 ATTAAGATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 1 0.04
15 22 0.88
16 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
TAATAATAATAATTA
Found at i:354 original size:9 final size:9
Alignment explanation
Indices: 314--355 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
304 CATACCACTA
314 ATAATAATT
1 ATAATAATT
* *
323 ATTATAATA
1 ATAATAATT
332 ATAATAAGTT
1 ATAATAA-TT
342 -TAATAATT
1 ATAATAATT
350 ATAATA
1 ATAATA
356 TTAAGATGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
8 2 0.07
9 24 0.89
10 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (9 bp):
ATAATAATT
Found at i:366 original size:24 final size:24
Alignment explanation
Indices: 318--368 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
308 CCACTAATAA
* *
318 TAATTATTATAATAATAATAAGTT
1 TAATAATTATAATAATAAGAAGTT
* *
342 TAATAATTATAATATTAAGATGTT
1 TAATAATTATAATAATAAGAAGTT
366 TAA
1 TAA
369 CGTAAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (24 bp):
TAATAATTATAATAATAAGAAGTT
Found at i:5497 original size:13 final size:14
Alignment explanation
Indices: 5463--5498 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
5453 TGTTCCTTCA
5463 ACATGAATTAAGGC
1 ACATGAATTAAGGC
5477 ACATGAATTAAGGC
1 ACATGAATTAAGGC
5491 A-ATGAATT
1 ACATGAATT
5499 TTCCCTCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.25
Consensus pattern (14 bp):
ACATGAATTAAGGC
Found at i:11793 original size:7 final size:6
Alignment explanation
Indices: 11775--11800 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
11765 ATATATGCAC
11775 ATAAAA ATAAAA ATAAAA ATAAAA AT
1 ATAAAA ATAAAA ATAAAA ATAAAA AT
11801 TAAATACTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:15609 original size:13 final size:13
Alignment explanation
Indices: 15591--15615 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15581 AAGAGTTCTG
15591 AAAAAAAAAATTA
1 AAAAAAAAAATTA
15604 AAAAAAAAAATT
1 AAAAAAAAAATT
15616 TCTTAAAACT
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAAAAAAATTA
Found at i:19138 original size:48 final size:48
Alignment explanation
Indices: 19082--19180 Score: 128
Period size: 49 Copynumber: 2.1 Consensus size: 48
19072 TTCGGAATTT
* ** *
19082 AAAAGAAAGATTGGAGCCCAA-AAAACCTATGTACTAGATTAAAGCCC
1 AAAAGAAAGAATAAAGCCCAACAAAACCTATGTACCAGATTAAAGCCC
* *
19129 AAAAGGAAAGAATAAAGCCCAACGAAACCTATGTACCAGATTGAAGCCC
1 AAAA-GAAAGAATAAAGCCCAACAAAACCTATGTACCAGATTAAAGCCC
19178 AAA
1 AAA
19181 GCAATTTATG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
47 4 0.09
48 14 0.32
49 26 0.59
ACGTcount: A:0.48, C:0.20, G:0.17, T:0.14
Consensus pattern (48 bp):
AAAAGAAAGAATAAAGCCCAACAAAACCTATGTACCAGATTAAAGCCC
Found at i:19563 original size:17 final size:17
Alignment explanation
Indices: 19541--19580 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
19531 AAATTAAATA
**
19541 TTTTTATTTTAATGTAT
1 TTTTTATTAAAATGTAT
*
19558 TTTTTATTAAAATTTAT
1 TTTTTATTAAAATGTAT
19575 TTTTTA
1 TTTTTA
19581 ATAATAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTTTATTAAAATGTAT
Done.