Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009246.1 Corchorus capsularis cultivar CVL-1 contig09267, 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: 37537
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:3047 original size:2 final size:2
Alignment explanation
Indices: 3036--3064 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3026 TAGTATAATT
3036 TA TA -A 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 TA TA
3065 AAAGAGGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:23514 original size:12 final size:12
Alignment explanation
Indices: 23499--23528 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
23489 TTAAAATGCA
23499 AAAAAAAAAAAG
1 AAAAAAAAAAAG
23511 AAAAAAAAAAAG
1 AAAAAAAAAAAG
23523 AAAAAA
1 AAAAAA
23529 GGAGAAGCGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:24803 original size:17 final size:17
Alignment explanation
Indices: 24781--24813 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
24771 TGTTTTGAAG
24781 TTTG-TTAAATGTTTCTA
1 TTTGTTTAAAT-TTTCTA
24798 TTTGTTTAAATTTTCT
1 TTTGTTTAAATTTTCT
24814 TTGTTTTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.21, C:0.06, G:0.09, T:0.64
Consensus pattern (17 bp):
TTTGTTTAAATTTTCTA
Found at i:29184 original size:18 final size:18
Alignment explanation
Indices: 29161--29196 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
29151 GGGTGTACAA
29161 AAACCGACCGAATCGAAT
1 AAACCGACCGAATCGAAT
*
29179 AAACCGACTGAATCGAAT
1 AAACCGACCGAATCGAAT
29197 CGTAAATGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.25, G:0.17, T:0.14
Consensus pattern (18 bp):
AAACCGACCGAATCGAAT
Found at i:30419 original size:107 final size:107
Alignment explanation
Indices: 30294--30535 Score: 376
Period size: 107 Copynumber: 2.3 Consensus size: 107
30284 AATAAATTAC
* *
30294 ATATTTTATTTCTAAAACCCTATAATAATAAGTTATTAATTATGAAATTTACCCTTAAAATAAAA
1 ATATTTTATTTCTAAAACCATATAATAATAAATTATTAATTATGAAATTTACCCTTAAAATAAAA
* ** *
30359 ATAAAATTTTAATTTGGGCCTAAACTTAGTGAAATTAGTTTT
66 ATAAAATTTTAATTTAGAACTAAACTTAGTGAAATTAGTTTA
* * * *
30401 GTATTTTATTTCTAAAACCATATAACAATAAATTATTAATTTTGAAATTTACCCTTAAAATAGAA
1 ATATTTTATTTCTAAAACCATATAATAATAAATTATTAATTATGAAATTTACCCTTAAAATAAAA
30466 ATAAAATTTTAATTTAGAACTAAACTTAGTGAAATTAGTTTA
66 ATAAAATTTTAATTTAGAACTAAACTTAGTGAAATTAGTTTA
**
30508 ATATTTTATTTCTAAAACTTTATAATAA
1 ATATTTTATTTCTAAAACCATATAATAA
30536 AAAAATGTTT
Statistics
Matches: 121, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
107 121 1.00
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (107 bp):
ATATTTTATTTCTAAAACCATATAATAATAAATTATTAATTATGAAATTTACCCTTAAAATAAAA
ATAAAATTTTAATTTAGAACTAAACTTAGTGAAATTAGTTTA
Found at i:30568 original size:107 final size:106
Alignment explanation
Indices: 30294--30566 Score: 370
Period size: 107 Copynumber: 2.6 Consensus size: 106
30284 AATAAATTAC
* *
30294 ATATTTTATTTCTAAAACCCTATAATAATAAGTTATTAATTATGAAATTTACCCTTAAAATAAAA
1 ATATTTTATTTCTAAAACCATATAATAATAAATTATTAATT-TGAAATTTACCCTTAAAATAAAA
* ** *
30359 ATAAAATTTTAATTTGGGCCTAAACTTAGTGAAATTAGTTTT
65 ATAAAATTTTAATTTAGAACTAAACTTAGTGAAATTAGTTTA
* * *
30401 GTATTTTATTTCTAAAACCATATAACAATAAATTATTAATTTTGAAATTTACCCTTAAAATAGAA
1 ATATTTTATTTCTAAAACCATATAATAATAAATTATTAA-TTTGAAATTTACCCTTAAAATAAAA
30466 ATAAAATTTTAATTTAGAACTAAACTTAGTGAAATTAGTTTA
65 ATAAAATTTTAATTTAGAACTAAACTTAGTGAAATTAGTTTA
** * * *
30508 ATATTTTATTTCTAAAACTTTATAATAAAAAAATGT-TTAATTT-CAATTTACTCTTAAAA
1 ATATTTTATTTCTAAAACCATATAAT-AATAAAT-TATTAATTTGAAATTTACCCTTAAAA
30567 ATCAAATTAA
Statistics
Matches: 147, Mismatches: 16, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
106 14 0.10
107 120 0.82
108 12 0.08
109 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.42
Consensus pattern (106 bp):
ATATTTTATTTCTAAAACCATATAATAATAAATTATTAATTTGAAATTTACCCTTAAAATAAAAA
TAAAATTTTAATTTAGAACTAAACTTAGTGAAATTAGTTTA
Found at i:32260 original size:15 final size:16
Alignment explanation
Indices: 32238--32275 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
32228 CGCTCAAATG
32238 TCGGGTCAT-TTGGGT
1 TCGGGTCATGTTGGGT
* *
32253 TTGGGTCATGTTTGGT
1 TCGGGTCATGTTGGGT
32269 TCGGGTC
1 TCGGGTC
32276 TTTTTCAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.05, C:0.13, G:0.39, T:0.42
Consensus pattern (16 bp):
TCGGGTCATGTTGGGT
Done.