Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013072.1 Corchorus capsularis cultivar CVL-1 contig13093, 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: 45353
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:160 original size:12 final size:11
Alignment explanation
Indices: 131--167 Score: 65
Period size: 11 Copynumber: 3.3 Consensus size: 11
121 CTTTAATCCT
131 TTTCCTTATAA
1 TTTCCTTATAA
142 TTTCCTTATAA
1 TTTCCTTATAA
153 TATTCCTTATAA
1 T-TTCCTTATAA
165 TTT
1 TTT
168 TGGATATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.27, C:0.16, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTCCTTATAA
Found at i:2819 original size:17 final size:17
Alignment explanation
Indices: 2797--2842 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
2787 CCCTCATGGT
2797 ACTAGGTAGCATGAGGC
1 ACTAGGTAGCATGAGGC
*
2814 ACTAGGTAGCATGAGGT
1 ACTAGGTAGCATGAGGC
2831 ACTAGGTAGCAT
1 ACTAGGTAGCAT
2843 CTGTTATATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.30, C:0.15, G:0.33, T:0.22
Consensus pattern (17 bp):
ACTAGGTAGCATGAGGC
Found at i:17101 original size:28 final size:28
Alignment explanation
Indices: 17067--17143 Score: 145
Period size: 28 Copynumber: 2.8 Consensus size: 28
17057 CTACTCCCTC
17067 TGTTCCTTTTTATTTGTCATCACCCTTT
1 TGTTCCTTTTTATTTGTCATCACCCTTT
17095 TGTTCCTTTTTATTTGTCATCACCCTTT
1 TGTTCCTTTTTATTTGTCATCACCCTTT
*
17123 TGTTTCTTTTTATTTGTCATC
1 TGTTCCTTTTTATTTGTCATC
17144 TTACCCTACC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.10, C:0.22, G:0.08, T:0.60
Consensus pattern (28 bp):
TGTTCCTTTTTATTTGTCATCACCCTTT
Found at i:19943 original size:2 final size:2
Alignment explanation
Indices: 19936--19963 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19926 AAAATAGCAA
19936 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19964 TACAAAGAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22748 original size:20 final size:20
Alignment explanation
Indices: 22723--22763 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
22713 TACTTTAAAC
* *
22723 AATTTAATGAGAAGTTATAA
1 AATTTAAAGAGAAATTATAA
*
22743 AATTTAAAGTGAAATTATAA
1 AATTTAAAGAGAAATTATAA
22763 A
1 A
22764 CACAATATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.34
Consensus pattern (20 bp):
AATTTAAAGAGAAATTATAA
Found at i:38350 original size:19 final size:19
Alignment explanation
Indices: 38311--38353 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
38301 ATTGTGTTTC
*
38311 ATAA-AATAAGGAAGAACA
1 ATAAGAATAAGGAAGAAAA
38329 ATAAGAATAA-GAAGAAGAA
1 ATAAGAATAAGGAAGAA-AA
38348 ATAAGA
1 ATAAGA
38354 GAGAGAACTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.67, C:0.02, G:0.19, T:0.12
Consensus pattern (19 bp):
ATAAGAATAAGGAAGAAAA
Found at i:42647 original size:27 final size:27
Alignment explanation
Indices: 42609--42690 Score: 85
Period size: 27 Copynumber: 2.9 Consensus size: 27
42599 AAAAAGTCAG
*
42609 ATTTTTACAATATTTTAATATAAA-AAT
1 ATTTTTAAAATATTTTAAT-TAAATAAT
42636 ATTTTTAAAATATTTTAAATTTAAAATAAT
1 ATTTTTAAAATATTTT-AA-TT-AAATAAT
*
42666 AGTTTTAAAATGATTTTTAATTAAA
1 ATTTTTAAAAT-A-TTTTAATTAAA
42691 CAATCGGACT
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
27 15 0.32
28 3 0.06
29 7 0.15
30 15 0.32
31 3 0.06
32 4 0.09
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (27 bp):
ATTTTTAAAATATTTTAATTAAATAAT
Found at i:42690 original size:30 final size:28
Alignment explanation
Indices: 42611--42690 Score: 83
Period size: 30 Copynumber: 2.8 Consensus size: 28
42601 AAAGTCAGAT
* *
42611 TTTTACAATA-TTTTAA-TATAAAAATAT
1 TTTTAAAATATTTTTAATTA-AAAAATAG
*
42638 TTTTAAAATATTTTAAATTTAAAATAATAG
1 TTTTAAAATATTTTTAA-TTAAAA-AATAG
42668 TTTTAAAATGATTTTTAATTAAA
1 TTTTAAAAT-ATTTTTAATTAAA
42691 CAATCGGACT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
27 9 0.20
28 5 0.11
29 3 0.07
30 20 0.45
31 7 0.16
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (28 bp):
TTTTAAAATATTTTTAATTAAAAAATAG
Done.