Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007915.1 Corchorus capsularis cultivar CVL-1 contig07936, 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: 10977
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2884 original size:17 final size:19
Alignment explanation
Indices: 2862--2897 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
2852 CCAATGTCTT
2862 CTAAACTAA-ATA-AATAA
1 CTAAACTAAGATAGAATAA
2879 CTAAACTAAGATAGAATAA
1 CTAAACTAAGATAGAATAA
2898 AGGCCCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 3 0.18
19 5 0.29
ACGTcount: A:0.61, C:0.11, G:0.06, T:0.22
Consensus pattern (19 bp):
CTAAACTAAGATAGAATAA
Found at i:5079 original size:2 final size:2
Alignment explanation
Indices: 5072--5105 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5062 ATTTTTCATC
5072 AT AT AT 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 AT AT AT
5106 TTTGCCAAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8272 original size:6 final size:6
Alignment explanation
Indices: 8252--8337 Score: 82
Period size: 6 Copynumber: 15.7 Consensus size: 6
8242 AGTCAACGTT
8252 CCGAAC CCG--C CCGAAC CCGAAC CCGAGA- -C-AAC CCGAAC CCGAAC
1 CCGAAC CCGAAC CCGAAC CCGAAC CCGA-AC CCGAAC CCGAAC CCGAAC
* *
8296 CCG--C CCGAAC CCGAAC GCAAAC CCGAAC CCG-AC CCG-AC CCGA
1 CCGAAC CCGAAC CCGAAC CCGAAC CCGAAC CCGAAC CCGAAC CCGA
8338 GATCAAAATA
Statistics
Matches: 67, Mismatches: 4, Indels: 18
0.75 0.04 0.20
Matches are distributed among these distances:
3 1 0.01
4 9 0.13
5 12 0.18
6 44 0.66
7 1 0.01
ACGTcount: A:0.30, C:0.51, G:0.19, T:0.00
Consensus pattern (6 bp):
CCGAAC
Found at i:8306 original size:22 final size:23
Alignment explanation
Indices: 8261--8337 Score: 81
Period size: 22 Copynumber: 3.5 Consensus size: 23
8251 TCCGAACCCG
**
8261 CCCGAACCCGAACCCGAGAC-AA
1 CCCGAACCCGAACCCGACCCGAA
8283 CCCGAACCCGAACCCG-CCCGAA
1 CCCGAACCCGAACCCGACCCGAA
* *
8305 CCCGAACGCAAACCCGAACCCG-A
1 CCCGAACCCGAACCCG-ACCCGAA
8328 CCCG-ACCCGA
1 CCCGAACCCGA
8338 GATCAAAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.02
22 36 0.78
23 5 0.11
24 4 0.09
ACGTcount: A:0.31, C:0.51, G:0.18, T:0.00
Consensus pattern (23 bp):
CCCGAACCCGAACCCGACCCGAA
Found at i:8337 original size:16 final size:16
Alignment explanation
Indices: 8252--8337 Score: 77
Period size: 16 Copynumber: 5.2 Consensus size: 16
8242 AGTCAACGTT
8252 CCGAACCCG-CCCGAAC
1 CCGAACCCGACCCG-AC
** *
8268 CCGAACCCGAGACAAC
1 CCGAACCCGACCCGAC
8284 CCGAACCCGAACCCG-C
1 CCGAACCCG-ACCCGAC
**
8300 CCGAACCCGAACGCAAAC
1 CCGAACCCG-AC-CCGAC
8318 CCGAACCCGACCCGAC
1 CCGAACCCGACCCGAC
8334 CCGA
1 CCGA
8338 GATCAAAATA
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
16 40 0.71
17 6 0.11
18 10 0.18
ACGTcount: A:0.30, C:0.51, G:0.19, T:0.00
Consensus pattern (16 bp):
CCGAACCCGACCCGAC
Found at i:9141 original size:15 final size:16
Alignment explanation
Indices: 9092--9149 Score: 82
Period size: 16 Copynumber: 3.7 Consensus size: 16
9082 CCCGACCCGG
* *
9092 ACCCGAACCCAAAAAA
1 ACCCGAACCCGAAAAT
9108 ACCCGAACCCGAAAAT
1 ACCCGAACCCGAAAAT
*
9124 ACCCGAACCCG-AAGT
1 ACCCGAACCCGAAAAT
9139 ACCCGAACCCG
1 ACCCGAACCCG
9150 CCCGAACCCG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
15 14 0.36
16 25 0.64
ACGTcount: A:0.41, C:0.41, G:0.14, T:0.03
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:9155 original size:10 final size:10
Alignment explanation
Indices: 9140--9182 Score: 86
Period size: 10 Copynumber: 4.3 Consensus size: 10
9130 ACCCGAAGTA
9140 CCCGAACCCG
1 CCCGAACCCG
9150 CCCGAACCCG
1 CCCGAACCCG
9160 CCCGAACCCG
1 CCCGAACCCG
9170 CCCGAACCCG
1 CCCGAACCCG
9180 CCC
1 CCC
9183 AATTGCCAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.19, C:0.63, G:0.19, T:0.00
Consensus pattern (10 bp):
CCCGAACCCG
Done.