Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014581.1 Corchorus capsularis cultivar CVL-1 contig14602, 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: 39081
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Found at i:7406 original size:18 final size:19
Alignment explanation
Indices: 7372--7409 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
7362 ATCCATCGTT
*
7372 ATCTCCATGGTCTCCATGC
1 ATCTCCATGGCCTCCATGC
7391 ATCTCCAT-GCCTCCATGC
1 ATCTCCATGGCCTCCATGC
7409 A
1 A
7410 GCCCATGCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.18, C:0.39, G:0.13, T:0.29
Consensus pattern (19 bp):
ATCTCCATGGCCTCCATGC
Found at i:7487 original size:30 final size:30
Alignment explanation
Indices: 7453--7515 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
7443 CATCTTCAAG
* *
7453 TCCATGATAACTCCTT-GGTGCATCATTCCC
1 TCCATGATAA-GCCTTGGGCGCATCATTCCC
*
7483 TCCATGATAAGCCTTGGGCGCATTATTCCC
1 TCCATGATAAGCCTTGGGCGCATCATTCCC
7513 TCC
1 TCC
7516 CCCTTGAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.19, C:0.33, G:0.16, T:0.32
Consensus pattern (30 bp):
TCCATGATAAGCCTTGGGCGCATCATTCCC
Found at i:7924 original size:19 final size:18
Alignment explanation
Indices: 7900--7938 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
7890 TGAAGATTTG
*
7900 TTGAAGATAATTTGAAGAA
1 TTGAAGACAA-TTGAAGAA
*
7919 TTGAAGACCATTGAAGAA
1 TTGAAGACAATTGAAGAA
7937 TT
1 TT
7939 ATTTCAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.31
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAA
Found at i:13050 original size:6 final size:6
Alignment explanation
Indices: 13039--13065 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
13029 ATTAATTTGC
13039 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
13066 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:14226 original size:40 final size:40
Alignment explanation
Indices: 14169--14273 Score: 165
Period size: 40 Copynumber: 2.6 Consensus size: 40
14159 AATTTTATTA
* *
14169 ATTTCGAAAAGTCTTCTCTTGGATTTCTAAAAAAACTCTT
1 ATTTCCAAAAGTCTTCTCTTGGATTACTAAAAAAACTCTT
*
14209 ATTTCCAAAAGTTTTCTCTTGGAATTACTAAAAAAACTCTT
1 ATTTCCAAAAGTCTTCTCTTGG-ATTACTAAAAAAACTCTT
14250 ATTTTCCAAAAGTCTTCTCTTGGA
1 A-TTTCCAAAAGTCTTCTCTTGGA
14274 ATTGTTTGAA
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
40 20 0.34
41 19 0.32
42 20 0.34
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40
Consensus pattern (40 bp):
ATTTCCAAAAGTCTTCTCTTGGATTACTAAAAAAACTCTT
Found at i:14256 original size:42 final size:41
Alignment explanation
Indices: 14169--14276 Score: 173
Period size: 42 Copynumber: 2.6 Consensus size: 41
14159 AATTTTATTA
* *
14169 ATTTCGAAAAGTCTTCTCTTGG-ATTTCTAAAAAAACTCTT
1 ATTTCCAAAAGTCTTCTCTTGGAATTACTAAAAAAACTCTT
*
14209 ATTTCCAAAAGTTTTCTCTTGGAATTACTAAAAAAACTCTT
1 ATTTCCAAAAGTCTTCTCTTGGAATTACTAAAAAAACTCTT
14250 ATTTTCCAAAAGTCTTCTCTTGGAATT
1 A-TTTCCAAAAGTCTTCTCTTGGAATT
14277 GTTTGAATAG
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
40 20 0.32
41 18 0.29
42 24 0.39
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (41 bp):
ATTTCCAAAAGTCTTCTCTTGGAATTACTAAAAAAACTCTT
Found at i:24644 original size:21 final size:20
Alignment explanation
Indices: 24615--24662 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
24605 TAGATTTAGA
* *
24615 TTTAATTTACTTTGCTTTGTT
1 TTTAATTTA-ATTGCTTTCTT
*
24636 TTTAGTTTAATTGCTTTCTT
1 TTTAATTTAATTGCTTTCTT
24656 TTTAATT
1 TTTAATT
24663 AATCTGTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.17, C:0.08, G:0.08, T:0.67
Consensus pattern (20 bp):
TTTAATTTAATTGCTTTCTT
Found at i:27659 original size:21 final size:19
Alignment explanation
Indices: 27634--27672 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
27624 TATGACTCAT
27634 ATGCTATGAATGCTATGATTG
1 ATGCTATGAAT-CT-TGATTG
*
27655 ATGCTTTGAATCTTGATT
1 ATGCTATGAATCTTGATT
27673 TGCTTGATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.26, C:0.10, G:0.21, T:0.44
Consensus pattern (19 bp):
ATGCTATGAATCTTGATTG
Done.