Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012149.1 Corchorus capsularis cultivar CVL-1 contig12170, 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: 25608
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:622 original size:23 final size:23
Alignment explanation
Indices: 590--635 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
580 GTTAGTCACC
590 TGCACATACATGACTGAATTCAG
1 TGCACATACATGACTGAATTCAG
*
613 TGCACGTACATGACTGAATTCAG
1 TGCACATACATGACTGAATTCAG
636 GTACGACATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26
Consensus pattern (23 bp):
TGCACATACATGACTGAATTCAG
Found at i:1056 original size:32 final size:32
Alignment explanation
Indices: 1019--1095 Score: 118
Period size: 32 Copynumber: 2.4 Consensus size: 32
1009 ATACAAAATT
*
1019 GGGATTATACATAACTAATAAATGGGTTGATG
1 GGGATTATACATAACTAATAAATGGGTTAATG
* *
1051 GGGATTATACATAATTAATCAATGGGTTAATG
1 GGGATTATACATAACTAATAAATGGGTTAATG
*
1083 CGGATTATACATA
1 GGGATTATACATA
1096 TTTTTCAGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (32 bp):
GGGATTATACATAACTAATAAATGGGTTAATG
Found at i:2007 original size:11 final size:11
Alignment explanation
Indices: 1993--2034 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
1983 ATTCATAACA
1993 AATTTATAATT
1 AATTTATAATT
2004 AATTTATAATT
1 AATTTATAATT
2015 -ATTTGATAAATT
1 AATTT-AT-AATT
*
2027 ATTTTATA
1 AATTTATA
2035 TAGGAAAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 4 0.15
11 14 0.52
12 6 0.22
13 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (11 bp):
AATTTATAATT
Found at i:2766 original size:13 final size:13
Alignment explanation
Indices: 2748--2774 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2738 GTTATACTTT
2748 TTATACTTTTTAA
1 TTATACTTTTTAA
2761 TTATACTTTTTAA
1 TTATACTTTTTAA
2774 T
1 T
2775 CTTTTTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (13 bp):
TTATACTTTTTAA
Found at i:2767 original size:22 final size:22
Alignment explanation
Indices: 2739--2780 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2729 AATTACATTG
2739 TTATACTTTTT-ATACTTTTTAA
1 TTATACTTTTTAAT-CTTTTTAA
2761 TTATACTTTTTAATCTTTTT
1 TTATACTTTTTAATCTTTTT
2781 TTTCTGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.67
Consensus pattern (22 bp):
TTATACTTTTTAATCTTTTTAA
Found at i:4114 original size:2 final size:2
Alignment explanation
Indices: 4065--4097 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
4055 GATATCTCAA
4065 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4098 TAGGAATTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:11259 original size:30 final size:28
Alignment explanation
Indices: 11188--11265 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 28
11178 GAACTTACAC
*
11188 AAAACGGCCAAATAAGCCCCTGAACTCT
1 AAAAAGGCCAAATAAGCCCCTGAACTCT
**
11216 -AATTGCAGCCAAATAAGCCCCTGAACTCTTT
1 AAAAAG--GCCAAATAAGCCCCTGAACTC--T
11247 AAAAAGGCCAAATAAGCCC
1 AAAAAGGCCAAATAAGCCC
11266 TTTTCTGATG
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
27 3 0.07
29 21 0.51
30 13 0.32
31 1 0.02
32 3 0.07
ACGTcount: A:0.40, C:0.29, G:0.14, T:0.17
Consensus pattern (28 bp):
AAAAAGGCCAAATAAGCCCCTGAACTCT
Found at i:16428 original size:4 final size:4
Alignment explanation
Indices: 16419--16447 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
16409 ATATTTCCAG
16419 TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT T
16448 GGATTTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:25233 original size:26 final size:26
Alignment explanation
Indices: 25204--25256 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
25194 GATGAAAAAT
25204 TAAATATATACTTGGCATTTATTTCC
1 TAAATATATACTTGGCATTTATTTCC
25230 TAAATATATACTTGGCATTTATTTCC
1 TAAATATATACTTGGCATTTATTTCC
25256 T
1 T
25257 TTTCACCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.08, T:0.47
Consensus pattern (26 bp):
TAAATATATACTTGGCATTTATTTCC
Done.