Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010270.1 Corchorus capsularis cultivar CVL-1 contig10291, 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: 78901
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:15719 original size:1 final size:1
Alignment explanation
Indices: 15713--15738 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
15703 ATACAATTAC
15713 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
15739 GGACAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:20288 original size:12 final size:13
Alignment explanation
Indices: 20249--20290 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
20239 TTTATGTCCC
20249 AAAAT-AACAAAT
1 AAAATGAACAAAT
20261 AGAAATGAACAAAT
1 A-AAATGAACAAAT
*
20275 AAAATG-ATAAAT
1 AAAATGAACAAAT
20287 AAAA
1 AAAA
20291 AGGGACGGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 10 0.37
13 9 0.33
14 8 0.30
ACGTcount: A:0.71, C:0.05, G:0.07, T:0.17
Consensus pattern (13 bp):
AAAATGAACAAAT
Found at i:20805 original size:29 final size:29
Alignment explanation
Indices: 20760--20830 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 29
20750 TGAGAAAGGG
20760 CAAAACGTCCTAAAATTGAGAGTTC-ATGGA
1 CAAAACGTCC-AAAATTGA-AGTTCAATGGA
* *
20790 CAAAATGTCCAAAATTGAAGTTCAATGGG
1 CAAAACGTCCAAAATTGAAGTTCAATGGA
20819 CAAAACGTCCAA
1 CAAAACGTCCAA
20831 GCGCTACAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.14
29 23 0.62
30 9 0.24
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.21
Consensus pattern (29 bp):
CAAAACGTCCAAAATTGAAGTTCAATGGA
Found at i:26577 original size:30 final size:30
Alignment explanation
Indices: 26543--26604 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
26533 TATTATCCTT
* *
26543 TTTGCCCTTGAATTATGGAGTTAAAGATAC
1 TTTGCCCCTGAATTATGGAGTTAAAGACAC
* *
26573 TTTGCCCCTGAGTTATGGGGTTAAAGACAC
1 TTTGCCCCTGAATTATGGAGTTAAAGACAC
26603 TT
1 TT
26605 CGCTCCTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (30 bp):
TTTGCCCCTGAATTATGGAGTTAAAGACAC
Found at i:48586 original size:13 final size:13
Alignment explanation
Indices: 48568--48592 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48558 AACATCAGCA
48568 AAAAATAAAAAAT
1 AAAAATAAAAAAT
48581 AAAAATAAAAAA
1 AAAAATAAAAAA
48593 ATCCTCCACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:49287 original size:31 final size:31
Alignment explanation
Indices: 49251--49310 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
49241 TTTGGTGGAA
* **
49251 AAAGTA-CAGAATTGGTCCCTTGAGTGGAACC
1 AAAGTAGCA-AATTAGTCCCTCAAGTGGAACC
49282 AAAGTAGCAAATTAGTCCCTCAAGTGGAA
1 AAAGTAGCAAATTAGTCCCTCAAGTGGAA
49311 AAATAAGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 23 0.92
32 2 0.08
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (31 bp):
AAAGTAGCAAATTAGTCCCTCAAGTGGAACC
Found at i:50971 original size:17 final size:18
Alignment explanation
Indices: 50935--50975 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
50925 TATTAATAAA
*
50935 CATGTTTAATTAGTTAGC
1 CATGTTCAATTAGTTAGC
50953 CATGTTCAATTAG-TAGC
1 CATGTTCAATTAGTTAGC
50970 CATGTT
1 CATGTT
50976 TGTTTTGGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (18 bp):
CATGTTCAATTAGTTAGC
Found at i:62968 original size:2 final size:2
Alignment explanation
Indices: 62961--62992 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
62951 AAATCAGAGC
62961 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
62993 GTTGCCATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:76954 original size:37 final size:35
Alignment explanation
Indices: 76858--76957 Score: 114
Period size: 34 Copynumber: 2.8 Consensus size: 35
76848 AAAATGAGGT
76858 TATTTTCCAGAAAACGTAATATTTTCTGTTGTTTGG
1 TATTTTCCAGAAAAC-TAATATTTTCTGTTGTTTGG
* *
76894 T-TGTTTCGA-AAAACAAATATTTTCTGTTGTTTGG
1 TAT-TTTCCAGAAAACTAATATTTTCTGTTGTTTGG
* *
76928 CTATTTTCCAGAAAATTAGTATTTTTCTGT
1 -TATTTTCCAGAAAACTAATA-TTTTCTGT
76958 GAAGGATGTA
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
34 19 0.36
35 12 0.23
36 14 0.26
37 8 0.15
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.48
Consensus pattern (35 bp):
TATTTTCCAGAAAACTAATATTTTCTGTTGTTTGG
Found at i:77006 original size:16 final size:16
Alignment explanation
Indices: 76987--77017 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
76977 AAAATGATTA
*
76987 TATATAAAAATTAAAC
1 TATATAAAAAATAAAC
77003 TATATAAAAAATAAA
1 TATATAAAAAATAAA
77018 ATCATCCTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
TATATAAAAAATAAAC
Found at i:77283 original size:2 final size:2
Alignment explanation
Indices: 77272--77306 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
77262 TTAAAAGTTC
77272 AT AT -T 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 AT
77307 TATCCTACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:78387 original size:22 final size:23
Alignment explanation
Indices: 78352--78397 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
78342 ATTTCCCGTG
*
78352 TTTTGTGTATATTTTCCGTGGAC
1 TTTTATGTATATTTTCCGTGGAC
*
78375 TTTTATGT-TATTTTCCGTTGAC
1 TTTTATGTATATTTTCCGTGGAC
78397 T
1 T
78398 ACCCTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.13, C:0.13, G:0.17, T:0.57
Consensus pattern (23 bp):
TTTTATGTATATTTTCCGTGGAC
Found at i:78645 original size:31 final size:29
Alignment explanation
Indices: 78610--78668 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
78600 AACTTTATGT
78610 TTTCCGATTATACCATTGTTTTTAAAATTTA
1 TTTCCGATTATACC-TT-TTTTTAAAATTTA
* *
78641 TTTCCGATTGTATCTTTTTTTAAAATTT
1 TTTCCGATTATACCTTTTTTTAAAATTT
78669 CTAAATTGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 12 0.46
30 2 0.08
31 12 0.46
ACGTcount: A:0.25, C:0.12, G:0.07, T:0.56
Consensus pattern (29 bp):
TTTCCGATTATACCTTTTTTTAAAATTTA
Found at i:78873 original size:2 final size:2
Alignment explanation
Indices: 78862--78901 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
78852 CTTTTATAAG
78862 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.