Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015523.1 Corchorus capsularis cultivar CVL-1 contig15544, 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: 20784
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2641 original size:20 final size:19
Alignment explanation
Indices: 2596--2653 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
2586 AATGTCACGG
2596 GATATCCGTCGATATATCC
1 GATATCCGTCGATATATCC
*
2615 GTGTATCCGTCGATATTTAT-C
1 G-ATATCCGTCGATA--TATCC
2636 GATAT-C-TCGATATATCC
1 GATATCCGTCGATATATCC
2653 G
1 G
2654 TAAATATCCG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
16 3 0.09
17 2 0.06
18 6 0.18
19 2 0.06
20 15 0.45
21 2 0.06
22 3 0.09
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.36
Consensus pattern (19 bp):
GATATCCGTCGATATATCC
Found at i:4104 original size:13 final size:12
Alignment explanation
Indices: 4081--4123 Score: 77
Period size: 12 Copynumber: 3.5 Consensus size: 12
4071 TTAATACAGG
4081 TATCGACGGATA
1 TATCGACGGATA
4093 TATCGAACGGATA
1 TATCG-ACGGATA
4106 TATCGACGGATA
1 TATCGACGGATA
4118 TATCGA
1 TATCGA
4124 GGTATCGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 18 0.60
13 12 0.40
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:5898 original size:32 final size:30
Alignment explanation
Indices: 5816--5902 Score: 117
Period size: 32 Copynumber: 2.9 Consensus size: 30
5806 TTGTCTTCTA
5816 AACTT-CAAA-TCAAGACATTTTACCCATG
1 AACTTCCAAATTCAAGACATTTTACCCATG
*
5844 AACTTCCAAATT-AAGGATATTTTACTCCATG
1 AACTTCCAAATTCAA-GACATTTTAC-CCATG
5875 AACTTCCCAAATTCAAGACATTTTACCC
1 AACTT-CCAAATTCAAGACATTTTACCC
5903 CTTGACAGAG
Statistics
Matches: 51, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
28 5 0.10
29 6 0.12
30 10 0.20
31 12 0.24
32 16 0.31
33 2 0.04
ACGTcount: A:0.37, C:0.25, G:0.07, T:0.31
Consensus pattern (30 bp):
AACTTCCAAATTCAAGACATTTTACCCATG
Found at i:7233 original size:68 final size:68
Alignment explanation
Indices: 7119--7255 Score: 265
Period size: 68 Copynumber: 2.0 Consensus size: 68
7109 TGTAAGTACC
7119 ACTGTAAGCCCTCTCTGAGATCTTTGGCATGCCCTGACCCTAAACTGAAATAGCCTCTCCTCATC
1 ACTGTAAGCCCTCTCTGAGATCTTTGGCATGCCCTGACCCTAAACTGAAATAGCCTCTCCTCATC
7184 TAA
66 TAA
*
7187 ACTGTAAGCCCTCTCTGAGATCTTTGGCATGCCCTGACCCTGAACTGAAATAGCCTCTCCTCATC
1 ACTGTAAGCCCTCTCTGAGATCTTTGGCATGCCCTGACCCTAAACTGAAATAGCCTCTCCTCATC
7252 TAA
66 TAA
7255 A
1 A
7256 ATTTTTTAAC
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (68 bp):
ACTGTAAGCCCTCTCTGAGATCTTTGGCATGCCCTGACCCTAAACTGAAATAGCCTCTCCTCATC
TAA
Found at i:9642 original size:21 final size:21
Alignment explanation
Indices: 9616--9659 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
9606 TACTCATAGA
9616 ACCTTCCCTCTCAAAGGGTCC
1 ACCTTCCCTCTCAAAGGGTCC
9637 ACCTTCCCTCTCAAAGGGTCC
1 ACCTTCCCTCTCAAAGGGTCC
9658 AC
1 AC
9660 AGCGCTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.43, G:0.14, T:0.23
Consensus pattern (21 bp):
ACCTTCCCTCTCAAAGGGTCC
Found at i:20744 original size:2 final size:2
Alignment explanation
Indices: 20737--20769 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20727 TGATTCCTTA
20737 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20770 CACCATGATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.