Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011709.1 Corchorus capsularis cultivar CVL-1 contig11730, 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: 21883
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:10080 original size:14 final size:13
Alignment explanation
Indices: 10060--10098 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
10050 AGAACAATTC
10060 TTTTTACTTTTTA
1 TTTTTACTTTTTA
10073 TCTTTTACATTTTTA
1 T-TTTTAC-TTTTTA
10088 TTTTT-CTTTTT
1 TTTTTACTTTTT
10099 CCATATCATC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 5 0.21
13 2 0.08
14 10 0.42
15 7 0.29
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTACTTTTTA
Found at i:13845 original size:13 final size:13
Alignment explanation
Indices: 13824--13894 Score: 54
Period size: 13 Copynumber: 5.2 Consensus size: 13
13814 CTGAGGACGG
* *
13824 CAAATATTACTTA
1 CAAAAATTACATA
13837 CAAAAATTACATA
1 CAAAAATTACATA
13850 CAATAATAATTAACATA
1 C-A-AA-AATT-ACATA
*
13867 -AAAAATTACTTA
1 CAAAAATTACATA
**
13879 CATCAATTACATA
1 CAAAAATTACATA
13892 CAA
1 CAA
13895 TAATAATTAC
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.09
13 27 0.59
14 3 0.07
15 3 0.07
16 4 0.09
17 5 0.11
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (13 bp):
CAAAAATTACATA
Found at i:14040 original size:12 final size:13
Alignment explanation
Indices: 14015--14043 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
14005 ATTAACATAA
14015 AAAATTATTTTTT
1 AAAATTATTTTTT
14028 AAAATTA-TTTTT
1 AAAATTATTTTTT
14040 AAAA
1 AAAA
14044 AAATTGATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AAAATTATTTTTT
Found at i:14044 original size:13 final size:13
Alignment explanation
Indices: 14014--14044 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
14004 AATTAACATA
14014 AAAAATTATTTTT
1 AAAAATTATTTTT
*
14027 TAAAATTATTTTT
1 AAAAATTATTTTT
14040 AAAAA
1 AAAAA
14045 AATTGATCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AAAAATTATTTTT
Found at i:14835 original size:7 final size:7
Alignment explanation
Indices: 14823--14850 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
14813 ACATTCACAT
14823 CTCTTTC
1 CTCTTTC
14830 CTCTTTC
1 CTCTTTC
14837 CTCTTTC
1 CTCTTTC
14844 CTCTTTC
1 CTCTTTC
14851 TTCTCCTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (7 bp):
CTCTTTC
Found at i:16183 original size:31 final size:31
Alignment explanation
Indices: 16112--16194 Score: 130
Period size: 31 Copynumber: 2.7 Consensus size: 31
16102 GCCAAATGTC
*
16112 CAATTTGAACCTGAACCTTTACGAACTTGCT
1 CAATTTGAGCCTGAACCTTTACGAACTTGCT
16143 CAATTTGAGCCTGAACCTTTACGAACTTGCT
1 CAATTTGAGCCTGAACCTTTACGAACTTGCT
* * *
16174 CAATATGAGCCTAAAGCTTTA
1 CAATTTGAGCCTGAACCTTTA
16195 AAGTGCACCA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.31
Consensus pattern (31 bp):
CAATTTGAGCCTGAACCTTTACGAACTTGCT
Done.