Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014370.1 Corchorus olitorius cultivar O-4 contig14403, 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: 24230
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33
Found at i:769 original size:6 final size:6
Alignment explanation
Indices: 758--815 Score: 55
Period size: 6 Copynumber: 9.7 Consensus size: 6
748 TATATACATG
* * ** *
758 TCGAGC TCGAGC TCGAGC TCGAAC TCG-GTA TCGAAT TCGAGC TCGAAC
1 TCGAGC TCGAGC TCGAGC TCGAGC TCGAG-C TCGAGC TCGAGC TCGAGC
806 TCGAGC TCGA
1 TCGAGC TCGA
816 CCTTGAATTT
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.22, C:0.29, G:0.28, T:0.21
Consensus pattern (6 bp):
TCGAGC
Found at i:775 original size:12 final size:12
Alignment explanation
Indices: 758--815 Score: 73
Period size: 12 Copynumber: 4.8 Consensus size: 12
748 TATATACATG
*
758 TCGAGCTCGAGC
1 TCGAGCTCGAAC
770 TCGAGCTCGAAC
1 TCGAGCTCGAAC
* *
782 TCG-GTATCGAAT
1 TCGAG-CTCGAAC
794 TCGAGCTCGAAC
1 TCGAGCTCGAAC
806 TCGAGCTCGA
1 TCGAGCTCGA
816 CCTTGAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
11 1 0.03
12 37 0.95
13 1 0.03
ACGTcount: A:0.22, C:0.29, G:0.28, T:0.21
Consensus pattern (12 bp):
TCGAGCTCGAAC
Found at i:2893 original size:2 final size:2
Alignment explanation
Indices: 2886--2932 Score: 58
Period size: 2 Copynumber: 21.5 Consensus size: 2
2876 TTGTTATTAT
2886 TA TA TA TA TA TGA TA TA TA TGA TA TA TA TGA TA TA TA TGA TA TA
1 TA TA TA TA TA T-A TA TA TA T-A TA TA TA T-A TA TA TA T-A TA TA
2930 TA T
1 TA T
2933 GATTAGCCTC
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
2 33 0.80
3 8 0.20
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2903 original size:9 final size:9
Alignment explanation
Indices: 2889--2935 Score: 94
Period size: 9 Copynumber: 5.2 Consensus size: 9
2879 TTATTATTAT
2889 ATATATATG
1 ATATATATG
2898 ATATATATG
1 ATATATATG
2907 ATATATATG
1 ATATATATG
2916 ATATATATG
1 ATATATATG
2925 ATATATATG
1 ATATATATG
2934 AT
1 AT
2936 TAGCCTCAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.45
Consensus pattern (9 bp):
ATATATATG
Found at i:8158 original size:15 final size:14
Alignment explanation
Indices: 8133--8163 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
8123 ATATATAGGA
8133 TAAATAATAATTAT
1 TAAATAATAATTAT
8147 TAAATAAATAATTAT
1 TAAAT-AATAATTAT
8162 TA
1 TA
8164 TTTATTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TAAATAATAATTAT
Found at i:10794 original size:21 final size:20
Alignment explanation
Indices: 10765--10804 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
10755 TGCCTTCTGC
10765 AAACAGGGAGGCATCTCCTG
1 AAACAGGGAGGCATCTCCTG
* *
10785 AAACAAGGGATGCATTTCCT
1 AAAC-AGGGAGGCATCTCCT
10805 TTGTTGCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.20
Consensus pattern (20 bp):
AAACAGGGAGGCATCTCCTG
Found at i:19518 original size:16 final size:16
Alignment explanation
Indices: 19497--19529 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
19487 CGAATTAGCA
19497 TGGAATTTGACTTACT
1 TGGAATTTGACTTACT
19513 TGGAATTTGACTTACT
1 TGGAATTTGACTTACT
19529 T
1 T
19530 AATTGAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.45
Consensus pattern (16 bp):
TGGAATTTGACTTACT
Found at i:20647 original size:40 final size:45
Alignment explanation
Indices: 20567--20648 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 45
20557 TTTAGTAATT
* *
20567 AAATATATATTATTTATTTATTTTGAACTCATTATTTATTATTTA
1 AAATATATATTATTTATTTATTTTGAACTCAGTATATATTATTTA
*
20612 AAATATAT-TTATTTTTTTA-TTT-AA-T-AGTATATATTAT
1 AAATATATATTATTTATTTATTTTGAACTCAGTATATATTAT
20649 ATCTAAGATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
40 10 0.29
41 1 0.03
42 2 0.06
43 3 0.09
44 10 0.29
45 8 0.24
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (45 bp):
AAATATATATTATTTATTTATTTTGAACTCAGTATATATTATTTA
Found at i:22632 original size:18 final size:18
Alignment explanation
Indices: 22609--22650 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
22599 CTTGTGTGGG
*
22609 AAAGTT-GGTTTTCAATGC
1 AAAGTTGGGTTTT-AAAGC
22627 AAAGTTGGGTTTTAAAGC
1 AAAGTTGGGTTTTAAAGC
22645 AAAGTT
1 AAAGTT
22651 TTTTAGGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (18 bp):
AAAGTTGGGTTTTAAAGC
Done.