Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018896.1 Corchorus olitorius cultivar O-4 contig18929, 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: 26095
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:5923 original size:20 final size:20
Alignment explanation
Indices: 5898--5937 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5888 ACAGCATTAG
5898 CAGGTGATTTTAACACTTAT
1 CAGGTGATTTTAACACTTAT
*
5918 CAGGTGATTTTACCACTTAT
1 CAGGTGATTTTAACACTTAT
5938 AAACACAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (20 bp):
CAGGTGATTTTAACACTTAT
Found at i:6768 original size:1 final size:1
Alignment explanation
Indices: 6762--6791 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
6752 AATTACACAG
6762 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
6792 CCCGGCCTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:12505 original size:31 final size:31
Alignment explanation
Indices: 12470--12608 Score: 154
Period size: 31 Copynumber: 4.5 Consensus size: 31
12460 TTGCCACATA
*
12470 TACCAAAAAGCAACATGTAGCACGCCACGTG
1 TACCAAAAAGCGACATGTAGCACGCCACGTG
12501 TACCAAAAAGCGACATG-AGACACGCCACGTG
1 TACCAAAAAGCGACATGTAG-CACGCCACGTG
* * *
12532 TACCAAAAAGTGACATGTATCACGCCATGTG
1 TACCAAAAAGCGACATGTAGCACGCCACGTG
* * * * *
12563 TACCCAAAAGTGACATGTGGCATGCCATGTG
1 TACCAAAAAGCGACATGTAGCACGCCACGTG
** *
12594 TTTCAAAAAGTGACA
1 TACCAAAAAGCGACA
12609 CATGGCATGC
Statistics
Matches: 95, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
30 2 0.02
31 92 0.97
32 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (31 bp):
TACCAAAAAGCGACATGTAGCACGCCACGTG
Found at i:12564 original size:62 final size:62
Alignment explanation
Indices: 12470--12608 Score: 170
Period size: 62 Copynumber: 2.2 Consensus size: 62
12460 TTGCCACATA
**
12470 TACCAAAAAGCAACATGTAGCACGCCACGTGTACCAAAAAGCGACATGAGACACGCCACGTG
1 TACCAAAAAGTGACATGTAGCACGCCACGTGTACCAAAAAGCGACATGAGACACGCCACGTG
* * * * * * * *
12532 TACCAAAAAGTGACATGTATCACGCCATGTGTACCCAAAAGTGACATGTGGCATGCCATGTG
1 TACCAAAAAGTGACATGTAGCACGCCACGTGTACCAAAAAGCGACATGAGACACGCCACGTG
**
12594 TTTCAAAAAGTGACA
1 TACCAAAAAGTGACA
12609 CATGGCATGC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
62 65 1.00
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (62 bp):
TACCAAAAAGTGACATGTAGCACGCCACGTGTACCAAAAAGCGACATGAGACACGCCACGTG
Found at i:14786 original size:129 final size:130
Alignment explanation
Indices: 14637--14898 Score: 386
Period size: 129 Copynumber: 2.0 Consensus size: 130
14627 TTGTTTAAAC
* * * *
14637 TTTTATAGTTTTACTCAACTAAAAACTTTATTTTTATT-TAATTAAATCTAATATCCTTATAACT
1 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTGT-ATAAAATCTAATATCCTTATAACT
* * * *
14701 ATTTTATTTTTACCATTTTACTATTTTAATTAAAAAAACTT-ATATATTGGAATTTTT-TAATAT
65 ATTTTATTTATACCATTTTACTAATTTAATT-AAAAAACTTAATATATTAGAATTTTTAAAATAT
14764 AT
129 AT
* *
14766 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTGTATAAAATCTAATATCTTTATACCTA
1 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTGTATAAAATCTAATATCCTTATAACTA
14831 TTTTATTTATACCATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTTAAAATATA
66 TTTTATTTATACCATTTTACTAATTTAATTAAAAAACTTA-ATATATTAGAATTTTTAAAATATA
14896 T
130 T
14897 TT
1 TT
14899 CTTAAATGAC
Statistics
Matches: 119, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
128 9 0.08
129 85 0.71
130 16 0.13
131 9 0.08
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (130 bp):
TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTGTATAAAATCTAATATCCTTATAACTA
TTTTATTTATACCATTTTACTAATTTAATTAAAAAACTTAATATATTAGAATTTTTAAAATATAT
Found at i:14849 original size:14 final size:15
Alignment explanation
Indices: 14821--14849 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
14811 ATCTAATATC
14821 TTTATACCTATTTTA
1 TTTATACCTATTTTA
14836 TTTATACC-ATTTTA
1 TTTATACCTATTTTA
14850 CTAATTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.28, C:0.14, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTATACCTATTTTA
Found at i:22717 original size:4 final size:4
Alignment explanation
Indices: 22708--22732 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
22698 TTAGAGTTGT
22708 GAAA GAAA GAAA GAAA GAAA GAAA G
1 GAAA GAAA GAAA GAAA GAAA GAAA G
22733 GAAGGAGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
GAAA
Done.