Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008365.1 Corchorus capsularis cultivar CVL-1 contig08386, 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: 42654
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:2868 original size:2 final size:2
Alignment explanation
Indices: 2861--2890 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2851 GTTCATAATC
2861 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
2891 TAAGTATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6230 original size:15 final size:15
Alignment explanation
Indices: 6210--6239 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6200 ATATTTACTC
6210 TTTCTACTTAGAACA
1 TTTCTACTTAGAACA
*
6225 TTTCTACTTGGAACA
1 TTTCTACTTAGAACA
6240 ACCCTCATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (15 bp):
TTTCTACTTAGAACA
Found at i:7834 original size:4 final size:4
Alignment explanation
Indices: 7827--7926 Score: 74
Period size: 4 Copynumber: 24.5 Consensus size: 4
7817 CATTCATTAT
* * *
7827 TATA TATA TATA TATA TATA TATA TATA TCATA TATG TAGTG TATG TATA
1 TATA TATA TATA TATA TATA TATA TATA T-ATA TATA TA-TA TATA TATA
** * * * * * * *
7877 TGCA TACA TACA TACA TACA TACA TACA TACA TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
7925 TA
1 TA
7927 AAAGATTACC
Statistics
Matches: 88, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
4 80 0.91
5 8 0.09
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (4 bp):
TATA
Found at i:8021 original size:2 final size:2
Alignment explanation
Indices: 8014--8047 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
8004 TTAAAGATTA
8014 AT 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 AT
8048 TATGTGTGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16713 original size:23 final size:23
Alignment explanation
Indices: 16687--16733 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
16677 CTTGCTTTGA
*
16687 ACATATATTACATTTACTAATGC
1 ACATATATTACATTAACTAATGC
16710 ACATATATTACATTAACTAATGC
1 ACATATATTACATTAACTAATGC
16733 A
1 A
16734 GGCTCATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.17, G:0.04, T:0.36
Consensus pattern (23 bp):
ACATATATTACATTAACTAATGC
Found at i:20936 original size:24 final size:23
Alignment explanation
Indices: 20883--20937 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
20873 ATTTTGATTG
*
20883 TTATTCCTTACCATTCCAAAACG
1 TTATTCCTTACCATTCCAAAACA
*
20906 TTATTCCTTACCAATTCCAGAACA
1 TTATTCCTTACC-ATTCCAAAACA
*
20930 TTTTTCCT
1 TTATTCCT
20938 CAAGCCAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 12 0.43
24 16 0.57
ACGTcount: A:0.27, C:0.29, G:0.04, T:0.40
Consensus pattern (23 bp):
TTATTCCTTACCATTCCAAAACA
Found at i:30989 original size:24 final size:24
Alignment explanation
Indices: 30957--31005 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
30947 GCAATTCAGT
30957 TGCTCATGAGTTAACTCGCTATGG
1 TGCTCATGAGTTAACTCGCTATGG
* *
30981 TGCTCATGAGTTAGCTCGTTATGG
1 TGCTCATGAGTTAACTCGCTATGG
31005 T
1 T
31006 TATCATTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (24 bp):
TGCTCATGAGTTAACTCGCTATGG
Found at i:31011 original size:24 final size:24
Alignment explanation
Indices: 30960--31011 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
30950 ATTCAGTTGC
*
30960 TCATGAGTTAACTCGCTATGGTGC
1 TCATGAGTTAACTCGCTATGGTGA
* * *
30984 TCATGAGTTAGCTCGTTATGGTTA
1 TCATGAGTTAACTCGCTATGGTGA
31008 TCAT
1 TCAT
31012 TAGATGAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.38
Consensus pattern (24 bp):
TCATGAGTTAACTCGCTATGGTGA
Found at i:40782 original size:78 final size:78
Alignment explanation
Indices: 40700--40945 Score: 323
Period size: 78 Copynumber: 3.1 Consensus size: 78
40690 GGTTTTTATA
* *
40700 ATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATAT-CTTCATAACTATTTTAT
1 ATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTT-ATAACTATTATAT
*
40764 TTTACCATGTTACT
65 TTTACCATTTTACT
* *
40778 ATTTTATTCAACTAAAAACTCTATTTTTATATAATTAAATATAATGAGTGAATCCTTATGACTAT
1 ATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATAT-A--A-T--ATCCTTATAACTAT
40843 TATATTTTACCATTTTACT
60 TATATTTTACCATTTTACT
* * * *
40862 ATTTTACTCAACTAAAAAATCTATTTTTATATAATTAAATTTAATATCCTTGTAACTATTACATT
1 ATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTATTATATT
**
40927 TTAAAATTTTACT
66 TTACCATTTTACT
40940 ATTTTA
1 ATTTTA
40946 ATTAAAAAGC
Statistics
Matches: 148, Mismatches: 13, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
78 74 0.50
79 1 0.01
80 1 0.01
81 2 0.01
82 1 0.01
83 1 0.01
84 65 0.44
85 3 0.02
ACGTcount: A:0.37, C:0.12, G:0.02, T:0.48
Consensus pattern (78 bp):
ATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTATTATATT
TTACCATTTTACT
Found at i:42632 original size:2 final size:2
Alignment explanation
Indices: 42625--42654 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
42615 TTAAACTACT
42625 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.