Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008020.1 Corchorus capsularis cultivar CVL-1 contig08041, 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: 50550
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3058 original size:35 final size:35
Alignment explanation
Indices: 2568--3045 Score: 664
Period size: 35 Copynumber: 13.7 Consensus size: 35
2558 AGTAATAAGA
* *
2568 AACTTAATTCAGGGTAATTAAGTAAGT-AATAGGT-
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTA-ATC
* *
2602 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATT
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
*
2637 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* * * *
2672 AACTTAACTCAGGGTAATTAATTAATTCATTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
*
2707 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
*
2742 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
*
2777 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
*
2812 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
2847 AACTTAATTCAGGGTAATTAAG-AGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTA-AGTCAGTAATC
*
2882 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
*
2917 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* * * *
2952 AACTTTAATTC-GGGATAATTAAGTGAGTTAATGAGT-
1 AAC-TTAATTCAGGG-TAATTAAGTAAGTCAGT-AATC
*
2988 AACTTAATTCAGGGTAATTAAGT-AGTTCAATAAGT-
1 AACTTAATTCAGGGTAATTAAGTAAG-TCAGTAA-TC
3023 AACTTAATTCAGGGTAATTAAGT
1 AACTTAATTCAGGGTAATTAAGT
3046 TTAGTAAGAA
Statistics
Matches: 409, Mismatches: 25, Indels: 19
0.90 0.06 0.04
Matches are distributed among these distances:
34 30 0.07
35 348 0.85
36 29 0.07
37 2 0.00
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.33
Consensus pattern (35 bp):
AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
Found at i:21968 original size:2 final size:2
Alignment explanation
Indices: 21961--21990 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
21951 CTACCGACAA
21961 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
21991 CAATATAATT
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:25836 original size:27 final size:27
Alignment explanation
Indices: 25805--25857 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
25795 TCAAATTGCA
*
25805 TATTGATATGTTGGACATTTTGCACCC
1 TATTGATATGCTGGACATTTTGCACCC
25832 TATTGATATGCTGGACATTTTGCACC
1 TATTGATATGCTGGACATTTTGCACC
25858 TTGATCGACC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.40
Consensus pattern (27 bp):
TATTGATATGCTGGACATTTTGCACCC
Found at i:39337 original size:2 final size:2
Alignment explanation
Indices: 39330--39368 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
39320 CGACCCTAAC
39330 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
39369 CAAAAACTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:43496 original size:1 final size:1
Alignment explanation
Indices: 43490--43514 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
43480 AAATATCCTT
43490 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
43515 TCCATTTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:50196 original size:2 final size:2
Alignment explanation
Indices: 50191--50227 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
50181 ATCTATAAAT
50191 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
50228 GAACTGCAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.