Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014044.1 Corchorus capsularis cultivar CVL-1 contig14065, 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: 35720
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Found at i:159 original size:33 final size:32
Alignment explanation
Indices: 7--155 Score: 235
Period size: 32 Copynumber: 4.6 Consensus size: 32
1 CGCCTT
* * *
7 GCCGCCCTAGTGGGGCGGCTAACCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCTAGCCGTGGCAGA
*
39 GCCGTCCTAGTGGGGCGGCTAGCCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCTAGCCGTGGCAGA
*
71 GCCGTCCTAGTGGGAAGGCTAGCCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCTAGCCGTGGCAGA
*
103 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCT-AGCCGTGGCAGA
136 GCCGTCCTAGTGGGGAGGCT
1 GCCGTCCTAGTGGGGAGGCT
156 CCGCGTGACT
Statistics
Matches: 110, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 79 0.72
33 31 0.28
ACGTcount: A:0.14, C:0.28, G:0.42, T:0.15
Consensus pattern (32 bp):
GCCGTCCTAGTGGGGAGGCTAGCCGTGGCAGA
Found at i:12130 original size:12 final size:12
Alignment explanation
Indices: 12113--12139 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
12103 AGCCTTCTGT
12113 TTTCTGCCTTCA
1 TTTCTGCCTTCA
12125 TTTCTGCCTTCA
1 TTTCTGCCTTCA
12137 TTT
1 TTT
12140 TGGTAAAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.30, G:0.07, T:0.56
Consensus pattern (12 bp):
TTTCTGCCTTCA
Found at i:13915 original size:19 final size:19
Alignment explanation
Indices: 13891--13928 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
13881 CTTGAAACTG
13891 TATGATCTAACAGATTCTA
1 TATGATCTAACAGATTCTA
13910 TATGATCTAACAGATTCTA
1 TATGATCTAACAGATTCTA
13929 ACAAATTGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (19 bp):
TATGATCTAACAGATTCTA
Found at i:25517 original size:14 final size:14
Alignment explanation
Indices: 25500--25527 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
25490 TTTGTTACAA
25500 TGTTTTTTTTTTGG
1 TGTTTTTTTTTTGG
25514 TGTTTTTTTTTTGG
1 TGTTTTTTTTTTGG
25528 GGGTTCAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (14 bp):
TGTTTTTTTTTTGG
Found at i:33313 original size:14 final size:14
Alignment explanation
Indices: 33294--33321 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
33284 TTAACTAAAC
33294 TATATATATAATTA
1 TATATATATAATTA
33308 TATATATATAATTA
1 TATATATATAATTA
33322 AAGATAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATATATAATTA
Found at i:33495 original size:21 final size:22
Alignment explanation
Indices: 33446--33503 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
33436 TCGTGTCATT
*
33446 GTGTTAACTCGT-TAATTAAAGC
1 GTGTTAACTCGTGT-CTTAAAGC
33468 GTG-TAACTCGTGTCTTAAA-C
1 GTGTTAACTCGTGTCTTAAAGC
*
33488 GTGTTAAC-AGTGTCTT
1 GTGTTAACTCGTGTCTT
33504 GACACGATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 11 0.34
21 17 0.53
22 4 0.12
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.38
Consensus pattern (22 bp):
GTGTTAACTCGTGTCTTAAAGC
Done.