Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012321.1 Corchorus capsularis cultivar CVL-1 contig12342, 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: 31256
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:11 original size:2 final size:2
Alignment explanation
Indices: 5--49 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1 ATAG
5 TA TA 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 TA TA TA
46 TA TA
1 TA TA
50 GGTCATAACC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3363 original size:15 final size:15
Alignment explanation
Indices: 3343--3372 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3333 TTCAATTCAG
3343 GTGAAGCACAGTAAA
1 GTGAAGCACAGTAAA
*
3358 GTGAAGCAGAGTAAA
1 GTGAAGCACAGTAAA
3373 AATTTCAGAT
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:0.47, C:0.10, G:0.30, T:0.13
Consensus pattern (15 bp):
GTGAAGCACAGTAAA
Found at i:14907 original size:27 final size:28
Alignment explanation
Indices: 14877--14941 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 28
14867 AGCTGCGTTA
14877 GCCTCAACATCC-TCAGGATTGGAACTC
1 GCCTCAACATCCTTCAGGATTGGAACTC
14904 GCCTCAACA-CCTTCAGGATTGGAACTC
1 GCCTCAACATCCTTCAGGATTGGAACTC
* *
14931 GTCTCACCATC
1 GCCTCAACATC
14942 AACCTCCATA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 2 0.06
27 31 0.91
28 1 0.03
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (28 bp):
GCCTCAACATCCTTCAGGATTGGAACTC
Found at i:20210 original size:15 final size:15
Alignment explanation
Indices: 20190--20220 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
20180 GCGTGCAATT
20190 CTACCCAATCTGGTG
1 CTACCCAATCTGGTG
20205 CTACCCAATCTGGTG
1 CTACCCAATCTGGTG
20220 C
1 C
20221 AAGAACATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.35, G:0.19, T:0.26
Consensus pattern (15 bp):
CTACCCAATCTGGTG
Found at i:28423 original size:15 final size:16
Alignment explanation
Indices: 28403--28441 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
28393 TACGTTTTGA
28403 TTAAAAAATAT-CTTT
1 TTAAAAAATATACTTT
*
28418 TTAAAAAATATATTTT
1 TTAAAAAATATACTTT
28434 TTAAAAAA
1 TTAAAAAA
28442 AAATTGGGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAAAATATACTTT
Found at i:28586 original size:32 final size:31
Alignment explanation
Indices: 28539--28610 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
28529 ATTTGCCCCT
* *
28539 AATTTTTTTGTTTTTTTAATAAAAATAAAATC
1 AATTTTTTTGTTTTTTT-ATAAAAAAAAAAAC
*
28571 AATTTTTTCTG-TTTTTTCTAAAAAAAAAAAC
1 AATTTTTT-TGTTTTTTTATAAAAAAAAAAAC
*
28602 CATTTTTTT
1 AATTTTTTT
28611 CTTTCTTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
30 1 0.03
31 18 0.51
32 14 0.40
33 2 0.06
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (31 bp):
AATTTTTTTGTTTTTTTATAAAAAAAAAAAC
Found at i:28611 original size:32 final size:33
Alignment explanation
Indices: 28539--28612 Score: 100
Period size: 32 Copynumber: 2.3 Consensus size: 33
28529 ATTTGCCCCT
*
28539 AATTTTTT-TGTTTTTTTAATAAAAATAAAATC
1 AATTTTTTCTGTTTTTTTAATAAAAATAAAACC
28571 AATTTTTTCTGTTTTTTCTAA-AAAAA-AAAACC
1 AATTTTTTCTGTTTTTT-TAATAAAAATAAAACC
*
28603 ATTTTTTTCT
1 AATTTTTTCT
28613 TTCTTAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
32 22 0.58
33 13 0.34
34 3 0.08
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.53
Consensus pattern (33 bp):
AATTTTTTCTGTTTTTTTAATAAAAATAAAACC
Found at i:31187 original size:2 final size:2
Alignment explanation
Indices: 31180--31256 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
31170 TAAGCAGATA
31180 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
31222 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.