Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008437.1 Corchorus capsularis cultivar CVL-1 contig08458, 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: 47818
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:16622 original size:31 final size:30
Alignment explanation
Indices: 16581--16659 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 30
16571 TACATATCCT
* * *
16581 ATTTGGGTCTAAATCTTTTATAAGT-TACTCA
1 ATTTGAGTCTAAACCTTTTA-AAGTAAAC-CA
*
16612 ATTTGAGTCTAAAGC-TTTAAAGTAAACCA
1 ATTTGAGTCTAAACCTTTTAAAGTAAACCA
*
16641 AATTGAGTCTAAACCTTTT
1 ATTTGAGTCTAAACCTTTT
16660 TGGGATGTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 19 0.46
30 9 0.22
31 13 0.32
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (30 bp):
ATTTGAGTCTAAACCTTTTAAAGTAAACCA
Found at i:22078 original size:1 final size:1
Alignment explanation
Indices: 22072--22103 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
22062 CCTCATGTTG
22072 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
22104 GTCCAGGAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:24615 original size:22 final size:24
Alignment explanation
Indices: 24590--24636 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
24580 TATATGGTGT
*
24590 ATGATTGAA-TAAATT-GTTTTCA
1 ATGATTCAATTAAATTAGTTTTCA
*
24612 ATGATTCAATTAGATTAGTTTTCA
1 ATGATTCAATTAAATTAGTTTTCA
24636 A
1 A
24637 AATAATCCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 8 0.38
23 5 0.24
24 8 0.38
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.45
Consensus pattern (24 bp):
ATGATTCAATTAAATTAGTTTTCA
Found at i:27051 original size:20 final size:21
Alignment explanation
Indices: 27028--27092 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
27018 TATTAACAAT
* *
27028 TAAAAGGAAAGAA-TTACTAA
1 TAAAAGGAAAGAACATAATAA
* *
27048 TAAAAGAAAAGAACATAATGA
1 TAAAAGGAAAGAACATAATAA
*
27069 TAAAAGGAAAGAACATAACAA
1 TAAAAGGAAAGAACATAATAA
27090 TAA
1 TAA
27093 TGTAATTTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
20 12 0.32
21 25 0.68
ACGTcount: A:0.65, C:0.06, G:0.14, T:0.15
Consensus pattern (21 bp):
TAAAAGGAAAGAACATAATAA
Found at i:32898 original size:31 final size:31
Alignment explanation
Indices: 32860--32929 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
32850 ACCAAAAAGT
*
32860 CATGCCACATGTACCAAAAAGTGACACGTGG
1 CATGCCACATGTACCAAAAAATGACACGTGG
** *
32891 CATGCCACATGTTTCAAAAAATGGCACGTGG
1 CATGCCACATGTACCAAAAAATGACACGTGG
32922 CATGCCAC
1 CATGCCAC
32930 GTGCACAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.19
Consensus pattern (31 bp):
CATGCCACATGTACCAAAAAATGACACGTGG
Found at i:34427 original size:41 final size:41
Alignment explanation
Indices: 34379--34468 Score: 180
Period size: 41 Copynumber: 2.2 Consensus size: 41
34369 AGTTCAGTGA
34379 TTAAATTTGTAATGTACCCAATTTTTTAAAATGTTCAATAC
1 TTAAATTTGTAATGTACCCAATTTTTTAAAATGTTCAATAC
34420 TTAAATTTGTAATGTACCCAATTTTTTAAAATGTTCAATAC
1 TTAAATTTGTAATGTACCCAATTTTTTAAAATGTTCAATAC
34461 TTAAATTT
1 TTAAATTT
34469 ATTTGATATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.46
Consensus pattern (41 bp):
TTAAATTTGTAATGTACCCAATTTTTTAAAATGTTCAATAC
Done.