Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015400.1 Corchorus olitorius cultivar O-4 contig15433, 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: 58923
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:40606 original size:31 final size:31
Alignment explanation
Indices: 40568--40629 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
40558 GAGGATTCGA
40568 GTCCTTGCCATGCATATATCATCTAATATGC
1 GTCCTTGCCATGCATATATCATCTAATATGC
40599 GTCCTTGCCATGCATATATCATCTAATATGC
1 GTCCTTGCCATGCATATATCATCTAATATGC
40630 TAGTGTTAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (31 bp):
GTCCTTGCCATGCATATATCATCTAATATGC
Found at i:42272 original size:19 final size:20
Alignment explanation
Indices: 42248--42295 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
42238 TTTTTTTTCT
*
42248 AATTAAGAACTGC-ATAAAA
1 AATTAAGAACTGCAAAAAAA
*
42267 AATTAAAAACTGCAAAAAAA
1 AATTAAGAACTGCAAAAAAA
42287 AATTAAGAA
1 AATTAAGAA
42296 AAATTAAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.65, C:0.08, G:0.08, T:0.19
Consensus pattern (20 bp):
AATTAAGAACTGCAAAAAAA
Found at i:42288 original size:20 final size:19
Alignment explanation
Indices: 42248--42292 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
42238 TTTTTTTTCT
* *
42248 AATTAAGAACTGCATAAAA
1 AATTAAAAACTGCAAAAAA
42267 AATTAAAAACTGCAAAAAAA
1 AATTAAAAACTGC-AAAAAA
42287 AATTAA
1 AATTAA
42293 GAAAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.64, C:0.09, G:0.07, T:0.20
Consensus pattern (19 bp):
AATTAAAAACTGCAAAAAA
Found at i:48990 original size:11 final size:11
Alignment explanation
Indices: 48974--48998 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
48964 TTTGATCTTT
48974 AATTATATAAA
1 AATTATATAAA
48985 AATTATATAAA
1 AATTATATAAA
48996 AAT
1 AAT
48999 AAATTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AATTATATAAA
Found at i:53878 original size:2 final size:2
Alignment explanation
Indices: 53871--53907 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
53861 GTAATTTGTT
53871 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
53908 CAAGACAATT
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
Found at i:54816 original size:61 final size:61
Alignment explanation
Indices: 54721--54841 Score: 233
Period size: 61 Copynumber: 2.0 Consensus size: 61
54711 CAAGTGGGTT
54721 GTGGAGTTGACACATGTCTATTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAATCG
1 GTGGAGTTGACACATGTCTATTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAATCG
*
54782 GTGGAGTTGACATATGTCTATTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAATC
1 GTGGAGTTGACACATGTCTATTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAATC
54842 CCTAGATGAC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.47
Consensus pattern (61 bp):
GTGGAGTTGACACATGTCTATTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAATCG
Found at i:56629 original size:2 final size:2
Alignment explanation
Indices: 56622--56646 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56612 TAATATGCAG
56622 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 T
56647 TAGTACTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57767 original size:3 final size:3
Alignment explanation
Indices: 57759--57792 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
57749 AATTAATTAC
57759 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
57793 AAAATATGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Done.