Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold288
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: 589160
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 14644 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:580003 original size:18 final size:20
Alignment explanation
Indices: 579982--580023 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
579972 TAAATAAATT
*
579982 TTAAGTATA-AAA-TATTCA
1 TTAAGTATATAAATTACTCA
*
580000 TTAATTATATAAATTACTCA
1 TTAAGTATATAAATTACTCA
580020 TTAA
1 TTAA
580024 TAAACTCAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.40
19 3 0.15
20 9 0.45
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (20 bp):
TTAAGTATATAAATTACTCA
Found at i:580012 original size:20 final size:20
Alignment explanation
Indices: 579987--580024 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
579977 AAATTTTAAG
*
579987 TATAAAATATTCATTAATTA
1 TATAAAATACTCATTAATTA
*
580007 TATAAATTACTCATTAAT
1 TATAAAATACTCATTAAT
580025 AAACTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (20 bp):
TATAAAATACTCATTAATTA
Found at i:586463 original size:31 final size:32
Alignment explanation
Indices: 586405--586469 Score: 96
Period size: 31 Copynumber: 2.0 Consensus size: 32
586395 CTCAATGAAA
586405 TCAAAGACATTATAAAAAAAAAATAAGCACCAC
1 TCAAAGACA-TATAAAAAAAAAATAAGCACCAC
* *
586438 TCAAAGACA-ATATAAAAAAAGTAAGCACCAC
1 TCAAAGACATATAAAAAAAAAATAAGCACCAC
586469 T
1 T
586470 TTATGTCTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 21 0.70
33 9 0.30
ACGTcount: A:0.58, C:0.18, G:0.08, T:0.15
Consensus pattern (32 bp):
TCAAAGACATATAAAAAAAAAATAAGCACCAC
Found at i:587648 original size:42 final size:42
Alignment explanation
Indices: 587589--587934 Score: 692
Period size: 42 Copynumber: 8.2 Consensus size: 42
587579 CCCCAGGCCT
587589 TGGGAATGATGGTATGGATGGCTTTGGGAATGATGGTATGGA
1 TGGGAATGATGGTATGGATGGCTTTGGGAATGATGGTATGGA
587631 TGGGAATGATGGTATGGATGGCTTTGGGAATGATGGTATGGA
1 TGGGAATGATGGTATGGATGGCTTTGGGAATGATGGTATGGA
587673 TGGGAATGATGGTATGGATGGCTTTGGGAATGATGGTATGGA
1 TGGGAATGATGGTATGGATGGCTTTGGGAATGATGGTATGGA
587715 TGGGAATGATGGTATGGATGGCTTTGGGAATGATGGTATGGA
1 TGGGAATGATGGTATGGATGGCTTTGGGAATGATGGTATGGA
587757 TGGGAATGATGGTATGGATGGCTTTGGGAATGATGGTATGGA
1 TGGGAATGATGGTATGGATGGCTTTGGGAATGATGGTATGGA
587799 TGGGAATGATGGTATGGATGGCTTTGGGAATGATGGTATGGA
1 TGGGAATGATGGTATGGATGGCTTTGGGAATGATGGTATGGA
587841 TGGGAATGATGGTATGGATGGCTTTGGGAATGATGGTATGGA
1 TGGGAATGATGGTATGGATGGCTTTGGGAATGATGGTATGGA
587883 TGGGAATGATGGTATGGATGGCTTTGGGAATGATGGTATGGA
1 TGGGAATGATGGTATGGATGGCTTTGGGAATGATGGTATGGA
587925 TGGGAATGAT
1 TGGGAATGAT
587935 CATTGGGGGT
Statistics
Matches: 304, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 304 1.00
ACGTcount: A:0.24, C:0.02, G:0.43, T:0.31
Consensus pattern (42 bp):
TGGGAATGATGGTATGGATGGCTTTGGGAATGATGGTATGGA
Found at i:588872 original size:25 final size:26
Alignment explanation
Indices: 588836--588893 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 26
588826 AAATCTTAAA
588836 AAAAAAACAACCTCCATCGTGAATCT
1 AAAAAAACAACCTCCATCGTGAATCT
*
588862 AAAAAAA-AACCTCCATCGTGAATTT
1 AAAAAAACAACCTCCATCGTGAATCT
*
588887 ACAAAAA
1 AAAAAAA
588894 TCACTATTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 23 0.77
26 7 0.23
ACGTcount: A:0.52, C:0.22, G:0.07, T:0.19
Consensus pattern (26 bp):
AAAAAAACAACCTCCATCGTGAATCT
Done.