Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold172
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: 1975206
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.26
Warning! 344189 characters in sequence are not A, C, G, or T
File 11 of 11
Found at i:1969315 original size:20 final size:20
Alignment explanation
Indices: 1969292--1969364 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1969282 ACAATTCAAA
1969292 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1969312 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1969333 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1969353 GTATCGATACAT
1 GTATCGATACAT
1969365 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1969336 original size:21 final size:21
Alignment explanation
Indices: 1969310--1969385 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1969300 ACATGTTGCA
1969310 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1969331 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
1969351 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
1969372 ATGTATCGATACAT
1 ATGTATCGATACAT
1969386 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1969343 original size:41 final size:41
Alignment explanation
Indices: 1969292--1969385 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1969282 ACAATTCAAA
*
1969292 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1969333 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1969374 GTATCGATACAT
1 GTATCGATACAT
1969386 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:1969442 original size:13 final size:13
Alignment explanation
Indices: 1969424--1969449 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1969414 TACAGCAAGT
1969424 ATGTATCGATACA
1 ATGTATCGATACA
1969437 ATGTATCGATACA
1 ATGTATCGATACA
1969450 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1973532 original size:15 final size:15
Alignment explanation
Indices: 1973512--1973542 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1973502 TAAAAATGTC
*
1973512 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1973527 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1973542 C
1 C
1973543 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Done.