Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3583
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, 430
Length: 718
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Found at i:251 original size:107 final size:104
Alignment explanation
Indices: 124--422 Score: 473
Period size: 107 Copynumber: 2.9 Consensus size: 104
114 GCAAAAAAAT
*
124 TTTCATTTTGAACAAAATGACGCCATTTTACTATTCTAAAAATTTTTTATTTTATTTTTTTATAA
1 TTTCATTTTGAACAAAATGACGCCATTTTACTATGCTAAAAATTTTTTATTTTATTTTTTTATAA
*
189 ATTGATTTATTTTTTGCAGCGTTTTTATAAAAAACGCCGCTA
66 ATTGATTTATTTTTTGCGGCGTTTTTAT---AAACGCCGCTA
* * *
231 TTTCATTTTGAACAAAATGACGCCATTTTGCTCTGCTAAAAATTTTTTATTTTATTTTTTTATAT
1 TTTCATTTTGAACAAAATGACGCCATTTTACTATGCTAAAAATTTTTTATTTTATTTTTTTATAA
296 ATTGATTTATTTTTTGCGGCG-TTTT-TAAACGCCGCTA
66 ATTGATTTATTTTTTGCGGCGTTTTTATAAACGCCGCTA
* *
333 TTTCATTTTCAACAAAATGACGCCGTTTTACTATGCTAAAAATTTTTTATTTTATTTTTTTATAA
1 TTTCATTTTGAACAAAATGACGCCATTTTACTATGCTAAAAATTTTTTATTTTATTTTTTTATAA
398 ATTGA--T-TTTTTTGCGGCGTTTTTAT
66 ATTGATTTATTTTTTGCGGCGTTTTTAT
423 TGCTTACCTT
Statistics
Matches: 180, Mismatches: 10, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
99 12 0.07
100 5 0.03
101 1 0.01
102 76 0.42
105 1 0.01
106 4 0.02
107 81 0.45
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.51
Consensus pattern (104 bp):
TTTCATTTTGAACAAAATGACGCCATTTTACTATGCTAAAAATTTTTTATTTTATTTTTTTATAA
ATTGATTTATTTTTTGCGGCGTTTTTATAAACGCCGCTA
Done.