Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1277
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: 2185
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.22
Warning! 662 characters in sequence are not A, C, G, or T
Found at i:300 original size:146 final size:147
Alignment explanation
Indices: 107--400 Score: 538
Period size: 146 Copynumber: 2.0 Consensus size: 147
97 AAACAAAAAT
107 ATTTTAAAAATTTCAGGAGGCTTACCTTTTGGAGCAGGAAAATAAAGTTCATTTTTACCTCGCTC
1 ATTTTAAAAA-TTCAGGAGGCTTACCTTTTGGAGCAGGAAAATAAAGTTCATTTTTACCTCGCTC
* *
172 GCTTAACAAAAACCTTCACTCCTCGGCGATG-TAGAGTAGTTGAAATTCCTTGCTTGAATTAACC
65 GCTTAACAAAAACCTTCACTCCTCGGCG-CGATAGAGTAGTCGAAATTCCTTGCTTGAATTAACC
236 TTTTCAAAATGGATCTCCA
129 TTTTCAAAATGGATCTCCA
255 ATTTTAAAAA-TCAGGAGGCTTACCTTTTGGAGCAGGAAAATAAAGTTCATTTTTACCTCGCTCG
1 ATTTTAAAAATTCAGGAGGCTTACCTTTTGGAGCAGGAAAATAAAGTTCATTTTTACCTCGCTCG
319 CTTAACAAAAACCTTCACTCCTCGGCGCGATAGAGTAGTCGAAATTCCTTGCTTGAATTAACCTT
66 CTTAACAAAAACCTTCACTCCTCGGCGCGATAGAGTAGTCGAAATTCCTTGCTTGAATTAACCTT
384 TTCAAAATGGATCTCCA
131 TTCAAAATGGATCTCCA
401 TACTCGACAA
Statistics
Matches: 143, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
145 1 0.01
146 132 0.92
148 10 0.07
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (147 bp):
ATTTTAAAAATTCAGGAGGCTTACCTTTTGGAGCAGGAAAATAAAGTTCATTTTTACCTCGCTCG
CTTAACAAAAACCTTCACTCCTCGGCGCGATAGAGTAGTCGAAATTCCTTGCTTGAATTAACCTT
TTCAAAATGGATCTCCA
Done.