Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold2704
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, 522
Length: 871
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Found at i:386 original size:137 final size:133
Alignment explanation
Indices: 195--581 Score: 463
Period size: 137 Copynumber: 2.9 Consensus size: 133
185 TCTAAAAAAA
* * * *
195 TAATTTTGAGAAGATGGTTCTAAAAAAATAGGGTATAAAACGCTTCAAGTAGGATGCAGTGTCAG
1 TAATTTTGAGAA-ATGGTT-TAAAAAAATAGCGTAAAAAACGCTTCAAGCAGGATGCACTGTCAG
*
260 CAAAAGTATTGAAAAAAGCTCTCACCTAGACGCTCTTTTTCTACAGTAGTTTCTGAAAAATAATT
64 CAAAAGTATTGAAAAAAGCTCTCACCTAGATGCTCTTTTTCTACAGTAGTTTCTGAAAAATAATT
325 TTGAAG
129 TTG-AG
* *
331 TAATTTTGAGAATATGAATTTAAAAAAAATAGCGTAAAAAACGCTTCAAGCAGGATGCACTTTCA
1 TAATTTTGAGAA-ATG-GTTT-AAAAAAATAGCGTAAAAAACGCTTCAAGCAGGATGCACTGTCA
* *
396 GCAAAAGTATTGAAAAAAGCTC-CTGCCTAGATGCTCTTTTTCTACAGTAGATTCTGAAAAATAA
63 GCAAAAGTATTGAAAAAAGCTCTC-ACCTAGATGCTCTTTTTCTACAGTAGTTTCTGAAAAATAA
460 TTTTGAG
127 TTTTGAG
* * *
467 --A-----AG--ATGGTTTTGAAAAAATAGTGTAAAAAATGCTTCAAGCAGGATGCACTGTCAGC
1 TAATTTTGAGAAATGG-TTTAAAAAAATAGCGTAAAAAACGCTTCAAGCAGGATGCACTGTCAGC
* * * * *
523 AAAAGTACTGAAAAATGCT-TCCACCTGGATACTATTTTTCTACAGTAGTTTCTGAAAAA
65 AAAAGTATTGAAAAAAGCTCT-CACCTAGATGCTCTTTTTCTACAGTAGTTTCTGAAAAA
582 ATAGGATAAA
Statistics
Matches: 223, Mismatches: 22, Indels: 23
0.83 0.08 0.09
Matches are distributed among these distances:
125 90 0.40
126 7 0.03
129 2 0.01
134 1 0.00
136 19 0.09
137 104 0.47
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.30
Consensus pattern (133 bp):
TAATTTTGAGAAATGGTTTAAAAAAATAGCGTAAAAAACGCTTCAAGCAGGATGCACTGTCAGCA
AAAGTATTGAAAAAAGCTCTCACCTAGATGCTCTTTTTCTACAGTAGTTTCTGAAAAATAATTTT
GAG
Found at i:561 original size:125 final size:126
Alignment explanation
Indices: 331--581 Score: 353
Period size: 125 Copynumber: 2.0 Consensus size: 126
321 AATTTTGAAG
* *
331 TAATTTTGAGAATATGAATTTAAAAAAAATAGCGTAAAAAACGCTTCAAGCAGGATGCACTTTCA
1 TAATTTTGAGAAGATGAATTTAAAAAAAATAGCGTAAAAAACGCTTCAAGCAGGATGCACTGTCA
* * * *
396 GCAAAAGTATTGAAAAAAGCTCCTGCCTAGATGCTCTTTTTCTACAGTAGATTCTGAAAAA
66 GCAAAAGTACTGAAAAAAGCTCCTACCTAGATACTATTTTTCTACAGTAGATTCTGAAAAA
* ** * *
457 TAATTTTGAGAAGATG-GTTTTGAAAAAATAGTGTAAAAAATGCTTCAAGCAGGATGCACTGTCA
1 TAATTTTGAGAAGATGAATTTAAAAAAAATAGCGTAAAAAACGCTTCAAGCAGGATGCACTGTCA
* * *
521 GCAAAAGTACTGAAAAATGCTTCC-ACCTGGATACTATTTTTCTACAGTAGTTTCTGAAAAA
66 GCAAAAGTACTGAAAAAAGC-TCCTACCTAGATACTATTTTTCTACAGTAGATTCTGAAAAA
582 ATAGGATAAA
Statistics
Matches: 110, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
125 92 0.84
126 18 0.16
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.29
Consensus pattern (126 bp):
TAATTTTGAGAAGATGAATTTAAAAAAAATAGCGTAAAAAACGCTTCAAGCAGGATGCACTGTCA
GCAAAAGTACTGAAAAAAGCTCCTACCTAGATACTATTTTTCTACAGTAGATTCTGAAAAA
Found at i:811 original size:31 final size:29
Alignment explanation
Indices: 750--811 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
740 GGTTTTAGAG
* * *
750 AAAATAAATTAGGGTTTATGGATTTTAAA
1 AAAATAAATTAGGGTTTAAGAACTTTAAA
779 AAAATTAAATTAGGGTTTAAAGAACTTTAAA
1 AAAA-TAAATTAGGGTTT-AAGAACTTTAAA
810 AA
1 AA
812 TAAATTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 4 0.14
30 13 0.46
31 11 0.39
ACGTcount: A:0.50, C:0.02, G:0.15, T:0.34
Consensus pattern (29 bp):
AAAATAAATTAGGGTTTAAGAACTTTAAA
Done.