Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold800
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: 6297
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.30
Found at i:2482 original size:274 final size:274
Alignment explanation
Indices: 1993--2533 Score: 929
Period size: 274 Copynumber: 2.0 Consensus size: 274
1983 ACTCAAAAAA
1993 TTGAGGGATGCTGTGTCCCTATTCCAGGACAAAGCTTATCAGTGGTGGTTGACAGTTGAACAAAG
1 TTGAGGGATGCTGTGTCCCTATTCCAGGACAAAGCTTATCAGTGGTGGTTGACAGTTGAACAAAG
2058 TGTTCAGCCTGAACAGGTGAACTGGGACTATTTCAAGAACACATTCCAAGGTTAGTATGTGAGGG
66 TGTTCAGCCTGAACAGGTGAACTGGGACTATTTCAAGAACACATTCCAAGGTTAGTATGTGAGGG
* *
2123 CAAATTATGTTGAGGCTCACCGATACGAGTTCATGAGCCTAGTTCAAGGCGACCGATCGGTGGCC
131 CAAATTATGTTGAAGCTCACCGATACGAGTTCATGAGCCTAGTTCAAGGCAACCGATCGGTGGCC
* * * * *
2188 AAATAGGAAGTCGAGTTTTTACGACTGAGTAGGTATGTATGGACTCTAGTAGCGTCTAATTATGA
196 AAATAGGAAGCCAAGTTTTTACGACTAAGTAGGTATGCATGGACTCTAGTAGCGTCTAATTACGA
2253 AAAGTGTTTAAAGT
261 AAAGTGTTTAAAGT
* * * * * *
2267 TTGAGGGGTGCTGTTTCCTTATTTCGGGACGAAGCTTATCAGTGGTGGTTGACAGTTGAACAAAG
1 TTGAGGGATGCTGTGTCCCTATTCCAGGACAAAGCTTATCAGTGGTGGTTGACAGTTGAACAAAG
2332 TGTTCAGCCTGAACAGGTGAACTGGGACTATTTCAAGAACACATTCCAAGGTTAGTATGTGAGGG
66 TGTTCAGCCTGAACAGGTGAACTGGGACTATTTCAAGAACACATTCCAAGGTTAGTATGTGAGGG
*
2397 CAAATTATGTTGAAGCTCACCGATACGAGTTCATGAGCCTAGTTCAGGGCAACCGATCGGTGGCC
131 CAAATTATGTTGAAGCTCACCGATACGAGTTCATGAGCCTAGTTCAAGGCAACCGATCGGTGGCC
* *
2462 AAATATGAAGCCAAGTTTTTACGACTAAGTAGGTATGCATGGACTCTAGTAGCGTCTGATTACGA
196 AAATAGGAAGCCAAGTTTTTACGACTAAGTAGGTATGCATGGACTCTAGTAGCGTCTAATTACGA
*
2527 TAAGTGT
261 AAAGTGT
2534 GTGAGGTTAG
Statistics
Matches: 250, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
274 250 1.00
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (274 bp):
TTGAGGGATGCTGTGTCCCTATTCCAGGACAAAGCTTATCAGTGGTGGTTGACAGTTGAACAAAG
TGTTCAGCCTGAACAGGTGAACTGGGACTATTTCAAGAACACATTCCAAGGTTAGTATGTGAGGG
CAAATTATGTTGAAGCTCACCGATACGAGTTCATGAGCCTAGTTCAAGGCAACCGATCGGTGGCC
AAATAGGAAGCCAAGTTTTTACGACTAAGTAGGTATGCATGGACTCTAGTAGCGTCTAATTACGA
AAAGTGTTTAAAGT
Found at i:2666 original size:157 final size:157
Alignment explanation
Indices: 2380--2698 Score: 620
Period size: 157 Copynumber: 2.0 Consensus size: 157
2370 ACACATTCCA
2380 AGGTTAGTATGTGAGGGCAAATTATGTTGAAGCTCACCGATACGAGTTCATGAGCCTAGTTCAGG
1 AGGTTAGTATGTGAGGGCAAATTATGTTGAAGCTCACCGATACGAGTTCATGAGCCTAGTTCAGG
2445 GCAACCGATCGGTGGCCAAATATGAAGCCAAGTTTTTACGACTAAGTAGGTATGCATGGACTCTA
66 GCAACCGATCGGTGGCCAAATATGAAGCCAAGTTTTTACGACTAAGTAGGTATGCATGGACTCTA
*
2510 GTAGCGTCTGATTACGATAAGTGTGTG
131 GTAGCATCTGATTACGATAAGTGTGTG
2537 AGGTTAGTATGTGAGGGCAAATTATGTTGAAGCTCACCGATACGAGTTCATGAGCCTAGTTCAGG
1 AGGTTAGTATGTGAGGGCAAATTATGTTGAAGCTCACCGATACGAGTTCATGAGCCTAGTTCAGG
2602 GCAACCGATCGGTGGCCAAATATGAAGCCAAGTTTTTACGACTAAGTAGGTATGCATGGACTCTA
66 GCAACCGATCGGTGGCCAAATATGAAGCCAAGTTTTTACGACTAAGTAGGTATGCATGGACTCTA
*
2667 GTAGCATCTGATTATGATAAGTGTGTG
131 GTAGCATCTGATTACGATAAGTGTGTG
2694 AGGTT
1 AGGTT
2699 TGAGGGATTG
Statistics
Matches: 160, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
157 160 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (157 bp):
AGGTTAGTATGTGAGGGCAAATTATGTTGAAGCTCACCGATACGAGTTCATGAGCCTAGTTCAGG
GCAACCGATCGGTGGCCAAATATGAAGCCAAGTTTTTACGACTAAGTAGGTATGCATGGACTCTA
GTAGCATCTGATTACGATAAGTGTGTG
Done.