Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1689
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, 841
Length: 1402
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Found at i:650 original size:133 final size:133
Alignment explanation
Indices: 412--678 Score: 493
Period size: 133 Copynumber: 2.0 Consensus size: 133
402 GCAAAGGCTT
412 CAAGAACTATAATTTTCTTGTATGTGGTACAACTTATTCCGTAGATTAAGTATATTTTAACATGT
1 CAAGAACTATAATTTTCTTGTATGTGGTACAACTTATTCCGTAGATTAAGTATATTTTAACATGT
477 TTGACCTCAGGCAATTACCCCTCCCCCCTCCCCCGCCCTGCGCACAGTAGGTTGAGAGGGCACTG
66 TTGACCTCAGGCAATTACCCCTCCCCCCTCCCCCGCCCTGCGCACAGTAGGTTGAGAGGGCACTG
542 AAA
131 AAA
545 CAAGAACTATAATTTTCTTGTATGTGGTACACAACTTATT-C-TAGATTAAGTATATTTTAACAT
1 CAAGAACTATAATTTTCTTGTATGTGGT--ACAACTTATTCCGTAGATTAAGTATATTTTAACAT
*
608 GTTTGACCTCAGGCAATTACCCCTCCCCCCTCCCCCGCCCTGCGCACAGTAGGTTGAGGGGGCAC
64 GTTTGACCTCAGGCAATTACCCCTCCCCCCTCCCCCGCCCTGCGCACAGTAGGTTGAGAGGGCAC
673 TGAAA
129 TGAAA
678 C
1 C
679 GCGATTCAAG
Statistics
Matches: 131, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
133 120 0.92
134 1 0.01
135 10 0.08
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (133 bp):
CAAGAACTATAATTTTCTTGTATGTGGTACAACTTATTCCGTAGATTAAGTATATTTTAACATGT
TTGACCTCAGGCAATTACCCCTCCCCCCTCCCCCGCCCTGCGCACAGTAGGTTGAGAGGGCACTG
AAA
Found at i:1389 original size:114 final size:114
Alignment explanation
Indices: 1184--1402 Score: 359
Period size: 114 Copynumber: 1.9 Consensus size: 114
1174 AATGTCTTCT
* * * * * *
1184 GCTGATTGTAGTTTTGTTTTCTTCTCTCCATCTTCGAGAGGGTTTTCTTTAGATAAAGCAGTTAC
1 GCTGATTGTAGTTTTATTCTCTTCTCGCCATCTTCGAGAGGGTTTTCGTCAGATAAAGCAATTAC
1249 CATTTTCCGTTTGCACTCAACAGAAATATC-TCTGTCAAAGAAAGAAAAC
66 CATTTTCCGTTTGCACTCAACAGAAATATCGT-TGTCAAAGAAAGAAAAC
*
1298 GCTGCTTGTAGTTTTATTCTCTTCTCGCCATCTTCGAGAGGGTTTTCGTCAGATAAAGCAATTAC
1 GCTGATTGTAGTTTTATTCTCTTCTCGCCATCTTCGAGAGGGTTTTCGTCAGATAAAGCAATTAC
1363 CATTTTCCGTTTGCACTCAACAGAAATATCGTTGTCAAAG
66 CATTTTCCGTTTGCACTCAACAGAAATATCGTTGTCAAAG
Statistics
Matches: 97, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
114 96 0.99
115 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.37
Consensus pattern (114 bp):
GCTGATTGTAGTTTTATTCTCTTCTCGCCATCTTCGAGAGGGTTTTCGTCAGATAAAGCAATTAC
CATTTTCCGTTTGCACTCAACAGAAATATCGTTGTCAAAGAAAGAAAAC
Done.