Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold527
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: 2222
ACGTcount: A:0.19, C:0.36, G:0.32, T:0.13
Found at i:914 original size:403 final size:403
Alignment explanation
Indices: 4--1110 Score: 1597
Period size: 403 Copynumber: 2.7 Consensus size: 403
1 GCG
4 CAATCCCCGACAGGCAACCGGCAGGACGTGCCCACCGTTGCCGATGCAA-GGCCACGAGACTGCC
1 CAATCCCCGACAGGCAACCGGCAGGACGTGCCCACCGTTGCCGATGCAAGGGCCACGAGACTGCC
*
68 CCTTGCCCGAGGGGCAATGGCCAGGCCAAGCCCTCACCTGCAGCTTCTGCCCACGCCACAACCGG
66 CC-TGCTCGAGGGGC-ATGGCCAGGCCAAGCCCTCACCTGCAGCTTCTGCCCACGCCACAACCGG
* *
133 GACAACCTACTCGAATTCGGGAACTTGGCAAGAATCACCGCAGGTGGCGAGCC-TGCCTTCCGGC
129 GACTACCAACTCGAATTCGGGAACTTGGC-AGAATCACCGCAGGT-GCGAGCCTTGCCTTCCGGC
* * **
197 A-GACCACGCCCCGTTACCCGCACACGCGTGCCAAACGATCGCGCACGTAGCGACCGGGGGCCTC
192 ACGACCACGCCCCGTTACCCGCACACGCGTGCCAAACGATCGCGCACGCAGAGACCGACGGCCTC
* *
261 ACCACGGATCACTTGGACCGCGTAGGGTCTCCATCACCGCAGCTGGGCATCCGGTCACCGAAAAC
257 ACCACGGATCACTTGGACCGCGAAGGGTCTCCATCACCGCAGCTGGGCATCCGGCCACCGAAAAC
* * * *
326 CACGATCGCAAGGCTCGCGCGACCTGGATTTTAATCGAGAGGGACACTGCCGGGGCGCGAACCAT
322 CACGATCGCAAGGCACGCGCGACCTGGATCTTAACCGAGAGGGACACTGCCGGGGCGCGAACAAT
* *
391 GCCAGGCGCATGGAGCG
387 GCCAGGCGCATCGAGCA
408 CAATCCCCGACAGGCAACCGGCAGGACGTGCCCACCGTTGCCGATGCAAGGGCCACGAGACTGCC
1 CAATCCCCGACAGGCAACCGGCAGGACGTGCCCACCGTTGCCGATGCAAGGGCCACGAGACTGCC
*
473 CCTGCTCGAGGGGCATGGCCAGGCCAAGCCCTCACCTGCAGCCTCTGCCCACGCCACAACCGGGA
66 CCTGCTCGAGGGGCATGGCCAGGCCAAGCCCTCACCTGCAGCTTCTGCCCACGCCACAACCGGGA
* *
538 CTACCGACTCGAATTCGGGAACTTGGCAGCATCACCGCAGGTGCGAGCCTTGCCTTCCGGCACGA
131 CTACCAACTCGAATTCGGGAACTTGGCAGAATCACCGCAGGTGCGAGCCTTGCCTTCCGGCACGA
*
603 CCACGCCCCGTTACCCGCACACGCGTGCCAACCGATCGCGCACGCAGAGACCGACGGCCTCACCA
196 CCACGCCCCGTTACCCGCACACGCGTGCCAAACGATCGCGCACGCAGAGACCGACGGCCTCACCA
*
668 CGGATCACTTGGACCGCGAAGGGTC-CCGTCACCCGCAGCT-GGCATCCGGCCACCGAAAACCAC
261 CGGATCACTTGGACCGCGAAGGGTCTCCATCA-CCGCAGCTGGGCATCCGGCCACCGAAAACCAC
*
731 GATCGCAAGGCACGCGCGACCTGGATCTTAACCGAGAGGGACACT-CTGCGTGGGCGCGATCAAT
325 GATCGCAAGGCACGCGCGACCTGGATCTTAACCGAGAGGGACACTGC--CG-GGGCGCGAACAAT
795 GCCAGGCGCATCGAGCA
387 GCCAGGCGCATCGAGCA
* * * * *
812 CAATCCCCGACAGACAACCGGCGGGACGAGCCCACCGTTGCCGAAGCAAGGGCCGCGAGACTGCC
1 CAATCCCCGACAGGCAACCGGCAGGACGTGCCCACCGTTGCCGATGCAAGGGCCACGAGACTGCC
877 CCTGCTC-ACGGGGCATGGCCAGGCCAAGCCC-CACCTGCAGCTTCTGCCCACGCCACAACCGGG
66 CCTGCTCGA-GGGGCATGGCCAGGCCAAGCCCTCACCTGCAGCTTCTGCCCACGCCACAACCGGG
* * * *
940 ACTACCAACTCGAATTCGGGAACTTGGCAGAATCAGCGCAGGTG-GAAG-CTTAACCCTACGGCA
130 ACTACCAACTCGAATTCGGGAACTTGGCAGAATCACCGCAGGTGCG-AGCCTT-GCCTTCCGGCA
** * ** ** * * *
1003 CGACCACGCCCCTTGTGCCCCACACACGCGTGCCATGCGATCGGCAGCATACGGCGACCG-GGGA
193 CGACCACGCCCC--GTTACCCGCACACGCGTGCCAAACGATC-GC-GCACGCAGAGACCGACGG-
** * *
1067 CCTTGCCACGGATCACCTGGACCGCGCAGGGTCTCCATCACCGC
253 CCTCACCACGGATCACTTGGACCGCGAAGGGTCTCCATCACCGC
1111 GACAAGGTTT
Statistics
Matches: 640, Mismatches: 47, Indels: 29
0.89 0.07 0.04
Matches are distributed among these distances:
401 8 0.01
402 99 0.15
403 266 0.42
404 175 0.27
405 40 0.06
406 4 0.01
407 43 0.07
408 5 0.01
ACGTcount: A:0.22, C:0.38, G:0.28, T:0.12
Consensus pattern (403 bp):
CAATCCCCGACAGGCAACCGGCAGGACGTGCCCACCGTTGCCGATGCAAGGGCCACGAGACTGCC
CCTGCTCGAGGGGCATGGCCAGGCCAAGCCCTCACCTGCAGCTTCTGCCCACGCCACAACCGGGA
CTACCAACTCGAATTCGGGAACTTGGCAGAATCACCGCAGGTGCGAGCCTTGCCTTCCGGCACGA
CCACGCCCCGTTACCCGCACACGCGTGCCAAACGATCGCGCACGCAGAGACCGACGGCCTCACCA
CGGATCACTTGGACCGCGAAGGGTCTCCATCACCGCAGCTGGGCATCCGGCCACCGAAAACCACG
ATCGCAAGGCACGCGCGACCTGGATCTTAACCGAGAGGGACACTGCCGGGGCGCGAACAATGCCA
GGCGCATCGAGCA
Done.