Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold762

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: 7057
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31


Found at i:3425 original size:39 final size:39

Alignment explanation


    Indices: 3366--3480  Score: 133
    Period size: 39  Copynumber: 2.9  Consensus size: 39

       3356 AATTTAGTTC

                *                                 *
       3366 GAGTATTTAATTATGTCATAATTTGAACATCATTAATAT
          1 GAGTTTTTAATTATGTCATAATTTGAACATCATTAATAA

                        *         *      *         
       3405 GAGTTTTTAATTTTGTCATAATCTGAACAACATTAATAA
          1 GAGTTTTTAATTATGTCATAATTTGAACATCATTAATAA

               *                *     *     *     
       3444 G-GGTTTTAATTATGTCATAGTTTAGGACATCTTTAAT
          1 GAGTTTTTAATTATGTCATAATTT-GAACATCATTAAT

       3481 GCATATTTTA


Statistics
Matches: 63,  Mismatches: 12, Indels: 2
        0.82            0.16        0.03

Matches are distributed among these distances:
  38   18  0.29
  39   45  0.71

ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43


Consensus pattern (39 bp):   
GAGTTTTTAATTATGTCATAATTTGAACATCATTAATAA

Found at i:4934 original size:52 final size:53

Alignment explanation


    Indices: 4854--4955  Score: 152
    Period size: 52  Copynumber: 1.9  Consensus size: 53

       4844 TTAAGAAGTC

                                   *             *    *          
       4854 TGACTTAATAACATGCATTGATGTTGTTCAAACTAGAGCATAGTTAATAGGTG
          1 TGACTTAATAACATGCATTGATGATGTTCAAACTAGAACATACTTAATAGGTG

                                         *  *                 
       4907 TGACTTAA-AACATGCATTGATGATGTTCGAATTAGAACATACTTAATAG
          1 TGACTTAATAACATGCATTGATGATGTTCAAACTAGAACATACTTAATAG

       4956 ACATAAATCA


Statistics
Matches: 44,  Mismatches: 5, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  52   36  0.82
  53    8  0.18

ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33


Consensus pattern (53 bp):   
TGACTTAATAACATGCATTGATGATGTTCAAACTAGAACATACTTAATAGGTG
Done.