Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1533

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, 956

Length: 1594
ACGTcount: A:0.26, C:0.18, G:0.11, T:0.22

Warning! 385 characters in sequence are not A, C, G, or T


Found at i:1075 original size:29 final size:29

Alignment explanation


    Indices: 1012--1079  Score: 84
    Period size: 29  Copynumber: 2.3  Consensus size: 29

       1002 TAATCAACCG

                              *          
       1012 CGCACACTTAGTGCCATGTACTTTAAACT
          1 CGCACACTTAGTGCCATGCACTTTAAACT

             *                         ** 
       1041 CACACACTTAGTGCCATGCA-TTTCAAGTT
          1 CGCACACTTAGTGCCATGCACTTT-AAACT

                      
       1070 CGCACACTTA
          1 CGCACACTTA

       1080 CCTTTTCCGC


Statistics
Matches: 33,  Mismatches: 5, Indels: 2
        0.82            0.12        0.05

Matches are distributed among these distances:
  28    3  0.09
  29   30  0.91

ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29


Consensus pattern (29 bp):   
CGCACACTTAGTGCCATGCACTTTAAACT

Found at i:1299 original size:29 final size:30

Alignment explanation


    Indices: 1260--1338  Score: 110
    Period size: 29  Copynumber: 2.7  Consensus size: 30

       1250 CTTAATAATC

                                           
       1260 AACCACGCACACTTAGTGCCATGTAC-TTTA
          1 AACC-CGCACACTTAGTGCCATGTACATTTA

               *                           
       1290 AACTCGCACACTTAGTG-C-TGTACAATTTA
          1 AACCCGCACACTTAGTGCCATGTAC-ATTTA

                                
       1319 AACCCGCACACTTAGTGCCA
          1 AACCCGCACACTTAGTGCCA

       1339 ATCTCATGAC


Statistics
Matches: 43,  Mismatches: 2, Indels: 7
        0.83            0.04        0.13

Matches are distributed among these distances:
  27    5  0.12
  28    1  0.02
  29   33  0.77
  30    4  0.09

ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25


Consensus pattern (30 bp):   
AACCCGCACACTTAGTGCCATGTACATTTA
Done.