Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold10822.1

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: 3276
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32


Found at i:954 original size:43 final size:44

Alignment explanation


    Indices: 891--984  Score: 154
    Period size: 43  Copynumber: 2.1  Consensus size: 44

        881 GCCAAGACAC

                                              *  *       
        891 ATTTAAAACATGTAATAAGTCAAAACATAATTATGAGCTGTAGTA
          1 ATTT-AAACATGTAATAAGTCAAAACATAATTATAAGATGTAGTA

                                                        
        936 ATTTAAA-ATGTAATAAGTCAAAACATAATTATAAGATGTAGTA
          1 ATTTAAACATGTAATAAGTCAAAACATAATTATAAGATGTAGTA

                  
        979 ATTTAA
          1 ATTTAA

        985 GCTAAATTAA


Statistics
Matches: 47,  Mismatches: 2, Indels: 2
        0.92            0.04        0.04

Matches are distributed among these distances:
  43   40  0.85
  44    3  0.06
  45    4  0.09

ACGTcount: A:0.49, C:0.06, G:0.12, T:0.33


Consensus pattern (44 bp):   
ATTTAAACATGTAATAAGTCAAAACATAATTATAAGATGTAGTA

Found at i:1084 original size:20 final size:19

Alignment explanation


    Indices: 1061--1125  Score: 51
    Period size: 20  Copynumber: 3.3  Consensus size: 19

       1051 AAGCTCAAAC

                                
       1061 GAGCTAAAGTAAGCTAAATT
          1 GAGCTAAAGT-AGCTAAATT

                                 
       1081 GAGCTCAAACG-AGCTAAATT
          1 GAGCT-AAA-GTAGCTAAATT

            *    * *           *
       1101 AAGCTCATGTGAGCTAAATC
          1 GAGCTAAAGT-AGCTAAATT

                 
       1121 GAGCT
          1 GAGCT

       1126 GGGAAAAACT


Statistics
Matches: 36,  Mismatches: 5, Indels: 8
        0.73            0.10        0.16

Matches are distributed among these distances:
  18    1  0.03
  19    1  0.03
  20   30  0.83
  21    3  0.08
  22    1  0.03

ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23


Consensus pattern (19 bp):   
GAGCTAAAGTAGCTAAATT

Found at i:2415 original size:17 final size:18

Alignment explanation


    Indices: 2393--2426  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       2383 ACAACACTCC

                        *     
       2393 TTTCTT-CTTCACTCTCG
          1 TTTCTTCCTTCAATCTCG

                             
       2410 TTTCTTCCTTCAATCTC
          1 TTTCTTCCTTCAATCTC

       2427 ACTCTCTTTT


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    6  0.40
  18    9  0.60

ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53


Consensus pattern (18 bp):   
TTTCTTCCTTCAATCTCG

Done.