Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1088

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: 2862
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.31


Found at i:2158 original size:47 final size:47

Alignment explanation


    Indices: 2107--2199  Score: 177
    Period size: 47  Copynumber: 2.0  Consensus size: 47

       2097 AAATCGAGTA

                                                           
       2107 AAAAAATAATGTGATGCTACATTAAATATACAATGCAATAATAAATT
          1 AAAAAATAATGTGATGCTACATTAAATATACAATGCAATAATAAATT

                   *                                      
       2154 AAAAAATGATGTGATGCTACATTAAATATACAATGCAATAATAAAT
          1 AAAAAATAATGTGATGCTACATTAAATATACAATGCAATAATAAAT

       2200 ATTACGATGG


Statistics
Matches: 45,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  47   45  1.00

ACGTcount: A:0.53, C:0.09, G:0.10, T:0.29


Consensus pattern (47 bp):   
AAAAAATAATGTGATGCTACATTAAATATACAATGCAATAATAAATT

Found at i:2375 original size:71 final size:71

Alignment explanation


    Indices: 2293--2429  Score: 229
    Period size: 71  Copynumber: 1.9  Consensus size: 71

       2283 AAACACAATT

                           *       *                                         
       2293 ATATAACGAATGAGGGAAGCAAATCAAATAAATGAAGAAAAGAATATATACAATATGAACATAGA
          1 ATATAACGAATGAGGAAAGCAAACCAAATAAATGAAGAAAAGAATATATACAATATGAACATAGA

                  
       2358 ATGTAA
         66 ATGTAA

                  *                              *            *              
       2364 ATATAATGAATGAGGAAAGCAAACCAAATAAATGAAGTAAAGAATATATATAATATGAACATAGA
          1 ATATAACGAATGAGGAAAGCAAACCAAATAAATGAAGAAAAGAATATATACAATATGAACATAGA

             
       2429 A
         66 A

       2430 ATTATGAAGA


Statistics
Matches: 61,  Mismatches: 5, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  71   61  1.00

ACGTcount: A:0.57, C:0.07, G:0.16, T:0.20


Consensus pattern (71 bp):   
ATATAACGAATGAGGAAAGCAAACCAAATAAATGAAGAAAAGAATATATACAATATGAACATAGA
ATGTAA
Done.