Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: COLO4_19856

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, 954

Length: 1590
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.25


Found at i:121 original size:12 final size:12

Alignment explanation


    Indices: 91--179  Score: 54
    Period size: 12  Copynumber: 7.2  Consensus size: 12

         81 GGTGGAGTAT

                   *   *
         91 GAAGAAGTGGAG
          1 GAAGAAGAGGAA

             *          
        103 GTAGAAGAGGAA
          1 GAAGAAGAGGAA

              *      *   
        115 GAGGAAGA-AATA
          1 GAAGAAGAGGA-A

                 *    **
        127 GAAGAGGAGGTG
          1 GAAGAAGAGGAA

                           
        139 GAAGAAGAGGTTGAA
          1 GAAGAAGA-G--GAA

                    *   
        154 GAAGAAGAAGAA
          1 GAAGAAGAGGAA

                        
        166 GAAGAAGAGGAA
          1 GAAGAAGAGGAA

              
        178 GA
          1 GA

        180 TCAAGATGTT


Statistics
Matches: 56,  Mismatches: 16, Indels: 10
        0.68            0.20        0.12

Matches are distributed among these distances:
  11    1  0.02
  12   45  0.80
  13    1  0.02
  15    9  0.16

ACGTcount: A:0.51, C:0.00, G:0.43, T:0.07


Consensus pattern (12 bp):   
GAAGAAGAGGAA

Found at i:128 original size:21 final size:21

Alignment explanation


    Indices: 104--144  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

         94 GAAGTGGAGG

                                 
        104 TAGAAGAGGAAGAGGAAGAAA
          1 TAGAAGAGGAAGAGGAAGAAA

                      * *       
        125 TAGAAGAGGAGGTGGAAGAA
          1 TAGAAGAGGAAGAGGAAGAA

        145 GAGGTTGAAG


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.51, C:0.00, G:0.41, T:0.07


Consensus pattern (21 bp):   
TAGAAGAGGAAGAGGAAGAAA
Done.