Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2422

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, 569

Length: 949
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Found at i:72 original size:13 final size:13

Alignment explanation


    Indices: 54--80  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

         44 ATTTCAATCA

                         
         54 CTCTTTTTTTTTT
          1 CTCTTTTTTTTTT

                         
         67 CTCTTTTTTTTTT
          1 CTCTTTTTTTTTT

             
         80 C
          1 C

         81 AATTTCGATT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81


Consensus pattern (13 bp):   
CTCTTTTTTTTTT

Found at i:100 original size:27 final size:28

Alignment explanation


    Indices: 61--138  Score: 115
    Period size: 27  Copynumber: 2.8  Consensus size: 28

         51 TCACTCTTTT

                                    *    
         61 TTTTTTCTCTTTTTTTTTTCAATTTCG-A
          1 TTTTTT-TCTTTTTTTTTTCAATTCCGAA

                                        
         89 TTTTTTTCTTTTTTTTTT-AATTCCGAA
          1 TTTTTTTCTTTTTTTTTTCAATTCCGAA

                                   
        116 TTTTTTTCTTTTTTTTCTTCAAT
          1 TTTTTTTCTTTTTTTT-TTCAAT

        139 ACTAAATACA


Statistics
Matches: 46,  Mismatches: 1, Indels: 5
        0.88            0.02        0.10

Matches are distributed among these distances:
  26    6  0.13
  27   29  0.63
  28    8  0.17
  29    3  0.07

ACGTcount: A:0.12, C:0.13, G:0.03, T:0.73


Consensus pattern (28 bp):   
TTTTTTTCTTTTTTTTTTCAATTCCGAA

Found at i:192 original size:13 final size:13

Alignment explanation


    Indices: 171--221  Score: 68
    Period size: 13  Copynumber: 4.0  Consensus size: 13

        161 AAATTGAATA

                *        
        171 CAAACTTTTTTTT
          1 CAAATTTTTTTTT

                         
        184 CAAATTTTTTTTT
          1 CAAATTTTTTTTT

             *           
        197 CGAATTTTTTTTT
          1 CAAATTTTTTTTT

              *          
        210 C-GATTTTTTTTT
          1 CAAATTTTTTTTT

        222 ACAATCTCAT


Statistics
Matches: 35,  Mismatches: 3, Indels: 1
        0.90            0.08        0.03

Matches are distributed among these distances:
  12   10  0.29
  13   25  0.71

ACGTcount: A:0.18, C:0.10, G:0.04, T:0.69


Consensus pattern (13 bp):   
CAAATTTTTTTTT

Done.