Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold3945

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, 372

Length: 621
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34


Found at i:57 original size:32 final size:34

Alignment explanation


    Indices: 1--70  Score: 90
    Period size: 32  Copynumber: 2.1  Consensus size: 34

                                              
          1 AAAAACTATAGAAAAAATTATTAAAAATTATAAA
          1 AAAAACTATAGAAAAAATTATTAAAAATTATAAA

                 *       *           **       
         35 AAAAAGTATAG-ACAAATT-TTAAATGTTATAAA
          1 AAAAACTATAGAAAAAATTATTAAAAATTATAAA

                
         67 AAAA
          1 AAAA

         71 TTTAGAATAA


Statistics
Matches: 32,  Mismatches: 4, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  32   16  0.50
  33    6  0.19
  34   10  0.31

ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27


Consensus pattern (34 bp):   
AAAAACTATAGAAAAAATTATTAAAAATTATAAA

Found at i:385 original size:22 final size:22

Alignment explanation


    Indices: 339--402  Score: 69
    Period size: 22  Copynumber: 3.0  Consensus size: 22

        329 TTCACTGTTT

                        *        *
        339 TAAAAA-TAATAAAAAATTATT
          1 TAAAAATTAATATAAAATTATA

                *                  
        360 TAAATATTAATTATAAAA-TATA
          1 TAAAAATTAA-TATAAAATTATA

                            *    
        382 TAAAAATTAATATAAACTTAT
          1 TAAAAATTAATATAAAATTAT

        403 TTTCTATTTA


Statistics
Matches: 35,  Mismatches: 5, Indels: 5
        0.78            0.11        0.11

Matches are distributed among these distances:
  21   11  0.31
  22   18  0.51
  23    6  0.17

ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38


Consensus pattern (22 bp):   
TAAAAATTAATATAAAATTATA
Done.