Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1005

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: 3408
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.27

Warning! 566 characters in sequence are not A, C, G, or T


Found at i:540 original size:15 final size:15

Alignment explanation


    Indices: 505--546  Score: 52
    Period size: 15  Copynumber: 2.9  Consensus size: 15

        495 TTAAGAATTT

                *          
        505 TATTAAATTAT-ATA
          1 TATTTAATTATAATA

                           
        519 T-TTTAATTATAATA
          1 TATTTAATTATAATA

                    *     
        533 TATTTAATAATAAT
          1 TATTTAATTATAAT

        547 TATGTTCTCC


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  13    8  0.33
  14    5  0.21
  15   11  0.46

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (15 bp):   
TATTTAATTATAATA

Found at i:3205 original size:23 final size:24

Alignment explanation


    Indices: 3170--3217  Score: 62
    Period size: 23  Copynumber: 2.0  Consensus size: 24

       3160 ATACATAAAC

                                    
       3170 TTCACACAAATAAAAAACAATCAA
          1 TTCACACAAATAAAAAACAATCAA

                    *      *   *    
       3194 TTCA-ACATATAAAACACATTCAA
          1 TTCACACAAATAAAAAACAATCAA

             
       3217 T
          1 T

       3218 CACCAACAAA


Statistics
Matches: 21,  Mismatches: 3, Indels: 1
        0.84            0.12        0.04

Matches are distributed among these distances:
  23   17  0.81
  24    4  0.19

ACGTcount: A:0.56, C:0.21, G:0.00, T:0.23


Consensus pattern (24 bp):   
TTCACACAAATAAAAAACAATCAA
Done.