Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_1006 ID=scaffold_1006-JGI_221_v2.0

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: 2864
ACGTcount: A:0.19, C:0.09, G:0.08, T:0.18

Warning! 1318 characters in sequence are not A, C, G, or T


Found at i:804 original size:20 final size:20

Alignment explanation


    Indices: 776--814  Score: 69
    Period size: 20  Copynumber: 1.9  Consensus size: 20

        766 AGTAAAATAT

                                
        776 TTTCCGGAAAATGATTTACA
          1 TTTCCGGAAAATGATTTACA

                *              
        796 TTTCTGGAAAATGATTTAC
          1 TTTCCGGAAAATGATTTAC

        815 TGAAAATATT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38


Consensus pattern (20 bp):   
TTTCCGGAAAATGATTTACA

Found at i:1012 original size:18 final size:18

Alignment explanation


    Indices: 989--1024  Score: 54
    Period size: 18  Copynumber: 2.0  Consensus size: 18

        979 AATTTATTTA

                              
        989 TAAATAAATAAATCAAAT
          1 TAAATAAATAAATCAAAT

                  *  *        
       1007 TAAATATATCAATCAAAT
          1 TAAATAAATAAATCAAAT

       1025 GGTTTAATTG


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31


Consensus pattern (18 bp):   
TAAATAAATAAATCAAAT
Done.