Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1401

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: 6016
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26


Found at i:5158 original size:11 final size:11

Alignment explanation


    Indices: 5142--5174  Score: 57
    Period size: 11  Copynumber: 2.9  Consensus size: 11

       5132 CCTCCGCAAA

                       
       5142 AAAAAAAAAAC
          1 AAAAAAAAAAC

                       
       5153 AAAAAAAAAAC
          1 AAAAAAAAAAC

                       
       5164 ACAAAAAAAAA
          1 A-AAAAAAAAA

       5175 TAACAACAAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  11   12  0.57
  12    9  0.43

ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00


Consensus pattern (11 bp):   
AAAAAAAAAAC

Found at i:5158 original size:13 final size:13

Alignment explanation


    Indices: 5140--5186  Score: 67
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       5130 ATCCTCCGCA

                         
       5140 AAAAAAAAAAAAC
          1 AAAAAAAAAAAAC

                      *  
       5153 AAAAAAAAAACAC
          1 AAAAAAAAAAAAC

                     *   
       5166 AAAAAAAAATAAC
          1 AAAAAAAAAAAAC

                    
       5179 AACAAAAA
          1 AA-AAAAA

       5187 GGGTCCGGAT


Statistics
Matches: 30,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  13   25  0.83
  14    5  0.17

ACGTcount: A:0.87, C:0.11, G:0.00, T:0.02


Consensus pattern (13 bp):   
AAAAAAAAAAAAC
Done.