Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_477 ID=scaffold_477-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: 6821
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.29

Warning! 200 characters in sequence are not A, C, G, or T


Found at i:4560 original size:18 final size:17

Alignment explanation


    Indices: 4537--4575  Score: 60
    Period size: 17  Copynumber: 2.3  Consensus size: 17

       4527 AAAAAATAAC

                   * *       
       4537 AAAAAAAGGGGAAAAAG
          1 AAAAAAAAGAGAAAAAG

                             
       4554 AAAAAAAAGAGAAAAAG
          1 AAAAAAAAGAGAAAAAG

                 
       4571 AAAAA
          1 AAAAA

       4576 GAACCCCGCT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  17   20  1.00

ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00


Consensus pattern (17 bp):   
AAAAAAAAGAGAAAAAG

Found at i:5091 original size:24 final size:23

Alignment explanation


    Indices: 5064--5108  Score: 63
    Period size: 24  Copynumber: 1.9  Consensus size: 23

       5054 AAAAAAGATG

                *                   
       5064 ATGAGAAATGAAAAAGTGAAAAAA
          1 ATGAAAAATGAAAAAGT-AAAAAA

                      *          
       5088 ATGAAAAATGGAAAAGTAAAA
          1 ATGAAAAATGAAAAAGTAAAA

       5109 TGGAGAGGCT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  23    4  0.21
  24   15  0.79

ACGTcount: A:0.67, C:0.00, G:0.20, T:0.13


Consensus pattern (23 bp):   
ATGAAAAATGAAAAAGTAAAAAA
Done.