Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_135 ID=scaffold_135-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: 11412
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35

Warning! 100 characters in sequence are not A, C, G, or T


Found at i:10468 original size:15 final size:16

Alignment explanation


    Indices: 10436--10473  Score: 60
    Period size: 15  Copynumber: 2.4  Consensus size: 16

      10426 TTTCCACCAT

                       *    
      10436 ATTTGTTGTTATTTTC
          1 ATTTGTTGTTAATTTC

                            
      10452 ATTTGTT-TTAATTTC
          1 ATTTGTTGTTAATTTC

                   
      10467 ATTTGTT
          1 ATTTGTT

      10474 AAAATATCTT


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  15   14  0.67
  16    7  0.33

ACGTcount: A:0.16, C:0.05, G:0.11, T:0.68


Consensus pattern (16 bp):   
ATTTGTTGTTAATTTC

Found at i:11200 original size:23 final size:23

Alignment explanation


    Indices: 11157--11199  Score: 70
    Period size: 23  Copynumber: 1.9  Consensus size: 23

      11147 AAAAATAAAT

                 *                 
      11157 TATTCTTTTCTTTATTATTTTAC
          1 TATTCGTTTCTTTATTATTTTAC

                                 
      11180 TATTCGTTTCTTT-TTATTTT
          1 TATTCGTTTCTTTATTATTTT

      11200 TTAATTTAAT


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  22    7  0.37
  23   12  0.63

ACGTcount: A:0.14, C:0.12, G:0.02, T:0.72


Consensus pattern (23 bp):   
TATTCGTTTCTTTATTATTTTAC
Done.