Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_559 ID=scaffold_559-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: 5702
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37


Found at i:4068 original size:2 final size:2

Alignment explanation


    Indices: 4057--4088  Score: 57
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       4047 CATATAATTT

                                                             
       4057 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       4089 GTGATATGTT


Statistics
Matches: 29,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   28  0.97

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:5702 original size:2 final size:2

Alignment explanation


    Indices: 5642--5694  Score: 106
    Period size: 2  Copynumber: 26.5  Consensus size: 2

       5632 TCATTATGAC

                                                                          
       5642 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                            
       5684 AT AT AT AT AT A
          1 AT AT AT AT AT A

       5695 CGTATATA


Statistics
Matches: 51,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   51  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT
Done.