Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_528 ID=scaffold_528-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: 6109
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.33

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


Found at i:367 original size:5 final size:5

Alignment explanation


    Indices: 349--388  Score: 53
    Period size: 5  Copynumber: 7.6  Consensus size: 5

        339 TGTTTTATGT

                                   *                       
        349 ATATA ATAATA ATATA ATATT ATAATA ATATA ATATA ATA
          1 ATATA AT-ATA ATATA ATATA AT-ATA ATATA ATATA ATA

        389 ACTTACTTAT


Statistics
Matches: 31,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
   5   22  0.71
   6    9  0.29

ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40


Consensus pattern (5 bp):   
ATATA

Found at i:373 original size:16 final size:16

Alignment explanation


    Indices: 349--389  Score: 73
    Period size: 16  Copynumber: 2.6  Consensus size: 16

        339 TGTTTTATGT

                            
        349 ATATAATAATAATATA
          1 ATATAATAATAATATA

                *           
        365 ATATTATAATAATATA
          1 ATATAATAATAATATA

                     
        381 ATATAATAA
          1 ATATAATAA

        390 CTTACTTATT


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  16   23  1.00

ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39


Consensus pattern (16 bp):   
ATATAATAATAATATA

Found at i:389 original size:8 final size:8

Alignment explanation


    Indices: 354--383  Score: 51
    Period size: 8  Copynumber: 3.8  Consensus size: 8

        344 TATGTATATA

                    
        354 ATAATAAT
          1 ATAATAAT

                  * 
        362 ATAATATT
          1 ATAATAAT

                    
        370 ATAATAAT
          1 ATAATAAT

                  
        378 ATAATA
          1 ATAATA

        384 TAATAACTTA


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

Matches are distributed among these distances:
   8   20  1.00

ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40


Consensus pattern (8 bp):   
ATAATAAT

Found at i:5947 original size:2 final size:2

Alignment explanation


    Indices: 5940--5970  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       5930 TAATTCATTT

                                                          
       5940 TA TA 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 T

       5971 CAAAATACAT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.