Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_399 ID=scaffold_399-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: 7493
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34


Found at i:5431 original size:20 final size:21

Alignment explanation


    Indices: 5408--5451  Score: 63
    Period size: 20  Copynumber: 2.1  Consensus size: 21

       5398 TATATGTATT

                                 
       5408 ATATATATTATAA-AATATAA
          1 ATATATATTATAATAATATAA

                * *              
       5428 ATATTTTTTATAATAATATAA
          1 ATATATATTATAATAATATAA

               
       5449 ATA
          1 ATA

       5452 AAGTCAATTT


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  20   11  0.52
  21   10  0.48

ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45


Consensus pattern (21 bp):   
ATATATATTATAATAATATAA

Found at i:5906 original size:13 final size:14

Alignment explanation


    Indices: 5882--5914  Score: 50
    Period size: 13  Copynumber: 2.4  Consensus size: 14

       5872 CTCTCTCAAC

                          
       5882 AAAAATTACAAAAA
          1 AAAAATTACAAAAA

                         *
       5896 AAAAATT-CAAAAT
          1 AAAAATTACAAAAA

                  
       5909 AAAAAT
          1 AAAAAT

       5915 ATTTATAAAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  13   11  0.61
  14    7  0.39

ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18


Consensus pattern (14 bp):   
AAAAATTACAAAAA
Done.