Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_500 ID=scaffold_500-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: 6390
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.31


Found at i:5412 original size:43 final size:42

Alignment explanation


    Indices: 5348--5494  Score: 113
    Period size: 42  Copynumber: 3.4  Consensus size: 42

       5338 AGCCAACGTC

                   *        *                         
       5348 CCAGACGTGTCTTACAAGTAATCAAATATCGATGCCACTGTT
          1 CCAGACGGGTCTTACACGTAATCAAATATCGATGCCACTGTT

                                     *       *    *    
       5390 CCAGACAGGGTCTTACACGTAATCATATAT-GACGCCAATG-T
          1 CCAGAC-GGGTCTTACACGTAATCAAATATCGATGCCACTGTT

                *   *   *              *                  *
       5431 CTCAAACATGGTATTACACGTAAATCTCAA-ATCGATGCCAAC-GTC
          1 C-CAGAC-GGGTCTTACACGT-AATC-AAATATCGATGCC-ACTGTT

                               
       5476 CCAGACGTGGTCTTACACG
          1 CCAGACG-GGTCTTACACG

       5495 ATAACACATT


Statistics
Matches: 81,  Mismatches: 16, Indels: 14
        0.73            0.14        0.13

Matches are distributed among these distances:
  41    2  0.02
  42   30  0.37
  43   26  0.32
  44   21  0.26
  45    2  0.02

ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25


Consensus pattern (42 bp):   
CCAGACGGGTCTTACACGTAATCAAATATCGATGCCACTGTT
Done.