Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_802 ID=scaffold_802-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: 4585
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.22

Warning! 990 characters in sequence are not A, C, G, or T


Found at i:2657 original size:19 final size:19

Alignment explanation


    Indices: 2629--2673  Score: 63
    Period size: 19  Copynumber: 2.3  Consensus size: 19

       2619 GCGAAAATAC

                            *   
       2629 AAAAGAAAAGAAAAATGAAA
          1 AAAAG-AAAGAAAAATCAAA

                         *     
       2649 AAAAGAAAGAAAATTCAAA
          1 AAAAGAAAGAAAAATCAAA

                  
       2668 AAAAGA
          1 AAAAGA

       2674 GAATGAAAAG


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  19   18  0.78
  20    5  0.22

ACGTcount: A:0.78, C:0.02, G:0.13, T:0.07


Consensus pattern (19 bp):   
AAAAGAAAGAAAAATCAAA

Found at i:2687 original size:15 final size:15

Alignment explanation


    Indices: 2649--2714  Score: 50
    Period size: 15  Copynumber: 4.5  Consensus size: 15

       2639 AAAAATGAAA

                      *    *
       2649 AAAAGAAAGAAAATTC
          1 AAAAGAAAGAGAA-TG

                           
       2665 AAAA-AAAGAGAATG
          1 AAAAGAAAGAGAATG

                      *    
       2679 AAAAGAAAG-CAA-G
          1 AAAAGAAAGAGAATG

                    *      
       2692 AAAAGAAAAAG-ATG
          1 AAAAGAAAGAGAATG

                     
       2706 AAAAAGAAA
          1 -AAAAGAAA

       2715 CATTGAGTGA


Statistics
Matches: 41,  Mismatches: 5, Indels: 9
        0.75            0.09        0.16

Matches are distributed among these distances:
  13   10  0.24
  14    8  0.20
  15   19  0.46
  16    4  0.10

ACGTcount: A:0.73, C:0.03, G:0.18, T:0.06


Consensus pattern (15 bp):   
AAAAGAAAGAGAATG
Done.