Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_416 ID=scaffold_416-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: 7435
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.30

Warning! 156 characters in sequence are not A, C, G, or T


Found at i:1727 original size:21 final size:21

Alignment explanation


    Indices: 1686--1727  Score: 66
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1676 CTTTGTTCAA

                          * *    
       1686 AGACTTTGTAAAGGTGTATTC
          1 AGACTTTGTAAAGGGGAATTC

                                 
       1707 AGACTTTGTAAAGGGGAATTC
          1 AGACTTTGTAAAGGGGAATTC

       1728 TTACCTGTTT


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.31, C:0.10, G:0.26, T:0.33


Consensus pattern (21 bp):   
AGACTTTGTAAAGGGGAATTC

Found at i:2026 original size:12 final size:12

Alignment explanation


    Indices: 2009--2041  Score: 50
    Period size: 12  Copynumber: 2.8  Consensus size: 12

       1999 CGTGAAGTAC

                        
       2009 AACAAAAATTGA
          1 AACAAAAATTGA

                     *  
       2021 AACAAAAATCGA
          1 AACAAAAATTGA

                      
       2033 AA-AAAAATT
          1 AACAAAAATT

       2042 CAAGTTGTAT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  11    6  0.32
  12   13  0.68

ACGTcount: A:0.70, C:0.09, G:0.06, T:0.15


Consensus pattern (12 bp):   
AACAAAAATTGA
Done.