Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_1068 ID=scaffold_1068-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, 684

Length: 1141
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26


Found at i:207 original size:13 final size:14

Alignment explanation


    Indices: 189--229  Score: 59
    Period size: 13  Copynumber: 3.1  Consensus size: 14

        179 TCCATTTCAA

                          
        189 ATACAGATA-ACAG
          1 ATACAGATATACAG

                          
        202 ATACAGATATACAG
          1 ATACAGATATACAG

                 *        
        216 AT-CAAATATACAG
          1 ATACAGATATACAG

             
        229 A
          1 A

        230 ATCTTACCCC


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  13   20  0.77
  14    6  0.23

ACGTcount: A:0.54, C:0.15, G:0.12, T:0.20


Consensus pattern (14 bp):   
ATACAGATATACAG

Found at i:901 original size:9 final size:9

Alignment explanation


    Indices: 887--917  Score: 53
    Period size: 9  Copynumber: 3.4  Consensus size: 9

        877 GTTAAACGAA

                     
        887 TCGAGTTAT
          1 TCGAGTTAT

                    *
        896 TCGAGTTAA
          1 TCGAGTTAT

                     
        905 TCGAGTTAT
          1 TCGAGTTAT

                
        914 TCGA
          1 TCGA

        918 ATCAACTCGA


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

Matches are distributed among these distances:
   9   20  1.00

ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39


Consensus pattern (9 bp):   
TCGAGTTAT
Done.