Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_537 ID=scaffold_537-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: 5937
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32


Found at i:5045 original size:42 final size:42

Alignment explanation


    Indices: 4986--5068  Score: 157
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       4976 GACAGATTAG

                       *                              
       4986 CAGGGTTGTATGTTTCAGAAATTGTCAAATTACATGGAGTGA
          1 CAGGGTTGTATATTTCAGAAATTGTCAAATTACATGGAGTGA

                                                     
       5028 CAGGGTTGTATATTTCAGAAATTGTCAAATTACATGGAGTG
          1 CAGGGTTGTATATTTCAGAAATTGTCAAATTACATGGAGTG

       5069 CCAGTCTCCA


Statistics
Matches: 40,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  42   40  1.00

ACGTcount: A:0.31, C:0.10, G:0.25, T:0.34


Consensus pattern (42 bp):   
CAGGGTTGTATATTTCAGAAATTGTCAAATTACATGGAGTGA

Found at i:5084 original size:42 final size:41

Alignment explanation


    Indices: 4998--5085  Score: 115
    Period size: 42  Copynumber: 2.1  Consensus size: 41

       4988 GGGTTGTATG

                                                 **   
       4998 TTTCAGAAATTGTCAAATTACATGGAGTGACAGGGTTGTATA
          1 TTTCAGAAATTGTCAAATTACATGGAGTGACA-GGTTCCATA

                                         *             
       5040 TTTCAGAAATTGTCAAATTACATGGAGTGCCA-GTCTCCATTA
          1 TTTCAGAAATTGTCAAATTACATGGAGTGACAGGT-TCCA-TA

                
       5082 TTTC
          1 TTTC

       5086 GGATAGAGCT


Statistics
Matches: 41,  Mismatches: 3, Indels: 4
        0.85            0.06        0.08

Matches are distributed among these distances:
  40    2  0.05
  41    2  0.05
  42   37  0.90

ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35


Consensus pattern (41 bp):   
TTTCAGAAATTGTCAAATTACATGGAGTGACAGGTTCCATA

Found at i:5226 original size:2 final size:2

Alignment explanation


    Indices: 5219--5244  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       5209 GTATAATTTG

                                                  
       5219 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

       5245 GAATGTGGCC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Done.