Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_530 ID=scaffold_530-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: 6006
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32


Found at i:2262 original size:6 final size:6

Alignment explanation


    Indices: 2248--2281  Score: 50
    Period size: 6  Copynumber: 5.7  Consensus size: 6

       2238 GAGTGAACAA

                       *         *                 
       2248 AAAAAG AAAACG AAAAAG TAAAAG AAAAAG AAAA
          1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA

       2282 GAACTTAAAA


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
   6   24  1.00

ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03


Consensus pattern (6 bp):   
AAAAAG

Found at i:2275 original size:11 final size:11

Alignment explanation


    Indices: 2248--2284  Score: 56
    Period size: 12  Copynumber: 3.2  Consensus size: 11

       2238 GAGTGAACAA

                        
       2248 AAAAAGAAAACG
          1 AAAAAGAAAA-G

                        
       2260 AAAAAGTAAAAG
          1 AAAAAG-AAAAG

                       
       2272 AAAAAGAAAAG
          1 AAAAAGAAAAG

              
       2283 AA
          1 AA

       2285 CTTAAAAAAG


Statistics
Matches: 24,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
  11    7  0.29
  12   13  0.54
  13    4  0.17

ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03


Consensus pattern (11 bp):   
AAAAAGAAAAG
Done.