Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1995

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: 2928
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.31


Found at i:2341 original size:12 final size:11

Alignment explanation


    Indices: 2322--2388  Score: 61
    Period size: 12  Copynumber: 6.2  Consensus size: 11

       2312 AGAGAAAGAA

                       
       2322 GAGATAGGAGG
          1 GAGATAGGAGG

                        
       2333 GATGATAGGAGG
          1 GA-GATAGGAGG

                        
       2345 AGAGATAGGA--
          1 -GAGATAGGAGG

                   *   
       2355 GAGATAGTA--
          1 GAGATAGGAGG

                     * 
       2364 GAGATAGGAAG
          1 GAGATAGGAGG

                        
       2375 GATGATAGGAGG
          1 GA-GATAGGAGG

              
       2387 GA
          1 GA

       2389 AATAAGAGAG


Statistics
Matches: 48,  Mismatches: 3, Indels: 9
        0.80            0.05        0.15

Matches are distributed among these distances:
   9   16  0.33
  11    4  0.08
  12   26  0.54
  13    2  0.04

ACGTcount: A:0.40, C:0.00, G:0.46, T:0.13


Consensus pattern (11 bp):   
GAGATAGGAGG

Found at i:2356 original size:9 final size:9

Alignment explanation


    Indices: 2342--2372  Score: 53
    Period size: 9  Copynumber: 3.4  Consensus size: 9

       2332 GGATGATAGG

                     
       2342 AGGAGAGAT
          1 AGGAGAGAT

                     
       2351 AGGAGAGAT
          1 AGGAGAGAT

              *      
       2360 AGTAGAGAT
          1 AGGAGAGAT

                
       2369 AGGA
          1 AGGA

       2373 AGGATGATAG


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:0.45, C:0.00, G:0.42, T:0.13


Consensus pattern (9 bp):   
AGGAGAGAT
Done.