Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga04g00650.F1

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, 440

Length: 734
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.31


Found at i:76 original size:17 final size:17

Alignment explanation


    Indices: 54--87  Score: 52
    Period size: 17  Copynumber: 2.0  Consensus size: 17

         44 AACGCAATAC

                              
         54 AAAGAAGAAAAAA-AAAA
          1 AAAGAA-AAAAAAGAAAA

                             
         71 AAAGAAAAAAAAGAAAA
          1 AAAGAAAAAAAAGAAAA

         88 GGGAAATGGA


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  16    6  0.38
  17   10  0.62

ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00


Consensus pattern (17 bp):   
AAAGAAAAAAAAGAAAA

Found at i:77 original size:14 final size:14

Alignment explanation


    Indices: 58--88  Score: 53
    Period size: 14  Copynumber: 2.2  Consensus size: 14

         48 CAATACAAAG

                          
         58 AAGAAAAAAAAAAA
          1 AAGAAAAAAAAAAA

                       *  
         72 AAGAAAAAAAAGAA
          1 AAGAAAAAAAAAAA

               
         86 AAG
          1 AAG

         89 GGAAATGGAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00


Consensus pattern (14 bp):   
AAGAAAAAAAAAAA

Found at i:78 original size:9 final size:9

Alignment explanation


    Indices: 54--87  Score: 52
    Period size: 9  Copynumber: 3.9  Consensus size: 9

         44 AACGCAATAC

                  *  
         54 AAAGAAGAA
          1 AAAGAAAAA

                     
         63 AAA-AAAAA
          1 AAAGAAAAA

                     
         71 AAAGAAAAA
          1 AAAGAAAAA

                    
         80 AAAGAAAA
          1 AAAGAAAA

         88 GGGAAATGGA


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
   8    7  0.30
   9   16  0.70

ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00


Consensus pattern (9 bp):   
AAAGAAAAA
Done.