Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga13g02332.M1

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: 2551
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.32


Found at i:35 original size:9 final size:9

Alignment explanation


    Indices: 12--58  Score: 71
    Period size: 9  Copynumber: 5.4  Consensus size: 9

          2 TCCTTGGTAG

                     
         12 AGAAG-AAA
          1 AGAAGAAAA

                     
         20 A-AAGAAAA
          1 AGAAGAAAA

                     
         28 AGAAGAAAA
          1 AGAAGAAAA

                     
         37 AGAAGAAAA
          1 AGAAGAAAA

                  *  
         46 AGAAGAGAA
          1 AGAAGAAAA

                
         55 AGAA
          1 AGAA

         59 CAAAGGAGAA


Statistics
Matches: 36,  Mismatches: 1, Indels: 3
        0.90            0.03        0.08

Matches are distributed among these distances:
   7    3  0.08
   8    5  0.14
   9   28  0.78

ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00


Consensus pattern (9 bp):   
AGAAGAAAA

Found at i:88 original size:21 final size:19

Alignment explanation


    Indices: 28--78  Score: 59
    Period size: 18  Copynumber: 2.7  Consensus size: 19

         18 AAAAAGAAAA

                  *      *    *
         28 AGAAGAAAAAGAAGAAA-A
          1 AGAAGAGAAAGAACAAAGG

                               
         46 AGAAGAGAAAGAACAAAGG
          1 AGAAGAGAAAGAACAAAGG

                          
         65 AGAAGGAGAAAGAA
          1 AGAA-GAGAAAGAA

         79 AAGTAGGAGA


Statistics
Matches: 28,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  18   15  0.54
  19    4  0.14
  20    9  0.32

ACGTcount: A:0.69, C:0.02, G:0.29, T:0.00


Consensus pattern (19 bp):   
AGAAGAGAAAGAACAAAGG

Found at i:2157 original size:7 final size:8

Alignment explanation


    Indices: 2130--2163  Score: 50
    Period size: 8  Copynumber: 4.0  Consensus size: 8

       2120 ATTTAAAGTA

                    
       2130 TTTTATTT
          1 TTTTATTT

                      
       2138 TTTTATTGCT
          1 TTTTATT--T

                    
       2148 TTTTATTT
          1 TTTTATTT

                    
       2156 TTTTATTT
          1 TTTTATTT

       2164 AAGAGTGAGA


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

Matches are distributed among these distances:
   8   16  0.67
  10    8  0.33

ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82


Consensus pattern (8 bp):   
TTTTATTT
Done.