Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g01403.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: 4015
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32


Found at i:21 original size:2 final size:2

Alignment explanation


    Indices: 16--50  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

          6 CATCTCTCGT

                                                                
         16 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T

         51 TCCCCACTCT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51


Consensus pattern (2 bp):   
TC

Found at i:414 original size:14 final size:14

Alignment explanation


    Indices: 395--442  Score: 62
    Period size: 14  Copynumber: 3.4  Consensus size: 14

        385 ACTTAGTTGG

                          
        395 TTTTTTTTT-GTTT
          1 TTTTTTTTTGGTTT

                          
        408 TTTTTTTTTGGTTT
          1 TTTTTTTTTGGTTT

               * *         
        422 TTTGTCTTTGGATTT
          1 TTTTTTTTTGG-TTT

                  
        437 TTTTTT
          1 TTTTTT

        443 CTTTTTTGGT


Statistics
Matches: 29,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
  13    9  0.31
  14   13  0.45
  15    7  0.24

ACGTcount: A:0.02, C:0.02, G:0.12, T:0.83


Consensus pattern (14 bp):   
TTTTTTTTTGGTTT

Found at i:587 original size:6 final size:6

Alignment explanation


    Indices: 552--583  Score: 55
    Period size: 6  Copynumber: 5.3  Consensus size: 6

        542 CTTTATGTTC

                                          *      
        552 CAGCAA CAGCAA CAGCAA CAGCAA CAACAA CA
          1 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CA

        584 ACAAGTTTTG


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   6   25  1.00

ACGTcount: A:0.53, C:0.34, G:0.12, T:0.00


Consensus pattern (6 bp):   
CAGCAA

Found at i:3434 original size:22 final size:22

Alignment explanation


    Indices: 3409--3454  Score: 83
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       3399 AAAATATAAA

                      *           
       3409 GGATTTATTATTAAACTCGTTC
          1 GGATTTATTACTAAACTCGTTC

                                  
       3431 GGATTTATTACTAAACTCGTTC
          1 GGATTTATTACTAAACTCGTTC

              
       3453 GG
          1 GG

       3455 GTAGATTTAT


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  22   23  1.00

ACGTcount: A:0.26, C:0.15, G:0.17, T:0.41


Consensus pattern (22 bp):   
GGATTTATTACTAAACTCGTTC
Done.