Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga10g00152.N1

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: 6807
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32


Found at i:3356 original size:3 final size:3

Alignment explanation


    Indices: 3348--3400  Score: 81
    Period size: 3  Copynumber: 17.7  Consensus size: 3

       3338 CGTTTACCCT

                                                               *        
       3348 GAA GAA GAA GAA GAA GAA GAA GATA -AA GAA GAA GAA GAT GAA GAA
          1 GAA GAA GAA GAA GAA GAA GAA GA-A GAA GAA GAA GAA GAA GAA GAA

                      
       3393 GAA GAA GA
          1 GAA GAA GA

       3401 TTATGAAGTA


Statistics
Matches: 46,  Mismatches: 2, Indels: 4
        0.88            0.04        0.08

Matches are distributed among these distances:
   2    1  0.02
   3   44  0.96
   4    1  0.02

ACGTcount: A:0.64, C:0.00, G:0.32, T:0.04


Consensus pattern (3 bp):   
GAA

Found at i:3401 original size:15 final size:15

Alignment explanation


    Indices: 3348--3415  Score: 91
    Period size: 15  Copynumber: 4.5  Consensus size: 15

       3338 CGTTTACCCT

                    *      
       3348 GAAGAAGAAGAAGAA
          1 GAAGAAGATGAAGAA

                     *     
       3363 GAAGAAGATAAAGAA
          1 GAAGAAGATGAAGAA

                           
       3378 GAAGAAGATGAAGAA
          1 GAAGAAGATGAAGAA

                     * *   
       3393 GAAGAAGATTATGAA
          1 GAAGAAGATGAAGAA

             *      
       3408 GTAGAAGA
          1 GAAGAAGA

       3416 CGATTTCAAG


Statistics
Matches: 47,  Mismatches: 6, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  15   47  1.00

ACGTcount: A:0.60, C:0.00, G:0.31, T:0.09


Consensus pattern (15 bp):   
GAAGAAGATGAAGAA

Found at i:3406 original size:18 final size:18

Alignment explanation


    Indices: 3354--3420  Score: 68
    Period size: 18  Copynumber: 3.9  Consensus size: 18

       3344 CCCTGAAGAA

                          **  
       3354 GAAGAAGAAGAAGAAGAT
          1 GAAGAAGAAGAAGATTAT

            *                 
       3372 AAAGAAGAAGAAG---AT
          1 GAAGAAGAAGAAGATTAT

                              
       3387 GAAGAAGAAGAAGATTAT
          1 GAAGAAGAAGAAGATTAT

                *      *    
       3405 GAAGTAGAAGACGATT
          1 GAAGAAGAAGAAGATT

       3421 TCAAGGTAAA


Statistics
Matches: 42,  Mismatches: 4, Indels: 6
        0.81            0.08        0.12

Matches are distributed among these distances:
  15   14  0.33
  18   28  0.67

ACGTcount: A:0.57, C:0.01, G:0.30, T:0.12


Consensus pattern (18 bp):   
GAAGAAGAAGAAGATTAT

Found at i:3509 original size:18 final size:18

Alignment explanation


    Indices: 3488--3526  Score: 69
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       3478 CAGAGAGTTA

                       *      
       3488 TACAGATGATATAGATGC
          1 TACAGATGATACAGATGC

                              
       3506 TACAGATGATACAGATGC
          1 TACAGATGATACAGATGC

               
       3524 TAC
          1 TAC

       3527 TCAAAAGAGA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  18   20  1.00

ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26


Consensus pattern (18 bp):   
TACAGATGATACAGATGC

Found at i:3512 original size:9 final size:9

Alignment explanation


    Indices: 3487--3522  Score: 54
    Period size: 9  Copynumber: 4.0  Consensus size: 9

       3477 GCAGAGAGTT

                     
       3487 ATACAGATG
          1 ATACAGATG

               *     
       3496 ATATAGATG
          1 ATACAGATG

            *        
       3505 CTACAGATG
          1 ATACAGATG

                     
       3514 ATACAGATG
          1 ATACAGATG

       3523 CTACTCAAAA


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
   9   23  1.00

ACGTcount: A:0.42, C:0.11, G:0.22, T:0.25


Consensus pattern (9 bp):   
ATACAGATG
Done.