Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga04g00001.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: 4183
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29


Found at i:2448 original size:20 final size:20

Alignment explanation


    Indices: 2410--2452  Score: 59
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       2400 TAAATTCTAA

                       * **     
       2410 AAAGATAAATACATTTAATT
          1 AAAGATAAATAAAGATAATT

                                
       2430 AAAGATAAATAAAGATAATT
          1 AAAGATAAATAAAGATAATT

               
       2450 AAA
          1 AAA

       2453 ATGAAATCCT


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28


Consensus pattern (20 bp):   
AAAGATAAATAAAGATAATT

Found at i:2501 original size:15 final size:15

Alignment explanation


    Indices: 2481--2510  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       2471 ATAATCCTAA

                    *      
       2481 TAATTATCTTAATAT
          1 TAATTATCCTAATAT

                           
       2496 TAATTATCCTAATAT
          1 TAATTATCCTAATAT

       2511 AAATAAAATG


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50


Consensus pattern (15 bp):   
TAATTATCCTAATAT

Found at i:3569 original size:9 final size:9

Alignment explanation


    Indices: 3555--3591  Score: 56
    Period size: 9  Copynumber: 4.1  Consensus size: 9

       3545 CGTATATGAC

                    *
       3555 GGCGCGTGA
          1 GGCGCGTGT

                     
       3564 GGCGCGTGT
          1 GGCGCGTGT

                *    
       3573 GGCGTGTGT
          1 GGCGCGTGT

                     
       3582 GGCGCGTGT
          1 GGCGCGTGT

             
       3591 G
          1 G

       3592 CAGGTACTGC


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
   9   25  1.00

ACGTcount: A:0.03, C:0.19, G:0.57, T:0.22


Consensus pattern (9 bp):   
GGCGCGTGT
Done.