Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga13g02525.F7

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: 3188
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26


Found at i:1411 original size:54 final size:53

Alignment explanation


    Indices: 1348--1459  Score: 162
    Period size: 48  Copynumber: 2.2  Consensus size: 53

       1338 TTACTCCAGG

                                             *                  * 
       1348 CGTAGATCTCAGTCTCGTTCTCCTTATCGGCGCGGGTCACCTACACCTGTGCGC
          1 CGTAGATCTCA-TCTCGTTCTCCTTATCGGCGCAGGTCACCTACACCTGTGCAC

                                                                 
       1402 CGTAG-----ATCTCGTTCTCCTTATCGGCGCAGGTCACCTACACCTGTGCAC
          1 CGTAGATCTCATCTCGTTCTCCTTATCGGCGCAGGTCACCTACACCTGTGCAC

                      
       1450 CGTAGATCTC
          1 CGTAGATCTC

       1460 GTTCACCCAT


Statistics
Matches: 51,  Mismatches: 2, Indels: 11
        0.80            0.03        0.17

Matches are distributed among these distances:
  48   45  0.88
  49    1  0.02
  54    5  0.10

ACGTcount: A:0.15, C:0.35, G:0.22, T:0.28


Consensus pattern (53 bp):   
CGTAGATCTCATCTCGTTCTCCTTATCGGCGCAGGTCACCTACACCTGTGCAC

Found at i:1415 original size:48 final size:48

Alignment explanation


    Indices: 1360--1463  Score: 190
    Period size: 48  Copynumber: 2.2  Consensus size: 48

       1350 TAGATCTCAG

                                 *                  *       
       1360 TCTCGTTCTCCTTATCGGCGCGGGTCACCTACACCTGTGCGCCGTAGA
          1 TCTCGTTCTCCTTATCGGCGCAGGTCACCTACACCTGTGCACCGTAGA

                                                            
       1408 TCTCGTTCTCCTTATCGGCGCAGGTCACCTACACCTGTGCACCGTAGA
          1 TCTCGTTCTCCTTATCGGCGCAGGTCACCTACACCTGTGCACCGTAGA

                    
       1456 TCTCGTTC
          1 TCTCGTTC

       1464 ACCCATCCGA


Statistics
Matches: 54,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  48   54  1.00

ACGTcount: A:0.13, C:0.36, G:0.22, T:0.29


Consensus pattern (48 bp):   
TCTCGTTCTCCTTATCGGCGCAGGTCACCTACACCTGTGCACCGTAGA

Found at i:2800 original size:21 final size:21

Alignment explanation


    Indices: 2776--2819  Score: 54
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       2766 GAAAGAAGCT

                                  
       2776 AAGAGGAGGAA-AAAGGAAGAA
          1 AAGA-GAGGAAGAAAGGAAGAA

                  **             
       2797 AAGAGATTAAGAAAGGAAGAA
          1 AAGAGAGGAAGAAAGGAAGAA

              
       2818 AA
          1 AA

       2820 ACGTAAACGT


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  20    4  0.20
  21   16  0.80

ACGTcount: A:0.64, C:0.00, G:0.32, T:0.05


Consensus pattern (21 bp):   
AAGAGAGGAAGAAAGGAAGAA
Done.