Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_20038

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: 2592
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23


Found at i:952 original size:54 final size:53

Alignment explanation


    Indices: 889--1000  Score: 162
    Period size: 48  Copynumber: 2.2  Consensus size: 53

        879 TTACTCCAGG

                                             *                  * 
        889 CGTAGATCTCAGTCTCGTTCTCCTTATCGGCGCGGGTCACCTACACCTGTGCGC
          1 CGTAGATCTCA-TCTCGTTCTCCTTATCGGCGCAGGTCACCTACACCTGTGCAC

                                                                 
        943 CGTAG-----ATCTCGTTCTCCTTATCGGCGCAGGTCACCTACACCTGTGCAC
          1 CGTAGATCTCATCTCGTTCTCCTTATCGGCGCAGGTCACCTACACCTGTGCAC

                      
        991 CGTAGATCTC
          1 CGTAGATCTC

       1001 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:956 original size:48 final size:48

Alignment explanation


    Indices: 901--1004  Score: 190
    Period size: 48  Copynumber: 2.2  Consensus size: 48

        891 TAGATCTCAG

                                 *                  *       
        901 TCTCGTTCTCCTTATCGGCGCGGGTCACCTACACCTGTGCGCCGTAGA
          1 TCTCGTTCTCCTTATCGGCGCAGGTCACCTACACCTGTGCACCGTAGA

                                                            
        949 TCTCGTTCTCCTTATCGGCGCAGGTCACCTACACCTGTGCACCGTAGA
          1 TCTCGTTCTCCTTATCGGCGCAGGTCACCTACACCTGTGCACCGTAGA

                    
        997 TCTCGTTC
          1 TCTCGTTC

       1005 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:2341 original size:21 final size:21

Alignment explanation


    Indices: 2317--2360  Score: 54
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       2307 GAAAGAAGCT

                                  
       2317 AAGAGGAGGAA-AAAGGAAGAA
          1 AAGA-GAGGAAGAAAGGAAGAA

                  **             
       2338 AAGAGATTAAGAAAGGAAGAA
          1 AAGAGAGGAAGAAAGGAAGAA

              
       2359 AA
          1 AA

       2361 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.