genome.fa.s12255.2.7.7.80.10.50.1000.txt.html

Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012255.1 Corchorus olitorius cultivar O-4 contig12288, whole genome shotgun sequence

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: 3067
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:931 original size:30 final size:30

Alignment explanation


    Indices: 875--1288  Score: 534
    Period size: 30  Copynumber: 13.7  Consensus size: 30

        865 GCTAATATAT

                                           
        875 ATTGACACCAGAAGTTGTCAATGGCCTTGCA
          1 ATTGACACCAGAAGTTGTC-ATGGCCTTGCA

             *                            
        906 AATGACACCAGAAGTTGTCATGGCCTTGCA
          1 ATTGACACCAGAAGTTGTCATGGCCTTGCA

                   *     **               
        936 ATTGACATCAGAACCTGTCATGGCCTTGCA
          1 ATTGACACCAGAAGTTGTCATGGCCTTGCA

             *                            
        966 AATGACACCAGAAGTTGTCATGGCCTTGCA
          1 ATTGACACCAGAAGTTGTCATGGCCTTGCA

                        *              *  
        996 ATTGACACCAGAGGTTGTCATGGCCTTACA
          1 ATTGACACCAGAAGTTGTCATGGCCTTGCA

                                   **      
       1026 ATTGACACCAGAAGTTGTCAATGATCTTGCA
          1 ATTGACACCAGAAGTTGTC-ATGGCCTTGCA

                         *            *    
       1057 ATTGACACCAGAAATTGTCAT-GCTCCTGCA
          1 ATTGACACCAGAAGTTGTCATGGC-CTTGCA

            *            *           *     
       1087 GTTGACACCAGAAATTGTCAT-GCTGTTGCA
          1 ATTGACACCAGAAGTTGTCATGGC-CTTGCA

                         *           *     
       1117 ATTGACACCAGAACTTGTCAT-GCTGTTGCA
          1 ATTGACACCAGAAGTTGTCATGGC-CTTGCA

                                     *     
       1147 ATTGACACCAGAAGTTGTCAT-GCTGTTGCA
          1 ATTGACACCAGAAGTTGTCATGGC-CTTGCA

                                           
       1177 ATTGACACCAGAAGTTGTCAT-GCTCTTGCA
          1 ATTGACACCAGAAGTTGTCATGGC-CTTGCA

                                           
       1207 ATTGACACCAGAAGTTGTCAT-GCTCTTGCA
          1 ATTGACACCAGAAGTTGTCATGGC-CTTGCA

                                  **      
       1237 ATTGACACCAGAAGTTGTCATGTTCTTGCA
          1 ATTGACACCAGAAGTTGTCATGGCCTTGCA

                *                 
       1267 ATTGTCACCAGAAGTTGTCATG
          1 ATTGACACCAGAAGTTGTCATG

       1289 ATTTTACCTT


Statistics
Matches: 350,  Mismatches: 30, Indels: 7
        0.90            0.08        0.02

Matches are distributed among these distances:
  30  306  0.87
  31   44  0.13

ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28


Consensus pattern (30 bp):   
ATTGACACCAGAAGTTGTCATGGCCTTGCA

Done.