Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012823.1 Corchorus olitorius cultivar O-4 contig12856, 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: 18455
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30


Found at i:678 original size:30 final size:30

Alignment explanation


    Indices: 644--869  Score: 341
    Period size: 30  Copynumber: 7.6  Consensus size: 30

        634 TACATACAAA

                                *    *    
        644 TGACACCAGAAGTTGTCATGGTCTTACAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                                *    *   *
        674 TGACACCAGAAGTTGTCATGGTCTTACAAA
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                               *          
        704 TGACACCAGAAGTTGTCATAATCTTGCAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                                *         
        734 TGACACCAGAAGTTGTCATGCTCTTGCAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                                  *       
        764 TGACACCAGAAGTTGTCATGATTTTGCAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                                  *       
        794 TGACACCAGAAGTTGTCATGATGTTGCAAT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                                  *       
        824 TGACACCAGAAGTTGTCATGATGTT---AT
          1 TGACACCAGAAGTTGTCATGATCTTGCAAT

                               
        851 TGACACCAGAAGTTGTCAT
          1 TGACACCAGAAGTTGTCAT

        870 ACCAAATTAT


Statistics
Matches: 186,  Mismatches: 10, Indels: 3
        0.93            0.05        0.02

Matches are distributed among these distances:
  27   21  0.11
  30  165  0.89

ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30


Consensus pattern (30 bp):   
TGACACCAGAAGTTGTCATGATCTTGCAAT

Found at i:930 original size:62 final size:62

Alignment explanation


    Indices: 823--1055  Score: 391
    Period size: 62  Copynumber: 3.8  Consensus size: 62

        813 GATGTTGCAA

                                   **                        *            
        823 TTGACACCAGAAGTTGTCATG-ATGTTATTGACACCAGAAGTTGTCATACCAAATTATTATC
          1 TTGACACCAGAAGTTGTCATGAAAATTATTGACACCAGAAGTTGTCATATCAAATTATTATC

                                                                          
        884 TTGACACCAGAAGTTGTCATGAAAATTATTGACACCAGAAGTTGTCATATCAAATTATTATC
          1 TTGACACCAGAAGTTGTCATGAAAATTATTGACACCAGAAGTTGTCATATCAAATTATTATC

                                                                          
        946 TTGACACCAGAAGTTGTCATGAAAATTATTGACACCAGAAGTTGTCATATCAAATTATTA--
          1 TTGACACCAGAAGTTGTCATGAAAATTATTGACACCAGAAGTTGTCATATCAAATTATTATC

                                *                             
       1006 TTGACACCAGAAGTTGTCATAAAAATTATCTTGACACCAGAAGTTGTCAT
          1 TTGACACCAGAAGTTGTCATGAAAATTA--TTGACACCAGAAGTTGTCAT

       1056 GCTGAGGAAA


Statistics
Matches: 165,  Mismatches: 4, Indels: 5
        0.95            0.02        0.03

Matches are distributed among these distances:
  60   27  0.16
  61   21  0.13
  62  117  0.71

ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32


Consensus pattern (62 bp):   
TTGACACCAGAAGTTGTCATGAAAATTATTGACACCAGAAGTTGTCATATCAAATTATTATC

Done.