Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021918.1 Corchorus olitorius cultivar O-4 contig21951, 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: 13683
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:914 original size:50 final size:48

Alignment explanation


    Indices: 813--955  Score: 164
    Period size: 49  Copynumber: 3.0  Consensus size: 48

        803 CAAGCAATCA

                *      *                     **          *  
        813 TTTACTTTTCACTGCACTTTTTATCAATTTTTACTACAAAATTGAACT
          1 TTTAATTTTCATTGCACTTTTTATCAATTTTTAAGACAAAATTGATCT

                     *              *                          
        861 TTT-ATTTTTACTTGCATCTTTTTCTCAATTTTTAAAGACAAAATTGATCT
          1 TTTAATTTTCA-TTGCA-CTTTTTATCAATTTTT-AAGACAAAATTGATCT

                        *                    *            
        911 TTTAATTTTCATCGCACTTTTTATCAATTTTT-TGACAAAATTGAT
          1 TTTAATTTTCATTGCACTTTTTATCAATTTTTAAGACAAAATTGAT

        956 TGGCACGCTC


Statistics
Matches: 80,  Mismatches: 11, Indels: 9
        0.80            0.11        0.09

Matches are distributed among these distances:
  47   17  0.21
  48    7  0.09
  49   30  0.38
  50   20  0.25
  51    6  0.08

ACGTcount: A:0.29, C:0.15, G:0.06, T:0.50


Consensus pattern (48 bp):   
TTTAATTTTCATTGCACTTTTTATCAATTTTTAAGACAAAATTGATCT

Found at i:5703 original size:36 final size:37

Alignment explanation


    Indices: 5656--5730  Score: 134
    Period size: 36  Copynumber: 2.1  Consensus size: 37

       5646 CAGAGATGCC

                                                 
       5656 TGACTCTTGTTTCACCCTTTGTTTCAA-TTTTTTAAT
          1 TGACTCTTGTTTCACCCTTTGTTTCAATTTTTTTAAT

                         *                       
       5692 TGACTCTTGTTTCTCCCTTTGTTTCAATTTTTTTAAT
          1 TGACTCTTGTTTCACCCTTTGTTTCAATTTTTTTAAT

              
       5729 TG
          1 TG

       5731 TCATTAGATC


Statistics
Matches: 37,  Mismatches: 1, Indels: 1
        0.95            0.03        0.03

Matches are distributed among these distances:
  36   26  0.70
  37   11  0.30

ACGTcount: A:0.15, C:0.19, G:0.09, T:0.57


Consensus pattern (37 bp):   
TGACTCTTGTTTCACCCTTTGTTTCAATTTTTTTAAT
Done.