Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012333.1 Corchorus olitorius cultivar O-4 contig12366, 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: 11653
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:62 original size:2 final size:2

Alignment explanation


    Indices: 55--100  Score: 83
    Period size: 2  Copynumber: 23.0  Consensus size: 2

         45 GAAATCTTAT

                                                                      *   
         55 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                 
         97 TA TA
          1 TA TA

        101 CTAAATAGTA


Statistics
Matches: 42,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   42  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:1889 original size:36 final size:35

Alignment explanation


    Indices: 1804--1976  Score: 177
    Period size: 37  Copynumber: 4.7  Consensus size: 35

       1794 TCCTCCATAG

                                     *       *  
       1804 TTTTCAAATTGGGAAAGTTCCCACTAAGTTTTTGAA
          1 TTTTCAAATTGGGAAAGTTCCCA-TCAGTTTTTTAA

                                                 
       1840 GTTTTCAAATTGGGAAAGTTCCCATCGAGTTTTTTAA
          1 -TTTTCAAATTGGGAAAGTTCCCATC-AGTTTTTTAA

                   *        *           *      
       1877 TTTTCAAGTTGGGAAAATTCCCATCAG-GTTTTAA
          1 TTTTCAAATTGGGAAAGTTCCCATCAGTTTTTTAA

                   *               *     *         *
       1911 TTTTCAATTTAGGGAAAGTTCCCGTCATTTTTGGTTTTAG
          1 TTTTCAAATT-GGGAAAGTTCCCATCA--GTT--TTTTAA

                    *                 
       1951 TTTTCAAAGTGGGAAAGTTCCCATCA
          1 TTTTCAAATTGGGAAAGTTCCCATCA

       1977 AAAGCATTTT


Statistics
Matches: 115,  Mismatches: 14, Indels: 12
        0.82            0.10        0.09

Matches are distributed among these distances:
  34   15  0.13
  35   16  0.14
  36   24  0.21
  37   32  0.28
  39   15  0.13
  40   13  0.11

ACGTcount: A:0.27, C:0.14, G:0.18, T:0.40


Consensus pattern (35 bp):   
TTTTCAAATTGGGAAAGTTCCCATCAGTTTTTTAA
Done.