Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016073.1 Corchorus capsularis cultivar CVL-1 contig16094, 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: 9393
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.30


Found at i:2096 original size:42 final size:43

Alignment explanation


    Indices: 2027--2123  Score: 99
    Period size: 44  Copynumber: 2.3  Consensus size: 43

       2017 TATATATATT

                       *        *            **   *    
       2027 CATCATGCATTGTCCATCTCCTTGTAT-ATATGTGCATGCATC
          1 CATCATGCATTATCCATCTCATTGTATAATATGCCCATACATC

            *              *                             
       2069 GATCATGCATTATCCCT-TCATTAGTATACATATGCCCATACATC
          1 CATCATGCATTATCCATCTCATT-GTATA-ATATGCCCATACATC

                       
       2113 CATCATGCATT
          1 CATCATGCATT

       2124 CACTTGTATA


Statistics
Matches: 44,  Mismatches: 8, Indels: 4
        0.79            0.14        0.07

Matches are distributed among these distances:
  41    4  0.09
  42   18  0.41
  44   22  0.50

ACGTcount: A:0.26, C:0.27, G:0.11, T:0.36


Consensus pattern (43 bp):   
CATCATGCATTATCCATCTCATTGTATAATATGCCCATACATC

Found at i:4046 original size:21 final size:20

Alignment explanation


    Indices: 4020--4069  Score: 64
    Period size: 21  Copynumber: 2.4  Consensus size: 20

       4010 GAAGAAGAAA

                         *  *    
       4020 AAGAAGAAAGTGAGAACGAGG
          1 AAGAAGAAA-TGAAAAAGAGG

                                 
       4041 AAGAAGGAAATGAAAAAGAGG
          1 AAGAA-GAAATGAAAAAGAGG

                    
       4062 AAGAAGAA
          1 AAGAAGAA

       4070 GAATCTGATG


Statistics
Matches: 26,  Mismatches: 2, Indels: 3
        0.84            0.06        0.10

Matches are distributed among these distances:
  20    3  0.12
  21   19  0.73
  22    4  0.15

ACGTcount: A:0.60, C:0.02, G:0.34, T:0.04


Consensus pattern (20 bp):   
AAGAAGAAATGAAAAAGAGG
Done.