Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008331.1 Corchorus capsularis cultivar CVL-1 contig08352, 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: 10026
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.31


Found at i:3471 original size:20 final size:20

Alignment explanation


    Indices: 3432--3471  Score: 55
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       3422 CATCATTCGA

                      *         
       3432 ATTACATCATTCAAATTTTG
          1 ATTACATCATCCAAATTTTG

                                 
       3452 ATTACATCA-CCAAATATTTG
          1 ATTACATCATCCAAAT-TTTG

       3472 CCTGTTCAAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  19    5  0.28
  20   13  0.72

ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40


Consensus pattern (20 bp):   
ATTACATCATCCAAATTTTG

Found at i:7192 original size:49 final size:50

Alignment explanation


    Indices: 7068--7338  Score: 200
    Period size: 49  Copynumber: 5.5  Consensus size: 50

       7058 ACTTGTCTTT

                   *            **    *   *       *    *      
       7068 CGTCCGGAAAGGGCATTTT-AAGAAAAAGCGAGTAAAACTAA-CGCCTTC
          1 CGTCCGGGAAGGGCATTTTGGGGAAATAGCAAGTAAAAATAAGTGCCTTC

             *           **     * *   *             *         
       7116 CATCCGGGAAGGGTGTTTT-AGAAAAAAGCAAGTAAAAATTAGTGCCTTC
          1 CGTCCGGGAAGGGCATTTTGGGGAAATAGCAAGTAAAAATAAGTGCCTTC

                           *             * *        *   * *    
       7165 CGTCCGGGAAGGGCACTTTGGGGAAA-AGTAGGTAAAAAAAAAGCGTCTTC
          1 CGTCCGGGAAGGGCATTTTGGGGAAATAGCAAGT-AAAAATAAGTGCCTTC

             *                 *  *                           
       7215 CCTCCGGGAAGGGCATTTTTGGAAAATAGCAAGT-AAAATAAGTGCCTTC
          1 CGTCCGGGAAGGGCATTTTGGGGAAATAGCAAGTAAAAATAAGTGCCTTC

                       *                            **          
       7264 CGTCCGGGAAGAGCATTTT-GGGAAATAGC-AGATGAAAACCAA-TGCCTTC
          1 CGTCCGGGAAGGGCATTTTGGGGAAATAGCAAG-T-AAAAATAAGTGCCTTC

              *         *              
       7313 CGCCCGGGAAGGCCATTTT-GGGAAAT
          1 CGTCCGGGAAGGGCATTTTGGGGAAAT

       7339 GTAAAATTTG


Statistics
Matches: 177,  Mismatches: 39, Indels: 13
        0.77            0.17        0.06

Matches are distributed among these distances:
  47    2  0.01
  48   42  0.24
  49   85  0.48
  50   43  0.24
  51    5  0.03

ACGTcount: A:0.34, C:0.18, G:0.27, T:0.21


Consensus pattern (50 bp):   
CGTCCGGGAAGGGCATTTTGGGGAAATAGCAAGTAAAAATAAGTGCCTTC
Done.