Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000674.1 Corchorus olitorius cultivar O-4 contig00674, 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, 921

Length: 1536
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37


Found at i:291 original size:50 final size:50

Alignment explanation


    Indices: 231--480  Score: 412
    Period size: 50  Copynumber: 5.0  Consensus size: 50

        221 CTTCAATGTC

                                 *         *        *         
        231 CTTTGAAAAGCGAATTTTGATTTTGAACTCACAAATGGAATGCAATTTTA
          1 CTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTA

                       *     *             *                  
        281 CTTTGAAAAGCAAATTTAGATCTTGAACTCACAAATGGAAAGCAATTTTA
          1 CTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTA

                                                              
        331 CTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTA
          1 CTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTA

                         *                                    
        381 CTTTGAAAAGCGACTTTTGATCTTGAACTCATAAATGGAAAGCAATTTTA
          1 CTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTA

            *                                                  
        431 TTTTGAAAAGC-AACTTTTGATCTTGAACTCATAAATGGAAAGCAATTTTA
          1 CTTTGAAAAGCGAA-TTTTGATCTTGAACTCATAAATGGAAAGCAATTTTA

        481 TTGTAAAACT


Statistics
Matches: 189,  Mismatches: 10, Indels: 2
        0.94            0.05        0.01

Matches are distributed among these distances:
  49    1  0.01
  50  188  0.99

ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34


Consensus pattern (50 bp):   
CTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTA

Found at i:1138 original size:20 final size:20

Alignment explanation


    Indices: 1115--1152  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       1105 TCTGATTTGA

                 *              
       1115 TTTTTGATTTTTGAATTTTT
          1 TTTTTCATTTTTGAATTTTT

                  *           
       1135 TTTTTCTTTTTTGAATTT
          1 TTTTTCATTTTTGAATTT

       1153 CTTGATGGAG


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.13, C:0.03, G:0.08, T:0.76


Consensus pattern (20 bp):   
TTTTTCATTTTTGAATTTTT
Done.