Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000682.1 Corchorus olitorius cultivar O-4 contig00682, 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: 2020
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36


Found at i:297 original size:50 final size:50

Alignment explanation


    Indices: 243--385  Score: 196
    Period size: 51  Copynumber: 2.8  Consensus size: 50

        233 CTTAAATGCC

                                     *        *     *         
        243 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAACTGGAATGCAATCTTA
          1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA

                              *           **               *   
        293 CTTTGAAAAGCGAATTTTAATCTTTGAACTTTCAAATGGAAAGCAATTTTA
          1 CTTTGAAAAGCGAATTTTGATC-TTGAACTCACAAATGGAAAGCAATCTTA

            *                              *          
        344 TTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAG
          1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAG

        386 AAATTTTGTT


Statistics
Matches: 80,  Mismatches: 12, Indels: 2
        0.85            0.13        0.02

Matches are distributed among these distances:
  50   38  0.47
  51   42  0.52

ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34


Consensus pattern (50 bp):   
CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA

Found at i:391 original size:50 final size:50

Alignment explanation


    Indices: 243--392  Score: 194
    Period size: 50  Copynumber: 3.0  Consensus size: 50

        233 CTTAAATGCC

                                     *     *  *     *     *   
        243 CTTTGAAAAGCGAATTTTGATCTTGGACTCACAACTGGAATGCAATCTTA
          1 CTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTA

                              *            *                    
        293 CTTTGAAAAGCGAATTTTAATCTTTGAACT-TTCAAATGGAAAGCAATTTTA
          1 CTTTGAAAAGCGAATTTTGATC-TTGAACTCAT-AAATGGAAAGCAATTTTA

            *                                         *      
        344 TTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGAAATTTT
          1 CTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTT

        393 GTTATAAAAC


Statistics
Matches: 86,  Mismatches: 11, Indels: 6
        0.83            0.11        0.06

Matches are distributed among these distances:
  50   44  0.51
  51   42  0.49

ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35


Consensus pattern (50 bp):   
CTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTA
Done.