Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016977.1 Corchorus olitorius cultivar O-4 contig17010, 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: 2056
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37


Found at i:200 original size:50 final size:50

Alignment explanation


    Indices: 52--203  Score: 232
    Period size: 50  Copynumber: 3.0  Consensus size: 50

         42 CTTCAATGTC

                                       *              *     *   
         52 CTTTGAAAAGCTGAAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTA
          1 CTTTGAAAAGC-G-AATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA

                       *                                      
        104 CTTTGAAAAGCAAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
          1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA

                    *                      *                  
        154 CTTTGAAAGGCGAATTTTGATCTTGAACTCATAAATGGAAAGCAATTTTA
          1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA

        204 TTGTAAAACT


Statistics
Matches: 93,  Mismatches: 7, Indels: 2
        0.91            0.07        0.02

Matches are distributed among these distances:
  50   82  0.88
  52   11  0.12

ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33


Consensus pattern (50 bp):   
CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA

Found at i:813 original size:5 final size:5

Alignment explanation


    Indices: 797--839  Score: 70
    Period size: 5  Copynumber: 8.6  Consensus size: 5

        787 TCAATTCTCT

                                                                
        797 TTTGA TTTTGA TTTGA TTTGA TTTGA TTTGA TTTGA -TTGA TTT
          1 TTTGA -TTTGA TTTGA TTTGA TTTGA TTTGA TTTGA TTTGA TTT

        840 TTTTTATGTT


Statistics
Matches: 36,  Mismatches: 0, Indels: 3
        0.92            0.00        0.08

Matches are distributed among these distances:
   4    4  0.11
   5   27  0.75
   6    5  0.14

ACGTcount: A:0.19, C:0.00, G:0.19, T:0.63


Consensus pattern (5 bp):   
TTTGA

Done.