Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006077.1 Corchorus olitorius cultivar O-4 contig06102, 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: 1897
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28


Found at i:1785 original size:41 final size:41

Alignment explanation


    Indices: 1740--1897  Score: 219
    Period size: 41  Copynumber: 3.9  Consensus size: 41

       1730 TTTCCGTGTT

                  *                 *                
       1740 CAATTTGGCCCCTAATTTAGGATTTTATTTACTATTTGATA
          1 CAATTTAGCCCCTAATTTAGGATTCTATTTACTATTTGATA

                    *        *                       
       1781 CAATTTAGTCCCTAATTAAGGATTCTATTTACTATTTGATA
          1 CAATTTAGCCCCTAATTTAGGATTCTATTTACTATTTGATA

                  *                    *   *         
       1822 CAATTTGGCCCCTAATTTAGGATTCTACTTAATATTTGATA
          1 CAATTTAGCCCCTAATTTAGGATTCTATTTACTATTTGATA

                    *    *                      
       1863 CAATTTAGTCCCTGATTTAGGATTCT-TATTACTAT
          1 CAATTTAGCCCCTAATTTAGGATTCTAT-TTACTAT


Statistics
Matches: 102,  Mismatches: 14, Indels: 2
        0.86            0.12        0.02

Matches are distributed among these distances:
  41  102  1.00

ACGTcount: A:0.28, C:0.16, G:0.11, T:0.44


Consensus pattern (41 bp):   
CAATTTAGCCCCTAATTTAGGATTCTATTTACTATTTGATA

Found at i:1885 original size:82 final size:82

Alignment explanation


    Indices: 1740--1897  Score: 255
    Period size: 82  Copynumber: 1.9  Consensus size: 82

       1730 TTTCCGTGTT

                                    *  *   *                                 
       1740 CAATTTGGCCCCTAATTTAGGATTTTATTTACTATTTGATACAATTTAGTCCCTAATTAAGGATT
          1 CAATTTGGCCCCTAATTTAGGATTCTACTTAATATTTGATACAATTTAGTCCCTAATTAAGGATT

                              
       1805 C-TATTTACTATTTGATA
         66 CTTA-TTACTATTTGATA

                                                                  *   *      
       1822 CAATTTGGCCCCTAATTTAGGATTCTACTTAATATTTGATACAATTTAGTCCCTGATTTAGGATT
          1 CAATTTGGCCCCTAATTTAGGATTCTACTTAATATTTGATACAATTTAGTCCCTAATTAAGGATT

                       
       1887 CTTATTACTAT
         66 CTTATTACTAT


Statistics
Matches: 70,  Mismatches: 5, Indels: 2
        0.91            0.06        0.03

Matches are distributed among these distances:
  82   68  0.97
  83    2  0.03

ACGTcount: A:0.28, C:0.16, G:0.11, T:0.44


Consensus pattern (82 bp):   
CAATTTGGCCCCTAATTTAGGATTCTACTTAATATTTGATACAATTTAGTCCCTAATTAAGGATT
CTTATTACTATTTGATA
Done.