Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002667.1 Corchorus olitorius cultivar O-4 contig02669, 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, 662

Length: 1104
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.29


Found at i:143 original size:18 final size:18

Alignment explanation


    Indices: 120--172  Score: 106
    Period size: 18  Copynumber: 2.9  Consensus size: 18

        110 CCTGGGTCGC

                              
        120 TATCGGTACCAAGAGGAA
          1 TATCGGTACCAAGAGGAA

                              
        138 TATCGGTACCAAGAGGAA
          1 TATCGGTACCAAGAGGAA

                             
        156 TATCGGTACCAAGAGGA
          1 TATCGGTACCAAGAGGA

        173 GTAAAAGTAT


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   35  1.00

ACGTcount: A:0.38, C:0.17, G:0.28, T:0.17


Consensus pattern (18 bp):   
TATCGGTACCAAGAGGAA

Found at i:441 original size:24 final size:24

Alignment explanation


    Indices: 413--508  Score: 183
    Period size: 24  Copynumber: 4.0  Consensus size: 24

        403 AAATTACTTC

                           *        
        413 TTTTCAATTTTAATGAAAATGAAA
          1 TTTTCAATTTTAATGGAAATGAAA

                                    
        437 TTTTCAATTTTAATGGAAATGAAA
          1 TTTTCAATTTTAATGGAAATGAAA

                                    
        461 TTTTCAATTTTAATGGAAATGAAA
          1 TTTTCAATTTTAATGGAAATGAAA

                                    
        485 TTTTCAATTTTAATGGAAATGAAA
          1 TTTTCAATTTTAATGGAAATGAAA

        509 AAATTATAAA


Statistics
Matches: 71,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  24   71  1.00

ACGTcount: A:0.43, C:0.04, G:0.11, T:0.42


Consensus pattern (24 bp):   
TTTTCAATTTTAATGGAAATGAAA

Found at i:532 original size:23 final size:24

Alignment explanation


    Indices: 504--548  Score: 65
    Period size: 23  Copynumber: 1.9  Consensus size: 24

        494 TTAATGGAAA

                                    
        504 TGAAAAAATTA-TAAAAATATTAT
          1 TGAAAAAATTATTAAAAATATTAT

                  *      *        
        527 TGAAAATATTATTGAAAATATT
          1 TGAAAAAATTATTAAAAATATT

        549 GAAAATAAAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  23   10  0.53
  24    9  0.47

ACGTcount: A:0.56, C:0.00, G:0.07, T:0.38


Consensus pattern (24 bp):   
TGAAAAAATTATTAAAAATATTAT

Found at i:534 original size:12 final size:12

Alignment explanation


    Indices: 504--548  Score: 65
    Period size: 12  Copynumber: 3.8  Consensus size: 12

        494 TTAATGGAAA

                  *     
        504 TGAAAAAATTA-
          1 TGAAAATATTAT

             *          
        515 TAAAAATATTAT
          1 TGAAAATATTAT

                        
        527 TGAAAATATTAT
          1 TGAAAATATTAT

                      
        539 TGAAAATATT
          1 TGAAAATATT

        549 GAAAATAAAA


Statistics
Matches: 30,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  11    9  0.30
  12   21  0.70

ACGTcount: A:0.56, C:0.00, G:0.07, T:0.38


Consensus pattern (12 bp):   
TGAAAATATTAT
Done.