Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004305.1 Corchorus capsularis cultivar CVL-1 contig04313, 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, 709

Length: 1183
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.29


Found at i:860 original size:11 final size:11

Alignment explanation


    Indices: 844--884  Score: 50
    Period size: 11  Copynumber: 3.7  Consensus size: 11

        834 ATGTCTTATA

                       
        844 TATATTAAGAT
          1 TATATTAAGAT

                       
        855 TATATTAA-A-
          1 TATATTAAGAT

                         
        864 TATATATATAGAT
          1 TATAT-TA-AGAT

                    
        877 TATATTAA
          1 TATATTAA

        885 AAATGAAAAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 8
        0.76            0.00        0.24

Matches are distributed among these distances:
   9    5  0.19
  10    3  0.12
  11   10  0.38
  12    3  0.12
  13    5  0.19

ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46


Consensus pattern (11 bp):   
TATATTAAGAT

Found at i:888 original size:24 final size:24

Alignment explanation


    Indices: 840--885  Score: 78
    Period size: 22  Copynumber: 2.0  Consensus size: 24

        830 GAGGATGTCT

                                    
        840 TATATATATTAAGATTATATTAAA
          1 TATATATATTAAGATTATATTAAA

                                    
        864 TATATATA-T-AGATTATATTAAA
          1 TATATATATTAAGATTATATTAAA

        886 AATGAAAAAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  22   13  0.59
  23    1  0.05
  24    8  0.36

ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46


Consensus pattern (24 bp):   
TATATATATTAAGATTATATTAAA

Found at i:898 original size:22 final size:22

Alignment explanation


    Indices: 850--898  Score: 55
    Period size: 22  Copynumber: 2.2  Consensus size: 22

        840 TATATATATT

                          *     * 
        850 AAGATTATATTAAATATATATA
          1 AAGATTATATTAAAAATATAAA

            *                      
        872 TAGATTATATTAAAAATGA-AAA
          1 AAGATTATATTAAAAAT-ATAAA

                 
        894 AAGAT
          1 AAGAT

        899 GGACAATCAA


Statistics
Matches: 22,  Mismatches: 4, Indels: 2
        0.79            0.14        0.07

Matches are distributed among these distances:
  22   21  0.95
  23    1  0.05

ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35


Consensus pattern (22 bp):   
AAGATTATATTAAAAATATAAA
Done.