Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011227.1 Corchorus olitorius cultivar O-4 contig11260, 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: 6049
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31


Found at i:2667 original size:26 final size:26

Alignment explanation


    Indices: 2631--2684  Score: 99
    Period size: 26  Copynumber: 2.1  Consensus size: 26

       2621 TGTGTCAAGA

                            *         
       2631 GTTCATTAGTATTTCTTTTCTAACTG
          1 GTTCATTAGTATTTCTATTCTAACTG

                                      
       2657 GTTCATTAGTATTTCTATTCTAACTG
          1 GTTCATTAGTATTTCTATTCTAACTG

              
       2683 GT
          1 GT

       2685 ATTTATCACC


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  26   27  1.00

ACGTcount: A:0.20, C:0.15, G:0.13, T:0.52


Consensus pattern (26 bp):   
GTTCATTAGTATTTCTATTCTAACTG

Found at i:5378 original size:12 final size:12

Alignment explanation


    Indices: 5318--5400  Score: 68
    Period size: 12  Copynumber: 7.2  Consensus size: 12

       5308 GTTTAGTAAA

                    *   
       5318 TATATATACAAT
          1 TATATATATAAT

              *        * 
       5330 TAAATATATATTT
          1 TATATATATA-AT

                        
       5343 TATATATATAA-
          1 TATATATATAAT

                        
       5354 TA-ATAT-T-A-
          1 TATATATATAAT

            *     *     
       5362 GATATACATAAT
          1 TATATATATAAT

                        
       5374 TATATATATAAT
          1 TATATATATAAT

            *           
       5386 AATATATATAAT
          1 TATATATATAAT

               
       5398 TAT
          1 TAT

       5401 TAAACGGTCT


Statistics
Matches: 55,  Mismatches: 11, Indels: 10
        0.72            0.14        0.13

Matches are distributed among these distances:
   8    2  0.04
   9    4  0.07
  10    5  0.09
  11    3  0.05
  12   31  0.56
  13   10  0.18

ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46


Consensus pattern (12 bp):   
TATATATATAAT
Done.