Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019106.1 Corchorus olitorius cultivar O-4 contig19139, 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: 20716
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--40  Score: 80
    Period size: 2  Copynumber: 20.0  Consensus size: 2

                                                                       
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

         41 AGATAAGACT


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   38  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:8582 original size:2 final size:2

Alignment explanation


    Indices: 8575--8638  Score: 64
    Period size: 2  Copynumber: 33.0  Consensus size: 2

       8565 TTTTTGAATA

                                        *                         *         
       8575 AT AT AT AT AT AT AT AT -T CCT -T AT -T AT -T AT AT CAC AT AT AT
          1 AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT -AT AT AT AT

                                               
       8615 AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT

       8639 GAATAAGATT


Statistics
Matches: 54,  Mismatches: 2, Indels: 12
        0.79            0.03        0.18

Matches are distributed among these distances:
   1    4  0.07
   2   48  0.89
   3    2  0.04

ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:18661 original size:20 final size:20

Alignment explanation


    Indices: 18636--18673  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      18626 GTGAATATAC

                                 
      18636 TGAACTTT-TGTTATTTTACT
          1 TGAACTTTAT-TTATTTTACT

                              
      18656 TGAACTTTATTTATTTTA
          1 TGAACTTTATTTATTTTA

      18674 ATTTTGTTTA


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  20   16  0.94
  21    1  0.06

ACGTcount: A:0.24, C:0.08, G:0.08, T:0.61


Consensus pattern (20 bp):   
TGAACTTTATTTATTTTACT
Done.