Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002442.1 Corchorus olitorius cultivar O-4 contig02442, 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: 2879
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33


Found at i:2806 original size:19 final size:18

Alignment explanation


    Indices: 2782--2869  Score: 91
    Period size: 19  Copynumber: 5.1  Consensus size: 18

       2772 TTGCCACGTC

                               
       2782 ATATTTTTTTATTAAAAAA
          1 ATATTTTTTT-TTAAAAAA

                              
       2801 ATA--TTTTTTTAAAAAA
          1 ATATTTTTTTTTAAAAAA

                    *         
       2817 A-A----TATTTAAAAAA
          1 ATATTTTTTTTTAAAAAA

                               
       2830 ATATATTTTTTTTAAAAAA
          1 ATAT-TTTTTTTTAAAAAA

                               
       2849 ATATATTTTTTTTAAAAAA
          1 ATAT-TTTTTTTTAAAAAA

              
       2868 AT
          1 AT

       2870 GAGTTAAGGA


Statistics
Matches: 61,  Mismatches: 2, Indels: 12
        0.81            0.03        0.16

Matches are distributed among these distances:
  13   11  0.18
  14    1  0.02
  15    1  0.02
  16    9  0.15
  17    5  0.08
  19   34  0.56

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (18 bp):   
ATATTTTTTTTTAAAAAA

Found at i:2824 original size:13 final size:14

Alignment explanation


    Indices: 2793--2837  Score: 56
    Period size: 13  Copynumber: 3.1  Consensus size: 14

       2783 TATTTTTTTA

                          * 
       2793 TTAAAAAAATATTTTT
          1 TTAAAAAAATA--TAT

                          
       2809 TTAAAAAAA-ATAT
          1 TTAAAAAAATATAT

                          
       2822 TTAAAAAAATATAT
          1 TTAAAAAAATATAT

              
       2836 TT
          1 TT

       2838 TTTTTAAAAA


Statistics
Matches: 27,  Mismatches: 1, Indels: 4
        0.84            0.03        0.12

Matches are distributed among these distances:
  13   11  0.41
  14    6  0.22
  15    1  0.04
  16    9  0.33

ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42


Consensus pattern (14 bp):   
TTAAAAAAATATAT

Found at i:2836 original size:31 final size:30

Alignment explanation


    Indices: 2795--2852  Score: 98
    Period size: 31  Copynumber: 1.9  Consensus size: 30

       2785 TTTTTTTATT

                                          
       2795 AAAAAAATATTTTTTTAAAAAAAATATTTA
          1 AAAAAAATATTTTTTTAAAAAAAATATTTA

                             *          
       2825 AAAAAATATATTTTTTTTAAAAAAATAT
          1 AAAAAA-ATATTTTTTTAAAAAAAATAT

       2853 ATTTTTTTTA


Statistics
Matches: 26,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  30    6  0.23
  31   20  0.77

ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41


Consensus pattern (30 bp):   
AAAAAAATATTTTTTTAAAAAAAATATTTA
Done.