Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016017.1 Corchorus olitorius cultivar O-4 contig16050, 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: 6675
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34


Found at i:364 original size:22 final size:23

Alignment explanation


    Indices: 323--366  Score: 72
    Period size: 22  Copynumber: 2.0  Consensus size: 23

        313 ACATATATAA

                                   
        323 TATTTTCTATTTAAATTTTTTAT
          1 TATTTTCTATTTAAATTTTTTAT

                        *         
        346 TATTTTCTA-TTGAATTTTTTA
          1 TATTTTCTATTTAAATTTTTTA

        367 AAATATATTT


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  22   11  0.55
  23    9  0.45

ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68


Consensus pattern (23 bp):   
TATTTTCTATTTAAATTTTTTAT

Found at i:3743 original size:15 final size:16

Alignment explanation


    Indices: 3723--3774  Score: 54
    Period size: 16  Copynumber: 3.3  Consensus size: 16

       3713 TTTGGTAGAG

                            
       3723 AGGAAA-GAAATAGGA
          1 AGGAAAGGAAATAGGA

                       *  * 
       3738 AGGAAAGGAAACA-TA
          1 AGGAAAGGAAATAGGA

                            *
       3753 AGGAAAAGGAAATAGGG
          1 AGG-AAAGGAAATAGGA

                 
       3770 AGGAA
          1 AGGAA

       3775 GAGAAAGGAA


Statistics
Matches: 29,  Mismatches: 5, Indels: 5
        0.74            0.13        0.13

Matches are distributed among these distances:
  15   10  0.34
  16   16  0.55
  17    3  0.10

ACGTcount: A:0.58, C:0.02, G:0.35, T:0.06


Consensus pattern (16 bp):   
AGGAAAGGAAATAGGA

Found at i:4106 original size:16 final size:16

Alignment explanation


    Indices: 4085--4117  Score: 66
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       4075 AAATAAATGA

                            
       4085 TATCCAAATACAGTTT
          1 TATCCAAATACAGTTT

                            
       4101 TATCCAAATACAGTTT
          1 TATCCAAATACAGTTT

             
       4117 T
          1 T

       4118 TTTTCGCTAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.36, C:0.18, G:0.06, T:0.39


Consensus pattern (16 bp):   
TATCCAAATACAGTTT
Done.