Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011839.1 Corchorus olitorius cultivar O-4 contig11872, 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: 9218
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32


Found at i:739 original size:22 final size:22

Alignment explanation


    Indices: 690--740  Score: 59
    Period size: 22  Copynumber: 2.3  Consensus size: 22

        680 AAATATTACC

                         *   **   
        690 ATAATTATTTTTGGCAGCCATA
          1 ATAATTATTTTTGCCAGAAATA

                                   
        712 ATAATTATTTTTGCCAAGAAATA
          1 ATAATTATTTTTGCC-AGAAATA

                   
        735 A-AATTA
          1 ATAATTA

        741 GAGAATAATT


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  22   19  0.76
  23    6  0.24

ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39


Consensus pattern (22 bp):   
ATAATTATTTTTGCCAGAAATA

Found at i:6095 original size:16 final size:15

Alignment explanation


    Indices: 6057--6098  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       6047 ACAGAGATTG

                   *       
       6057 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
       6072 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       6087 ACTAGAAAACAA
          1 AC-AGAAAACAA

       6099 AGCAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:6870 original size:11 final size:11

Alignment explanation


    Indices: 6854--6879  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

       6844 CCTTTGCCTA

                       
       6854 AAAACTAGAAG
          1 AAAACTAGAAG

                       
       6865 AAAACTAGAAG
          1 AAAACTAGAAG

                
       6876 AAAA
          1 AAAA

       6880 GAAATTATCT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08


Consensus pattern (11 bp):   
AAAACTAGAAG
Done.