Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006044.1 Corchorus olitorius cultivar O-4 contig06069, 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: 1946
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.35


Found at i:106 original size:17 final size:18

Alignment explanation


    Indices: 69--106  Score: 60
    Period size: 18  Copynumber: 2.2  Consensus size: 18

         59 ATCTTAAAAG

                              
         69 AAACAAGTTCATAATTCA
          1 AAACAAGTTCATAATTCA

                            * 
         87 AAACAAGTTC-TAATTTA
          1 AAACAAGTTCATAATTCA

               
        104 AAA
          1 AAA

        107 GTATACCAAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  17    9  0.47
  18   10  0.53

ACGTcount: A:0.53, C:0.13, G:0.05, T:0.29


Consensus pattern (18 bp):   
AAACAAGTTCATAATTCA

Found at i:296 original size:18 final size:18

Alignment explanation


    Indices: 273--307  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

        263 TGAAGCTTAG

                       *      
        273 AGAGAGAGAGACAAATGT
          1 AGAGAGAGAGAAAAATGT

                             
        291 AGAGAGAGAGAAAAATG
          1 AGAGAGAGAGAAAAATG

        308 GAGTAGAAGT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.54, C:0.03, G:0.34, T:0.09


Consensus pattern (18 bp):   
AGAGAGAGAGAAAAATGT
Done.