Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023719.1 Corchorus olitorius cultivar O-4 contig23752, 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: 5340
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34


Found at i:3921 original size:29 final size:29

Alignment explanation


    Indices: 3880--3999  Score: 163
    Period size: 29  Copynumber: 4.1  Consensus size: 29

       3870 GAATAAAACC

                                          
       3880 AAAATGACCAAAATGCCCCT-AGATGTGCA
          1 AAAATGACCAAAATGCCCCTGA-ATGTGCA

                    *                     
       3909 AAAATGACTAAAATGCCCCT-AGATGTGCA
          1 AAAATGACCAAAATGCCCCTGA-ATGTGCA

                   *   *            *    
       3938 AAAATGATCAAGATGCCCCTGAATATGCA
          1 AAAATGACCAAAATGCCCCTGAATGTGCA

                      *                  
       3967 AAAATGACCATAATGCCCCTGAATGTGCA
          1 AAAATGACCAAAATGCCCCTGAATGTGCA

                
       3996 AAAA
          1 AAAA

       4000 GGTCAATTAA


Statistics
Matches: 81,  Mismatches: 9, Indels: 2
        0.88            0.10        0.02

Matches are distributed among these distances:
  29   80  0.99
  30    1  0.01

ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19


Consensus pattern (29 bp):   
AAAATGACCAAAATGCCCCTGAATGTGCA

Found at i:5152 original size:18 final size:17

Alignment explanation


    Indices: 5129--5164  Score: 54
    Period size: 18  Copynumber: 2.1  Consensus size: 17

       5119 CTCCTCTCGC

                     *        
       5129 ATGAAAACATTTCTTTTT
          1 ATGAAAACAATT-TTTTT

                             
       5147 ATGAAAACAATTTTTTT
          1 ATGAAAACAATTTTTTT

             
       5164 A
          1 A

       5165 ACAATTTTTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  17    6  0.35
  18   11  0.65

ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47


Consensus pattern (17 bp):   
ATGAAAACAATTTTTTT
Done.