Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024008.1 Corchorus olitorius cultivar O-4 contig24041, 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: 3579
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:347 original size:29 final size:28

Alignment explanation


    Indices: 314--391  Score: 111
    Period size: 29  Copynumber: 2.8  Consensus size: 28

        304 ATGTGAACTT

                                     *  
        314 AAAAATGACCAAAATGCCCCTGAATGTG
          1 AAAAATGACCAAAATGCCCCTGAATATG

                        * *    *         
        342 CAAAAATGACCATATTGCCACTGAATATG
          1 -AAAAATGACCAAAATGCCCCTGAATATG

                                 
        371 AAAAATGACCAAAATGCCCCT
          1 AAAAATGACCAAAATGCCCCT

        392 TGGACGTGTA


Statistics
Matches: 42,  Mismatches: 7, Indels: 1
        0.84            0.14        0.02

Matches are distributed among these distances:
  28   18  0.43
  29   24  0.57

ACGTcount: A:0.44, C:0.23, G:0.14, T:0.19


Consensus pattern (28 bp):   
AAAAATGACCAAAATGCCCCTGAATATG

Found at i:3224 original size:16 final size:15

Alignment explanation


    Indices: 3186--3227  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       3176 ACAGAGATTG

                   *       
       3186 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
       3201 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       3216 ACTAGAAAACAA
          1 AC-AGAAAACAA

       3228 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
Done.