Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002282.1 Corchorus olitorius cultivar O-4 contig02282, 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: 4814
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:2991 original size:39 final size:40

Alignment explanation


    Indices: 2937--3012  Score: 127
    Period size: 39  Copynumber: 1.9  Consensus size: 40

       2927 GCTGTTTTAT

                     *                              
       2937 TTTATAAGTTCTTTTAAGAAAATTCAGTTAA-AAAAGGAA
          1 TTTATAAGTGCTTTTAAGAAAATTCAGTTAAGAAAAGGAA

                                    *            
       2976 TTTATAAGTGCTTTTAAGAAAATTTAGTTAAGAAAAG
          1 TTTATAAGTGCTTTTAAGAAAATTCAGTTAAGAAAAG

       3013 AAAGTCATTA


Statistics
Matches: 34,  Mismatches: 2, Indels: 1
        0.92            0.05        0.03

Matches are distributed among these distances:
  39   29  0.85
  40    5  0.15

ACGTcount: A:0.45, C:0.04, G:0.14, T:0.37


Consensus pattern (40 bp):   
TTTATAAGTGCTTTTAAGAAAATTCAGTTAAGAAAAGGAA

Found at i:3595 original size:36 final size:36

Alignment explanation


    Indices: 3546--3618  Score: 103
    Period size: 36  Copynumber: 2.0  Consensus size: 36

       3536 CATTACCTAA

                  *             *                
       3546 ATTCTAGTACTCCATCTCTAGATAATTCAAT-AAAAT
          1 ATTCTACTACTCCATCTCTACATAATT-AATCAAAAT

                    *                           
       3582 ATTCTACTCCTCCATCTCTACATAATTAATCAAAAT
          1 ATTCTACTACTCCATCTCTACATAATTAATCAAAAT

             
       3618 A
          1 A

       3619 AAACTAGTAT


Statistics
Matches: 33,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
  35    3  0.09
  36   30  0.91

ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36


Consensus pattern (36 bp):   
ATTCTACTACTCCATCTCTACATAATTAATCAAAAT
Done.