Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000794.1 Corchorus olitorius cultivar O-4 contig00794, 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, 625

Length: 1043
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.42


Found at i:706 original size:126 final size:123

Alignment explanation


    Indices: 526--775  Score: 326
    Period size: 126  Copynumber: 2.0  Consensus size: 123

        516 CATTATTTAA

                   *       *                          *              *     * 
        526 ACTTTTATAGTTTTATTCAACTAAAAACTCTAATTTTATTTATTTAAATCTAATATCTTTA-AGA
          1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATACA

                            *                                               
        590 T-TTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATATATTAGAATTTTTTAAATAT
         66 TATTTTA--ATTTTACCATTTTAATTAAAAAAC---T-TATATATATTAGAATTTTTTAAATAT

                                            *                               *
        653 ACTTTTACAGTTTTACTCAACT-AAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
          1 ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATACA

                   *             *  *                                 
        717 TATTTTATTTTTACCATTTTATTTTAAAAACTTATATATATTAGAATTTTTTAAATAT
         66 TATTTTAATTTTACCATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT

             
        775 A
          1 A

        776 TTTCTTAAAT


Statistics
Matches: 110,  Mismatches: 11, Indels: 9
        0.85            0.08        0.07

Matches are distributed among these distances:
 122   27  0.25
 123    1  0.01
 126   55  0.50
 127   22  0.20
 128    5  0.05

ACGTcount: A:0.37, C:0.10, G:0.02, T:0.50


Consensus pattern (123 bp):   
ACTTTTACAGTTTTACTCAACTAAAAACTCTAATTTTATTTAATTAAATCTAATATCCTTATACA
TATTTTAATTTTACCATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT

Found at i:737 original size:14 final size:15

Alignment explanation


    Indices: 713--741  Score: 51
    Period size: 14  Copynumber: 2.0  Consensus size: 15

        703 AATATCCTTA

                           
        713 TACCTATTTTATTTT
          1 TACCTATTTTATTTT

                           
        728 TACC-ATTTTATTTT
          1 TACCTATTTTATTTT

        742 AAAAACTTAT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14   10  0.71
  15    4  0.29

ACGTcount: A:0.21, C:0.14, G:0.00, T:0.66


Consensus pattern (15 bp):   
TACCTATTTTATTTT

Found at i:797 original size:14 final size:13

Alignment explanation


    Indices: 761--799  Score: 51
    Period size: 14  Copynumber: 2.9  Consensus size: 13

        751 TATATATTAG

                         
        761 AATTTTTTAAATA
          1 AATTTTTTAAATA

            *    *        
        774 TATTTCTTAAATGA
          1 AATTTTTTAAAT-A

                        
        788 AATTTTTTAAAT
          1 AATTTTTTAAAT

        800 TTTACAATTT


Statistics
Matches: 21,  Mismatches: 4, Indels: 1
        0.81            0.15        0.04

Matches are distributed among these distances:
  13   10  0.48
  14   11  0.52

ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54


Consensus pattern (13 bp):   
AATTTTTTAAATA
Done.