Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005994.1 Corchorus olitorius cultivar O-4 contig06019, 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, 610

Length: 1017
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41


Found at i:292 original size:127 final size:130

Alignment explanation


    Indices: 90--349  Score: 391
    Period size: 127  Copynumber: 2.0  Consensus size: 130

         80 GCCATTAGAC

                                                                             
         90 TTTTATAGTTTTACTCAACTAAAAACTCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
          1 TTTTATAGTTTTACTCAACTAAAAACTCTATCTTTATTTAATTAAATATAATATCCTCATAACTA

                          *    *  *                            *    *        
        155 TTTAATTTTTACCATTTTACTATTTTAATT-AAAAACTT-ATATATTAGAATTTTTTAAATATAT
         66 TTTAATTTTTACCAATTTAATAATTTAATTAAAAAACTTAATATATTAGAAATTTTAAAATATAT

                                           *               *         *   *   
        218 TTTTATAGTTTTACTCAACTAAAAACTCT-TTTTTATTTAATTAAATCTAATATCCTTATACCTA
          1 TTTTATAGTTTTACTCAACTAAAAACTCTATCTTTATTTAATTAAATATAATATCCTCATAACTA

               *       *                                                     
        282 TTTTATTTTTATCAATTTAATAATTTAATTAAAAAACTTAGATATATTAGAAATTTTAAAATATA
         66 TTTAATTTTTACCAATTTAATAATTTAATTAAAAAACTTA-ATATATTAGAAATTTTAAAATATA

             
        347 T
        130 T

              
        348 TT
          1 TT

        350 CTTAAATGAC


Statistics
Matches: 118,  Mismatches: 11, Indels: 4
        0.89            0.08        0.03

Matches are distributed among these distances:
 127   56  0.47
 128   37  0.31
 130   25  0.21

ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49


Consensus pattern (130 bp):   
TTTTATAGTTTTACTCAACTAAAAACTCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
TTTAATTTTTACCAATTTAATAATTTAATTAAAAAACTTAATATATTAGAAATTTTAAAATATAT

Found at i:544 original size:30 final size:30

Alignment explanation


    Indices: 508--581  Score: 148
    Period size: 30  Copynumber: 2.5  Consensus size: 30

        498 TTTTTCAATC

                                          
        508 ATAATATAAACTAATTTGAACAAAAAGATT
          1 ATAATATAAACTAATTTGAACAAAAAGATT

                                          
        538 ATAATATAAACTAATTTGAACAAAAAGATT
          1 ATAATATAAACTAATTTGAACAAAAAGATT

                          
        568 ATAATATAAACTAA
          1 ATAATATAAACTAA

        582 CAAAAATCTT


Statistics
Matches: 44,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  30   44  1.00

ACGTcount: A:0.58, C:0.07, G:0.05, T:0.30


Consensus pattern (30 bp):   
ATAATATAAACTAATTTGAACAAAAAGATT

Done.