Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006824.1 Corchorus olitorius cultivar O-4 contig06849, 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, 751

Length: 1252
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36


Found at i:897 original size:109 final size:112

Alignment explanation


    Indices: 773--983  Score: 383
    Period size: 112  Copynumber: 1.9  Consensus size: 112

        763 TTATATTTCA

                                                                             
        773 TTTAGATCAATTAATTATGTTTCCTTTAATCT-CT-T-AATATCTAAAATAACCTAATCTTTAAA
          1 TTTAGATCAATTAATTATGTTTCCTTTAATCTGCTATAAATATCTAAAATAACCTAATCTTTAAA

                  *                                        
        835 AATTAAGATAAAGTCCAATCTTTTCTATCCTCTCTAAAATAATTATG
         66 AATTAAAATAAAGTCCAATCTTTTCTATCCTCTCTAAAATAATTATG

                                             *                               
        882 TTTAGATCAATTAATTATGTTTCCTTTAATCTGTTATAAATATCTAAAATAACCTAATCTTTAAA
          1 TTTAGATCAATTAATTATGTTTCCTTTAATCTGCTATAAATATCTAAAATAACCTAATCTTTAAA

                                                 
        947 AATTAAAATAAAGTCCAATCTTTTCTATCCTCTCTAA
         66 AATTAAAATAAAGTCCAATCTTTTCTATCCTCTCTAA

        984 TTAAATCTAA


Statistics
Matches: 97,  Mismatches: 2, Indels: 3
        0.95            0.02        0.03

Matches are distributed among these distances:
 109   32  0.33
 110    1  0.01
 111    1  0.01
 112   63  0.65

ACGTcount: A:0.38, C:0.16, G:0.04, T:0.42


Consensus pattern (112 bp):   
TTTAGATCAATTAATTATGTTTCCTTTAATCTGCTATAAATATCTAAAATAACCTAATCTTTAAA
AATTAAAATAAAGTCCAATCTTTTCTATCCTCTCTAAAATAATTATG

Found at i:953 original size:24 final size:28

Alignment explanation


    Indices: 908--957  Score: 72
    Period size: 24  Copynumber: 1.9  Consensus size: 28

        898 ATGTTTCCTT

                                        
        908 TAATCTGTTATAAATATCTAAAATAACC
          1 TAATCTGTTATAAATATCTAAAATAACC

                                      
        936 TAATCT-TTA-AAA-AT-TAAAATAA
          1 TAATCTGTTATAAATATCTAAAATAA

        958 AGTCCAATCT


Statistics
Matches: 22,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
  24    8  0.36
  25    2  0.09
  26    3  0.14
  27    3  0.14
  28    6  0.27

ACGTcount: A:0.52, C:0.10, G:0.02, T:0.36


Consensus pattern (28 bp):   
TAATCTGTTATAAATATCTAAAATAACC

Done.