Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020380.1 Corchorus olitorius cultivar O-4 contig20413, 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: 25166
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--198  Score: 396
    Period size: 2  Copynumber: 99.0  Consensus size: 2

                                                                          
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

                                                                          
         43 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

                                                                          
         85 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

                                                                          
        127 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

                                                        
        169 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

        199 CTTTGTAATG


Statistics
Matches: 196,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2  196  1.00

ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50


Consensus pattern (2 bp):   
TC

Found at i:3256 original size:23 final size:23

Alignment explanation


    Indices: 3212--3256  Score: 54
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       3202 CTTTTAAAAA

                            **     
       3212 TTATATTTTTAATTATTTAATTT
          1 TTATATTTTTAATTATGAAATTT

                *      *          
       3235 TTATTTTTTTAGTTATGAAATT
          1 TTATATTTTTAATTATGAAATT

       3257 CCAAATGACG


Statistics
Matches: 18,  Mismatches: 4, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  23   18  1.00

ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67


Consensus pattern (23 bp):   
TTATATTTTTAATTATGAAATTT

Found at i:8758 original size:17 final size:17

Alignment explanation


    Indices: 8719--8761  Score: 50
    Period size: 17  Copynumber: 2.5  Consensus size: 17

       8709 GGACTAATAA

                       *    *
       8719 TAATGTTTTATTACCAT
          1 TAATGTTTTATGACCAG

             *            *  
       8736 TCATGTTTTATGACTAG
          1 TAATGTTTTATGACCAG

                     
       8753 TAATGTTTT
          1 TAATGTTTT

       8762 CCTCTTCAAA


Statistics
Matches: 21,  Mismatches: 5, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  17   21  1.00

ACGTcount: A:0.26, C:0.09, G:0.12, T:0.53


Consensus pattern (17 bp):   
TAATGTTTTATGACCAG
Done.