Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012105.1 Corchorus olitorius cultivar O-4 contig12138, 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: 3929
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29


Found at i:2250 original size:51 final size:51

Alignment explanation


    Indices: 2192--2571  Score: 658
    Period size: 51  Copynumber: 7.5  Consensus size: 51

       2182 GGTTTTCTCG

                            *               *        *         
       2192 AGATTGAATTGGAAGATAGTTCAAAGGATAAGAGGAAGACGATCCTTTTTA
          1 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTA

                               *                               
       2243 AGATTGAATTGGAAGACAGCTCAAAGGATAAGCGGAAGACGGTCC-TTTTA
          1 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTA

                            *                                  
       2293 AGATTGAATTGGAAGATAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTA
          1 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTA

                *                         *                    
       2344 AGATAGAATTGGAAGACAGTTCAAAGGATATGCGGAAGACGGTCC-TTTTA
          1 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTA

                                                    *          
       2394 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACAGTCCTTTTTA
          1 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTA

                                                     *         
       2445 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGATCC-TTTTA
          1 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTA

                                                               
       2495 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTA
          1 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTA

                                      
       2546 AGATTGAATTGGAAGACAGTTCAAAG
          1 AGATTGAATTGGAAGACAGTTCAAAG

       2572 AAGTTGATCG


Statistics
Matches: 311,  Mismatches: 15, Indels: 6
        0.94            0.05        0.02

Matches are distributed among these distances:
  50  144  0.46
  51  167  0.54

ACGTcount: A:0.37, C:0.11, G:0.27, T:0.25


Consensus pattern (51 bp):   
AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTA

Found at i:2303 original size:101 final size:101

Alignment explanation


    Indices: 2192--2571  Score: 663
    Period size: 101  Copynumber: 3.8  Consensus size: 101

       2182 GGTTTTCTCG

                            *               *                                
       2192 AGATTGAATTGGAAGATAGTTCAAAGGATAAGAGGAAGACGATCCTTTTTAAGATTGAATTGGAA
          1 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTTTAAGATTGAATTGGAA

                 *                              
       2257 GACAGCTCAAAGGATAAGCGGAAGACGGTCCTTTTA
         66 GACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA

                            *                        *             *         
       2293 AGATTGAATTGGAAGATAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTAAGATAGAATTGGAA
          1 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTTTAAGATTGAATTGGAA

                            *                   
       2358 GACAGTTCAAAGGATATGCGGAAGACGGTCCTTTTA
         66 GACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA

                                                                             
       2394 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGAC-AGTCCTTTTTAAGATTGAATTGGA
          1 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGA-TCCTTTTTAAGATTGAATTGGA

                                        *        
       2458 AGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTTA
         65 AGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA

                                                     *                       
       2495 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTTAAGATTGAATTGGAA
          1 AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTTTAAGATTGAATTGGAA

                        
       2560 GACAGTTCAAAG
         66 GACAGTTCAAAG

       2572 AAGTTGATCG


Statistics
Matches: 266,  Mismatches: 11, Indels: 4
        0.95            0.04        0.01

Matches are distributed among these distances:
 101  266  1.00

ACGTcount: A:0.37, C:0.11, G:0.27, T:0.25


Consensus pattern (101 bp):   
AGATTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTTTAAGATTGAATTGGAA
GACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTA

Done.