Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001262.1 Corchorus capsularis cultivar CVL-1 contig01262, 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, 733

Length: 1223
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33


Found at i:156 original size:69 final size:69

Alignment explanation


    Indices: 1--354  Score: 487
    Period size: 68  Copynumber: 5.1  Consensus size: 69

                                    *              *   **             *      
          1 GTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAACATTTAGGGGCTTTTCCAGAAGCCA
          1 GTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA-GCAGGGGCTTTTCCACAAGCCA

                 
         66 AACTC
         65 AACTC

                                                         **                  
         71 GTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCAACGGCTTTTCCACAAGCCAA
          1 GTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTTCCACAAGCCAA

                
        136 ACTC
         66 ACTC

                                    *                     *               *  
        140 GTTTCCATACGAGTCAGTTCAA-CGTTGGTTCCATCCAAGCAGCAGCGGCTTTTCCACAAGCTAA
          1 GTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTTCCACAAGCCAA

                
        204 ACTC
         66 ACTC

                                    *                  **               *    
        208 GTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATTTAGGGGCTTTTCCACAGGCCA
          1 GTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA-GCAGGGGCTTTTCCACAAGCCA

                 
        273 AACTC
         65 AACTC

                   *        *   *                        *            *    * 
        278 GTTTCCACACGAGTCAATT-TAGCCTTGGTTCCATCCAAGCAGCAAGGGCTTTTCCACTAGCCGA
          1 GTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTTCCACAAGCCAA

                
        342 ACTC
         66 ACTC

            *        
        346 TTTTCCATA
          1 GTTTCCATA

        355 TAAGTTGAGC


Statistics
Matches: 254,  Mismatches: 28, Indels: 6
        0.88            0.10        0.02

Matches are distributed among these distances:
  68   93  0.37
  69   82  0.32
  70   79  0.31

ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28


Consensus pattern (69 bp):   
GTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCAGGGGCTTTTCCACAAGCCAA
ACTC

Found at i:308 original size:138 final size:136

Alignment explanation


    Indices: 1--354  Score: 467
    Period size: 138  Copynumber: 2.6  Consensus size: 136

                                    *              *   **             *      
          1 GTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAACATTTAGGGGCTTTTCCAGAAGCCA
          1 GTTTCCATACGAGTCAGTT-AAGCCTTGGTTCCATCCAAGCA-GCA-GGGCTTTTCCACAAGCCA

                                                                             
         66 AACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCAACGGCTTTTCCACAA
         63 AACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCAACGGCTTTTCCACAA

                     
        131 GCCAAACTC
        128 GCCAAACTC

                                    *                                     *  
        140 GTTTCCATACGAGTCAGTTCAA-CGTTGGTTCCATCCAAGCAGCAGCGGCTTTTCCACAAGCTAA
          1 GTTTCCATACGAGTCAGTT-AAGCCTTGGTTCCATCCAAGCAGCAG-GGCTTTTCCACAAGCCAA

                                        *                  ** **            *
        204 ACTCGTTTCCATACGAGTCAGTTCAAGCTTTGGTTCCATCCAAGCATTTAGGGGCTTTTCCACAG
         64 ACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCA-GCAACGGCTTTTCCACAA

                     
        269 GCCAAACTC
        128 GCCAAACTC

                   *        *  *                                     *    *  
        278 GTTTCCACACGAGTCAATTTAGCCTTGGTTCCATCCAAGCAGCAAGGGCTTTTCCACTAGCCGAA
          1 GTTTCCATACGAGTCAGTTAAGCCTTGGTTCCATCCAAGCAGC-AGGGCTTTTCCACAAGCCAAA

               *        
        343 CTCTTTTCCATA
         65 CTCGTTTCCATA

        355 TAAGTTGAGC


Statistics
Matches: 191,  Mismatches: 20, Indels: 9
        0.87            0.09        0.04

Matches are distributed among these distances:
 136    1  0.01
 137   63  0.33
 138  103  0.54
 139   24  0.13

ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28


Consensus pattern (136 bp):   
GTTTCCATACGAGTCAGTTAAGCCTTGGTTCCATCCAAGCAGCAGGGCTTTTCCACAAGCCAAAC
TCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAGCAACGGCTTTTCCACAAGCC
AAACTC
Done.