Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011187.1 Corchorus olitorius cultivar O-4 contig11220, 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: 1674
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27


Found at i:457 original size:153 final size:154

Alignment explanation


    Indices: 1--885  Score: 1174
    Period size: 153  Copynumber: 5.7  Consensus size: 154

                                                             * *             
          1 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACGAAAAGAAAAGCATT
          1 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT

                                 *              *          *  *     *      * 
         66 GAGGTTTGCCAAATCGAAGACAATTCAAAACAG-AATTAATGGTG-CTCGTTAGGCACAAAATTA
         66 GAGGTTTGCCAAATCGAAGACGATTCAAAAC-GTAACTAATGG-GCCCCGATAGGCCCAAAATAA

                                   *  
        129 CAAGTGTTCCAAATGAGCTAAAAGCT
        129 CAAGTGTTCCAAATGAGCTAAAAACT

              *   **                                                     *   
        155 TCTCAGAAGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGAATT
          1 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT

                       *  * *   *  *      *  *   *              *            
        220 GAGGTTTGCCAGATTGTAGATGACTCAAAATGTCACTGATGGGCCCCGATAGACCCAAAATAACA
         66 GAGGTTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGATAGGCCCAAAATAACA

                          *         
        285 AGTGTTCCAAATGAACTAAAAACT
        131 AGTGTTCCAAATGAGCTAAAAACT

                              *                    *                     * * 
        309 TCACAGTGGACTAATCTCCCCAAAATGATTATAGTTAGGGCATAAACAATGGAAAG-AAAGAAAT
          1 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT

                *                            *  *                            
        373 GAGGATTGCCAAATCGAAGACGATTCAAAACGTCACCAATGGGCCCCGATAGGCCCAAAATAACA
         66 GAGGTTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGATAGGCCCAAAATAACA

                        *            
        438 AGTGTTCCAAATTAGCT-AAAACTT
        131 AGTGTTCCAAATGAGCTAAAAAC-T

                 *         *                             *             *    *
        462 TCACATTGGACTAATATCACC-AAATGATTATAGTTAGGCCATAACCAATGGAAAGAAAGGCATC
          1 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT

                          *                   *        *    *                
        526 GAAGG-TTGCCAAAACGAAGACGATTCAAAACGTCACTAATGGTCCCCTATAGGCCCAAAATAAC
         66 G-AGGTTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGATAGGCCCAAAATAAC

               *                     
        590 AAGCGTTCCAAATGAGCTAAAAACT
        130 AAGTGTTCCAAATGAGCTAAAAACT

                       *                                          *          
        615 TCACAGTGGACAAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAATG-AAAGCATT
          1 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT

                                 *                        *                  
        679 GAGGTTTGCCAAATCGAAGACAATTCAAAACAG-AACTAATGGGCCTCGATAGGCCCAAAAAAAT
         66 GAGGTTTGCCAAATCGAAGACGATTCAAAAC-GTAACTAATGGGCCCCGATAGGCCC---AAAAT

                                        
        743 AACAAGTGTTCCAAATGAGCTAAAAACT
        127 AACAAGTGTTCCAAATGAGCTAAAAACT

                                *    *                                       
        771 TCACAGTGGACTAATCTCACAAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT
          1 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT

             *                  *    *      *         *       
        836 GGGGTTTGCCAAATCGAAGATGATTTAAAACGGAACTAATGGACCCCGAT
         66 GAGGTTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGAT

        886 GATGCGCTAA


Statistics
Matches: 637,  Mismatches: 80, Indels: 25
        0.86            0.11        0.03

Matches are distributed among these distances:
 152   40  0.06
 153  243  0.38
 154  219  0.34
 156   85  0.13
 157   50  0.08

ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21


Consensus pattern (154 bp):   
TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT
GAGGTTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCGATAGGCCCAAAATAACA
AGTGTTCCAAATGAGCTAAAAACT

Done.