Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010958.1 Corchorus olitorius cultivar O-4 contig10990, 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, 864

Length: 1440
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21


Found at i:322 original size:154 final size:154

Alignment explanation


    Indices: 1--1440  Score: 2142
    Period size: 154  Copynumber: 9.4  Consensus size: 154

                         *   *  *        * *                       *        *
          1 TCACAGTGGACTAGTCTGACGAAAATGATAAGAGTTAGGCCATAAACAATGGAAACAAAAGCATC
          1 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT

                *             *                               *     *        
         66 GAGGGTTGCCAAATCGAATACGATTCAAAACGGA-ACTAATG-GCCCCGAAAGGCCTAAAATAAC
         66 GAGGTTTGCCAAATCGAAGACGATTCAAAAC-GACACTAATGAGCCCCGATAGGCCCAAAATAAC

                         *           
        129 AAGTGTTCCAAATCAGCTAAAAACT
        130 AAGTGTTCCAAATGAGCTAAAAACT

                                              *                              
        154 TCACAGTGGACTAATCTCACCAAAATGATTATAGGTAGGCCATAAACAATGGAAAGAAAAGCATT
          1 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT

                   *       *           *                                     
        219 GAGGTTTCCCAAATCAAAGACGATTCAGAACGACACTAATGAGCCCCGATAGGCCCAAAATAACA
         66 GAGGTTTGCCAAATCGAAGACGATTCAAAACGACACTAATGAGCCCCGATAGGCCCAAAATAACA

             *                      
        284 ATTGTTCCAAATGAGCTAAAAACT
        131 AGTGTTCCAAATGAGCTAAAAACT

                                *              *                *            
        308 TCACAGTGGACTAATCTCACGAAAATGA-TAGTAGCTAGGCCATAAACAATGAAAAGAAAAGCAT
          1 TCACAGTGGACTAATCTCACCAAAATGATTA-TAGTTAGGCCATAAACAATGGAAAGAAAAGCAT

                                                            *   *          * 
        372 TGAGGTTT-CTCAAATCGAAGACGATTCAAAACGACACTAAT-AGGCCTCGAAAGGCCCAAAAAA
         65 TGAGGTTTGC-CAAATCGAAGACGATTCAAAACGACACTAATGA-GCCCCGATAGGCCCAAAATA

                                      *
        435 ACAAGTGTTCCAAATGAGCTAAAAACA
        128 ACAAGTGTTCCAAATGAGCTAAAAACT

                   *                          *                              
        462 TCACAGTCGACTAATCTCACCAAAATGATTATAGGTAGGCCATAAACAATGGAAAGAAAAGCATT
          1 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT

                   *                   *      *                              
        527 GAGGTTTCCCAAATCGAAGACGATTCAGAACGACTCTAATGAGCCCCGATAGGCCCAAAATAACA
         66 GAGGTTTGCCAAATCGAAGACGATTCAAAACGACACTAATGAGCCCCGATAGGCCCAAAATAACA

             *                      
        592 ATTGTTCCAAATGAGCTAAAAACT
        131 AGTGTTCCAAATGAGCTAAAAACT

                                *        * *     *            **             
        616 TCACAGTGGACTAATCTCACGAAAATGATAAGAGTTATGCCATAAACAATACAAAGAAAAGCATT
          1 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT

                            *                         *                      
        681 GAGGTTT-CTCAAATCAAAGACGATTCAAAACGACACTAATGGGCCCCGATAGGCCCAAAATAAC
         66 GAGGTTTGC-CAAATCGAAGACGATTCAAAACGACACTAATGAGCCCCGATAGGCCCAAAATAAC

                   *                 
        745 AAGTGTTTCAAATGAGCTAAAAACT
        130 AAGTGTTCCAAATGAGCTAAAAACT

                         *                                                   
        770 TCACAGTGGACTAGTCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT
          1 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT

            *                                         *   *                  
        835 AAGGTTTGCCAAATCGAAGACGATTCAAAACGGA-ACTAATGGGCCTCGATAGGCCCAAAATAAC
         66 GAGGTTTGCCAAATCGAAGACGATTCAAAAC-GACACTAATGAGCCCCGATAGGCCCAAAATAAC

                         *           
        899 AAGTGTTCCAAATAAGCTAAAAACT
        130 AAGTGTTCCAAATGAGCTAAAAACT

                     *                                                       
        924 TCACAGTGGCCTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT
          1 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT

                     *                * *   *  *     *                       
        989 GAGGTTTGCAAAATCGAAGACGATTCTATACGTCATTAATGGGCCCCGATAGGCCCAAAATAACA
         66 GAGGTTTGCCAAATCGAAGACGATTCAAAACGACACTAATGAGCCCCGATAGGCCCAAAATAACA

                                   *
       1054 AGTGTTCCAAATGAGCT-AAAACA
        131 AGTGTTCCAAATGAGCTAAAAACT

                              *                                              
       1077 TCACAGTGGACTAATCTCGCCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT
          1 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT

                            *                                          *     
       1142 GAGGTTTGCCAAATCGTAGACGATTCAAAACGGA-ACTAATGAGCCCCGATAGGCCCAAGATAAC
         66 GAGGTTTGCCAAATCGAAGACGATTCAAAAC-GACACTAATGAGCCCCGATAGGCCCAAAATAAC

                       *           * 
       1206 AAGTGTTCCAACTGAGCTAAAAAGT
        130 AAGTGTTCCAAATGAGCTAAAAACT

                 *               *                               *           
       1231 TCACAATGGACTAATCTCACCGAAATGATTATAGTTAGGCCATAAACAATGGATAGAAAAGCATT
          1 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT

                          *            *             *                       
       1296 GAGGTTTGCCAAATAGAAGACGATTCAGAACGACACTAATGGGCCCCGATAGGCCCAAAATAACA
         66 GAGGTTTGCCAAATCGAAGACGATTCAAAACGACACTAATGAGCCCCGATAGGCCCAAAATAACA

                  *               * 
       1361 AGTGTTTCAAATGAGCTAAAAAGT
        131 AGTGTTCCAAATGAGCTAAAAACT

                 *                                 **               
       1385 TCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGTTATAAACAATGGAAAG
          1 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG


Statistics
Matches: 1169,  Mismatches: 103, Indels: 29
        0.90            0.08        0.02

Matches are distributed among these distances:
 152    2  0.00
 153  237  0.20
 154  923  0.79
 155    7  0.01

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


Consensus pattern (154 bp):   
TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT
GAGGTTTGCCAAATCGAAGACGATTCAAAACGACACTAATGAGCCCCGATAGGCCCAAAATAACA
AGTGTTCCAAATGAGCTAAAAACT

Done.