Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011034.1 Corchorus olitorius cultivar O-4 contig11067, 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, 859

Length: 1432
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24


Found at i:283 original size:154 final size:154

Alignment explanation


    Indices: 3--1432  Score: 2135
    Period size: 154  Copynumber: 9.3  Consensus size: 154

          1 CA

                                             *      *                        
          3 TTGAGGTTTGCCAAATCGAAGTCGATTCAAAATGGAA-CTGATGGGCCCCGAAAGGCCCAAAATT
          1 TTGAGGTTTGCCAAATCGAAGTCGATTCAAAA-CGAATCTAATGGGCCCCGAAAGGCCCAAAATT

                                                         **                  
         67 ACAATTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCTTCAAAATGATTATAGTTAG
         65 ACAATTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAG

                                     
        132 GCCATAAACAATGGAAAGAAAAGCT
        130 GCCATAAACAATGGAAAGAAAAGCT

                                                         *                   
        157 TTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGAATCTAATGGGTCCCGAAAGGCCCAAAATTA
          1 TTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGAATCTAATGGGCCCCGAAAGGCCCAAAATTA

                              *         *               *                    
        222 CAATTGTTCCAACA-GAGTTAAAAACTTTACAGTGGACATATCTTACCAAAATGATTATAGTTAG
         66 CAATTGTTCCAA-ATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAG

                        *            
        286 GCCATAAACAATTGAAAGAAAAGCT
        130 GCCATAAACAATGGAAAGAAAAGCT

                                        *                                    
        311 TTGAGGTTTGCCAAATCGAAGTCGATTCCAAACGAATCTAATGGGCCCCGAAAGGCCCAAAATTA
          1 TTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGAATCTAATGGGCCCCGAAAGGCCCAAAATTA

                             *                       *                       
        376 CAATTGTTCCAAATGAGGTAAAAACTTCACAGTGGACATATGTCACCAAAATGATTATAGTTAGG
         66 CAATTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAGG

             *                      
        441 CAATAAACAATGGAAAGAAAAGCT
        131 CCATAAACAATGGAAAGAAAAGCT

                                             *      *             *         *
        465 TTGAGGTTTGCCAAATCGAAGTCGATTCAAAATTGAA-CTGATGGGCCCCGAAAAGCCCAAAATA
          1 TTGAGGTTTGCCAAATCGAAGTCGATTCAAAA-CGAATCTAATGGGCCCCGAAAGGCCCAAAATT

                *          *                                          *      
        529 ACAAGTGTTCCAAATAAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTAGAGTTAG
         65 ACAATTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAG

            *  *                   * 
        594 TCCGTAAACAATGGAAAGAAAAGTT
        130 GCCATAAACAATGGAAAGAAAAGCT

                                                     *   *  **              *
        619 TTGAGGTTTGCCAAATCGAAGTCGATTCAAAACAGAA-CTAGTGGTCCAAGAAAGGCCCAAAATA
          1 TTGAGGTTTGCCAAATCGAAGTCGATTCAAAAC-GAATCTAATGGGCCCCGAAAGGCCCAAAATT

                *                                                *           
        683 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATAATTATAGTTAG
         65 ACAATTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAG

            *  *               *     
        748 TCCGTAAACAATGGAAAGAGAAGCT
        130 GCCATAAACAATGGAAAGAAAAGCT

                     * *                *     *          *                   
        773 TTGAGGTTTTCTAAATCGAAGTCGATTCCAAACGGATCTAATGGGTCCCGAAAGGCCCAAAATTA
          1 TTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGAATCTAATGGGCCCCGAAAGGCCCAAAATTA

                         *   *                                               
        838 CAATTGTTCCAAAAGAGTTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAGG
         66 CAATTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAGG

                   **               
        903 CCATAAAGGATGGAAAGAAAAGCT
        131 CCATAAACAATGGAAAGAAAAGCT

                *                            *                              *
        927 TTGAAGTTTGCCAAATCGAAGTCGATTCAAAATGGAA-CTAATGGGCCCCGAAAGGCCCAAAATA
          1 TTGAGGTTTGCCAAATCGAAGTCGATTCAAAA-CGAATCTAATGGGCCCCGAAAGGCCCAAAATT

             *  *                                      *                     
        991 AGAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCACACCAAAATGATTATAGTTAG
         65 ACAATTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAG

            *                  *     
       1056 TCCATAAACAATGGAAAGAGAAGCT
        130 GCCATAAACAATGGAAAGAAAAGCT

                     * *                *     *          *                   
       1081 TTGAGGTTTTCTAAATCGAAGTCGATTCCAAACGGATCTAATGGGTCCCGAAAGGCCCAAAATTA
          1 TTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGAATCTAATGGGCCCCGAAAGGCCCAAAATTA

                         *   *                                               
       1146 CAATTGTTCCAAAAGAGTTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAGG
         66 CAATTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAGG

                              *     
       1211 CCATAAACAATGGAAAGATAAGCT
        131 CCATAAACAATGGAAAGAAAAGCT

                                   *   *            *                        
       1235 TTGAGGTTTGCCAAATCGAAGTCAATTTAAAACGAATCTAGTGGGCCCCG-AAGGCCC-AAATTA
          1 TTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGAATCTAATGGGCCCCGAAAGGCCCAAAATTA

                         *     *                                             
       1298 CAATTGTTCCAAAAGAG-TTAAAACTTCACAGTGGACATATCGTCACC-AAATGATTATAGTTAG
         66 CAATTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATC-TCACCAAAATGATTATAGTTAG

            **                       
       1361 AACAT-AACAATGGAAAG-AAAGCT
        130 GCCATAAACAATGGAAAGAAAAGCT

                                              *              
       1384 TTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGATCTAATGGGCCCC
          1 TTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGAATCTAATGGGCCCC


Statistics
Matches: 1157,  Mismatches: 110, Indels: 23
        0.90            0.09        0.02

Matches are distributed among these distances:
 149   50  0.04
 150   12  0.01
 151   42  0.04
 152   28  0.02
 153   15  0.01
 154  1004  0.87
 155    6  0.01

ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24


Consensus pattern (154 bp):   
TTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGAATCTAATGGGCCCCGAAAGGCCCAAAATTA
CAATTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAGG
CCATAAACAATGGAAAGAAAAGCT

Done.