Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020888.1 Corchorus olitorius cultivar O-4 contig20921, 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: 2549
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33


Found at i:633 original size:333 final size:332

Alignment explanation


    Indices: 27--2545  Score: 3578
    Period size: 333  Copynumber: 7.6  Consensus size: 332

         17 ATATATATAT

                         * **               *    * *                   *     
         27 ATATATAAATCATTGGTAAAAAGATTGAAGGGATTTTAAAGCTTCGAATATCGTTTTTCATATGC
          1 ATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCCTATGC

                                               *    *    *   *               
         92 TTTTCC-AGATTAATTT-CATATTAAATCGAAACTCGATTTTGATTCTCATAAAAACAAATCTTT
         66 TTTTCCGA-ATTAATTTCCA-ATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTT

                    *   *                           *   *   *                
        155 AAATCTTACGTGACTGAGATTTGGGTAGATGAATATAGATTTTCCAAGTAGTCTCT-GCGCCAAA
        129 AAATCTTATGTGGCTGAGATTTGGGTAGATGAATATAGATATTCAAAGGAGTCT-TGGCGCCAAA

                            *          *    *                           *    
        219 AATCATACAAAACTGAACCGGGCCCCGTAACGTGTTTTTAGCCGAAAACTGTGATGGTATCGCAC
        193 AATCATACAAAACTGAGCCGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGT-TAGCAC

                    *             *                                    *     
        284 ACGATTTCAGTCAAGATTTTGCGAAAATTGACCCGAATGATTTTTCCTAAATTTTTGGCTAAAAT
        257 ACGATTTCGGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTAAATTTTTGGCCAAAAT

            *          
        349 GCTCATAAAAA
        322 ACTCATAAAAA

                      *  *                 *                   *             
        360 ATATATAAATAATAGCCAAAAAGATTGAAGGCTATTTT-ACGCTTCGAATACCGTTTTTCCTATG
          1 ATATATAAATCATCGCCAAAAAGATTGAAGGGT-TTTTCACGCTTCGAATATCGTTTTTCCTATG

                                        *          *                         
        424 CTTTTCCGAATTAATTTCCAATTAAATCTAAACTGGATTTTGATGCTCGTAAAAACAAATCTTTA
         65 CTTTTCCGAATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTA

                        *                                         *          
        489 AATCTTATGTGGTTGAGATTTGGGTAGATGAATATAGATATTCAAAGGAGTCTTTGCGCCAAAAA
        130 AATCTTATGTGGCTGAGATTTGGGTAGATGAATATAGATATTCAAAGGAGTCTTGGCGCCAAAAA

                           * *     *                               *         
        554 TCATACAAAACTGAGGCTGGCCCTGGAACGCGTTTTTAGCCGAAAACTGTGATGGATAGCACACG
        195 TCATACAAAACTGAGCCGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACG

                  *             *      *                         *         * 
        619 ATTTTCAGTCAAGATTTTGCGAAAATTAACCCGAATGATTTTTCCTAAATTTTCGGCCAAAATGC
        260 A-TTTCGGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTAAATTTTTGGCCAAAATAC

                *    
        684 TCATGAAAA
        324 TCATAAAAA

                                                             * *            *
        693 ATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTCACGCTTCGAATCTTGTTTTTCCTATGT
          1 ATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCCTATGC

                                                                             
        758 TTTTCCGAATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAA
         66 TTTTCCGAATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAA

               *                                               *             
        823 ATCATATGTGGCTGAGATTTGGGTAGATGAATATAGA-ATGTCAAAGGAGTTTTGGCGCCAAAAA
        131 ATCTTATGTGGCTGAGATTTGGGTAGATGAATATAGATAT-TCAAAGGAGTCTTGGCGCCAAAAA

                           *  *    *                             *           
        887 TCATACAAAACTGAGTCGAGCCCTGGAACGCGTTTTTAGCCGAAAACTGTGATAGTTAGCACACG
        195 TCATACAAAACTGAGCCGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACG

                                       *                 *         *         
        952 ATTTCGGTCAAGATTTTGCAAAAATTGGCCCGAATGATTTTTCCTCAATTTTTGGACAAAATACT
        260 ATTTCGGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTAAATTTTTGGCCAAAATACT

                 *  
       1017 CATAACAA
        325 CATAAAAA

                                          *    *   *                        *
       1025 ATATATAAATCATCGCCAAAAAGATTGAAGAGTTTGTCATGCTTCGAATATCGTTTTTCCTATGT
          1 ATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCCTATGC

                                                          *                  
       1090 TTTTCCGAATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTTGTAAAAACAAATCTTTAA
         66 TTTTCCGAATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAA

            *  *                           *              *            *     
       1155 TTCCTATGTGGCTGAGATTTGGGTAGATGAAGATAGATATTCAAAGTAGTCTTGGCGCCCAAAAT
        131 ATCTTATGTGGCTGAGATTTGGGTAGATGAATATAGATATTCAAAGGAGTCTTGGCGCCAAAAAT

                   *                                               *         
       1220 CATACAAGACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGCTAGCACACG
        196 CATACAAAACTGAGCC-GGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACG

                                                    *                        
       1285 ATTTCGGTCAAGATTTTGCAAAAATTGACCCGAATGATTTATCCTTAAA-TTTTGGCCAAAATAC
        260 ATTTCGGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCC-TAAATTTTTGGCCAAAATAC

                     
       1349 TCATAAAAA
        324 TCATAAAAA

                                                                *            
       1358 AGTATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTCACGCTTCGAATATTGTTTTTCCTATG
          1 A-TATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCCTATG

                                                                             
       1423 CTTTTCCGAATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTA
         65 CTTTTCCGAATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTA

                *                                              *             
       1488 AATCATATGTGGCTGAGATTTGGGTAGATGAATATAGATATTCAAAGGAGTTTTGGCGCCAAAAA
        130 AATCTTATGTGGCTGAGATTTGGGTAGATGAATATAGATATTCAAAGGAGTCTTGGCGCCAAAAA

               *           *                                *          *     
       1553 TCACACAAAACTGAGTCGGGTCCCCGGAACGCGTTTTTAGCCGAAAACGGTGATGGTTAACACAC
        195 TCATACAAAACTGAGCCGGG-CCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACAC

             *       *                                  * *             * *  
       1618 GGTTTCGGTTAAGATTTTGCAAAAATTGACCCGAATGATTTTTCTTCAATTTTTGGCCAAGACAC
        259 GATTTCGGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTAAATTTTTGGCCAAAATAC

                    *
       1683 TCATAAAAG
        324 TCATAAAAA

               *          *                                    *             
       1692 ATAAATAAATCATCACCAAAAAGATTGAAGGGTTTTTCACGCTTCGAATATTGTTTTTCCTATGC
          1 ATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCCTATGC

                      *                      *      *                * *     
       1757 TTTTCCGAATCAATTTCCAATTAAATCGAAACTTGATTCTAATGCTCGTAAAAACAATTATTTAA
         66 TTTTCCGAATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAA

                       *        *                     *     *                
       1822 ATCTTATGTGGTTGAGATTTTGGTAGATGAATATAGATATTCCAAGGATTCTTGGCGCCAAAAAT
        131 ATCTTATGTGGCTGAGATTTGGGTAGATGAATATAGATATTCAAAGGAGTCTTGGCGCCAAAAAT

                          **    *                                            
       1887 CATACAAAACTGAGTTGGGTTCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACG
        196 CATACAAAACTGAGCCGGG-CCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACG

                   *         * *                                 *           
       1952 ATTTCGGCCAAGATTTTCCCAAAATTGACCCGAATGATTTTTCCTAAATTTTTAGCCAAAATACT
        260 ATTTCGGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTAAATTTTTGGCCAAAATACT

                    
       2017 CATAAAAA
        325 CATAAAAA

                          *             *      *   *                        *
       2025 ATATATAAATCATCTCCAAAAAGATTGATGGGTTTGTCATGCTTCGAATATCGTTTTTCCTATGT
          1 ATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCCTATGC

                                                          *   *              
       2090 TTTTCCGAATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTTGTATAAACAAATCTTTAA
         66 TTTTCCGAATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAA

            *  *                *               *         *            *     
       2155 TTCCTATGTGGCTGAGATTTAGGTAGATGAATATAGGTATTCAAAGTAGTCTTGGCGCCCAAAAT
        131 ATCTTATGTGGCTGAGATTTGGGTAGATGAATATAGATATTCAAAGGAGTCTTGGCGCCAAAAAT

                       *            **                                       
       2220 CATACAAAACTTAGCCGGGGCCCCAAAACGC-TTTTTCAGCCGAAAAC-----T-G-T---ACAC
        196 CATACAAAACTGAGCC-GGGCCCCGGAACGCGTTTTT-AGCCGAAAACTGTGATGGTTAGCACAC

                        *                                 *                  
       2274 GATTTCGGTCAATATTTTGCAAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATAC
        259 GATTTCGGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTAAATTTTTGGCCAAAATAC

               *     
       2339 TCAAAAAAA
        324 TCATAAAAA

                           *       **       *     * *    *       *      *    
       2348 TATATATAAATCATCTCCAAAAACTTTGAAGGATTTTTGATGCTTTGAATATCATTTTTCATATG
          1 -ATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCCTATG

                  *                          *                        *      
       2413 CTTTTCTGAATTAATTTCCAATTAAATCGAAACAGGATTCTGATGCTCGTAAAAACAATTCTTTA
         65 CTTTTCCGAATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTA

                     *                                *                      
       2478 AATCTTATGGGGCTGAGATTTGGGTAGATGAATATAGATATTTAAAGGAGTCTTGGCGCCAAAAA
        130 AATCTTATGTGGCTGAGATTTGGGTAGATGAATATAGATATTCAAAGGAGTCTTGGCGCCAAAAA

               
       2543 TCA
        195 TCA

       2546 CACA


Statistics
Matches: 1974,  Mismatches: 196, Indels: 41
        0.89            0.09        0.02

Matches are distributed among these distances:
 323   71  0.04
 324  174  0.09
 326    1  0.00
 327    1  0.00
 328    1  0.00
 332  277  0.14
 333  1137  0.58
 334  312  0.16

ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Consensus pattern (332 bp):   
ATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCCTATGC
TTTTCCGAATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAA
ATCTTATGTGGCTGAGATTTGGGTAGATGAATATAGATATTCAAAGGAGTCTTGGCGCCAAAAAT
CATACAAAACTGAGCCGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGA
TTTCGGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTAAATTTTTGGCCAAAATACTC
ATAAAAA

Done.