Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018134.1 Corchorus olitorius cultivar O-4 contig18167, 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: 1847
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33


Found at i:604 original size:331 final size:328

Alignment explanation


    Indices: 1--1847  Score: 2751
    Period size: 331  Copynumber: 5.6  Consensus size: 328

                                                 *  *                        
          1 TCATGCAAAACTGAGTCGGGACCCAGGAATGCGTTTTAAGACAAAAACTGTGATGGTTAGTACAC
          1 TCATGCAAAACTGAGTC-GGACCCAGGAATGCGTTTTTAGCCAAAAAC-GTGATGGTTAGTACAC

                   *                                                         
         66 GATTTCAACTAAAATTTTACAAAAATTGACCCGAAAGATTTTTCCTCAAATTTTAGCCACAATAA
         64 GATTTCAGCTAAAATTTTACAAAAATTGACCCGAAAGATTTTTCCTCAAATTTTAGCCACAATAA

                                  * *            *         *    *            
        131 TCATAGAAATATATAATTCAACATAAAAAAGATTGAAAGGCTTTTCATGCTTCTAATATCGTTTT
        129 TCATAGAAATATATAATTCAACTTCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTT

              *                     *        *                               
        196 TCCATTTTTTTCTGAATTAATTTCTAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAA
        194 T-TATTTTTTTCTGAATTAATTTCAAATAAAATTGAAACAAGATTCTGATGCTCGTAAAAACAAA

                 *                                                           
        261 TCCTTCAATCCACTGTGGCTGAGATTTGGTTAGATGAATATAGATTTTTCAAGGAGTCTTGGCGC
        258 TCCTTAAATCCACTGTGGCTGAGATTTGGTTAGATGAATATAGATTTTTCAAGGAGTCTTGGCGC

                  
        326 CAAAAA
        323 CAAAAA

                                                           *           *     
        332 TCATGCAAAACTGAGTCGTGACCCAGGAATGCGTTTTTAGCCCAAAATCGTGATGGTTAATACAC
          1 TCATGCAAAACTGAGTCG-GACCCAGGAATGCGTTTTTAG-CCAAAAACGTGATGGTTAGTACAC

                 **   *                *                             * *     
        397 GATTTTTGCTGAAATTTTACAAAAATTCACCCGAAAGATTTTTCCTCAAATTTTAGCTAAAATAA
         64 GATTTCAGCTAAAATTTTACAAAAATTGACCCGAAAGATTTTTCCTCAAATTTTAGCCACAATAA

                                                                             
        462 TCATAGAAATATATAATTCAACTTCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTATT
        129 TCATAGAAATATATAATTCAACTTCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGT-TT

                                             *                   *      *    
        527 TTTATTTTTTTCTGAATTAATTTCAAATAAAATCGAAACAAGATTCTGATGCTAGTAAAATCAAA
        193 TTTATTTTTTTCTGAATTAATTTCAAATAAAATTGAAACAAGATTCTGATGCTCGTAAAAACAAA

                                       *                     *               
        592 TCCTTAAATCCACTGTGGCTGAGATTTTGTTAGATGAATATAGATTTTTAAAGGAGTCTTGGCGC
        258 TCCTTAAATCCACTGTGGCTGAGATTTGGTTAGATGAATATAGATTTTTCAAGGAGTCTTGGCGC

                  
        657 CAAAAA
        323 CAAAAA

                                  *          *     *           *  *          
        663 TCATGCAAAACTGAGTCGGGACACAGGAATGCGATTTTACCCAAAAACCGTTATAGTTAGTACAC
          1 TCATGCAAAACTGAGTC-GGACCCAGGAATGCGTTTTTAGCCAAAAA-CGTGATGGTTAGTACAC

                   *         *                                               
        728 GATTTCATCTAAAATTTAACAAAAATTGACCCGAAAGATTTTTCCTCAAATTTTAGCCACAATAA
         64 GATTTCAGCTAAAATTTTACAAAAATTGACCCGAAAGATTTTTCCTCAAATTTTAGCCACAATAA

                              *  *          *                           *    
        793 TCATAGAAATATATAATTTAAGTTCAAAAAGAATGAAGGGCTTTTCACGCTTTTAATATCATTTT
        129 TCATAGAAATATATAATTCAACTTCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTT

                     *                                                 *     
        858 TTCATTTTTATCTGAATTAATTTCAAATAAAATTGAAACAAGATTCTGATGCTCGTAAACACAAA
        194 TT-ATTTTTTTCTGAATTAATTTCAAATAAAATTGAAACAAGATTCTGATGCTCGTAAAAACAAA

                                                                   *      *  
        923 TCCTTAAATCCACTGTGGCTGAGATTTGGTTAGATGAATATAGATTTTTCAAGGATTCTTGGTGC
        258 TCCTTAAATCCACTGTGGCTGAGATTTGGTTAGATGAATATAGATTTTTCAAGGAGTCTTGGCGC

                  
        988 CAAAAA
        323 CAAAAA

                        *     *                                              
        994 TCATGCAAAACTAAGTCAAGACCCAGGAATGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACAC
          1 TCATGCAAAACTGAGTC-GGACCCAGGAATGCGTTTTTAGCCAAAAA-CGTGATGGTTAGTACAC

                 **   *                   *                        *         
       1059 GATTTTTGCTGAAATTTTACAAAAATTGACACGAAAGATTTTTCCTCAAATTTTATCCACAATAA
         64 GATTTCAGCTAAAATTTTACAAAAATTGACCCGAAAGATTTTTCCTCAAATTTTAGCCACAATAA

                       *                           *                    *    
       1124 TCATAGAAATACATAATTCAACTTCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCATTTT
        129 TCATAGAAATATATAATTCAACTTCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTT

                         *  *                     *  *   *    *          *   
       1189 TTCATTTTTTTCTAAACTAATTTCAAATAAAATTGAAATAAAATTTTGATTCTCGTAAAAAGAAA
        194 TT-ATTTTTTTCTGAATTAATTTCAAATAAAATTGAAACAAGATTCTGATGCTCGTAAAAACAAA

                              *               *              *            *  
       1254 TCCTTAAATCCACTGTGGTTGAGATTTGGTTAGACGAATATAGATTTTTGAAGGAGTCTTGGTGC
        258 TCCTTAAATCCACTGTGGCTGAGATTTGGTTAGATGAATATAGATTTTTCAAGGAGTCTTGGCGC

                  
       1319 CAAAAA
        323 CAAAAA

                                                    *                        
       1325 TCATGCAAAACTGAGTCAGGACCCAGGAATGCGTTTTTAGACAAAAACGGTGATGGTTAGTACAC
          1 TCATGCAAAACTGAGTC-GGACCCAGGAATGCGTTTTTAGCCAAAAAC-GTGATGGTTAGTACAC

                                     *                                       
       1390 GATTTCAGCTAAAATTTTACAAAAAATGACCCGAAAGATTTTTCCTCAAATTTTAGCCACAATAA
         64 GATTTCAGCTAAAATTTTACAAAAATTGACCCGAAAGATTTTTCCTCAAATTTTAGCCACAATAA

                                                       *          *          
       1455 TCATAGAAATATATAATTCAACTTCAAAAAGATTGAAGGGCTTATCACGCTTTTGATATCGTATT
        129 TCATAGAAATATATAATTCAACTTCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGT-TT

              *                                                              
       1520 TTCATTTTTTTCCTGAATTAATTTCAAATAAAATTGAAACAAGATTCTGATGCTCGTAAAAACAA
        193 TTTATTTTTTT-CTGAATTAATTTCAAATAAAATTGAAACAAGATTCTGATGCTCGTAAAAACAA

              *            *           *                                    *
       1585 ATTCTTAAATCCACTATGGCTGAGATTAGGTTAGATGAATATAGATTTTTCAAGGAGTCTTGGCA
        257 ATCCTTAAATCCACTGTGGCTGAGATTTGGTTAGATGAATATAGATTTTTCAAGGAGTCTTGGCG

                  *
       1650 CCAAAAG
        322 CCAAAAA

               *           *         *   *               * *   *   *         
       1657 TCACGCAAAACTGAGCCGGAGCCCATGAACGCGTTTTTAGCCACATATCGTAATGATTAGTACAC
          1 TCATGCAAAACTGAGTCGGA-CCCAGGAATGCGTTTTTAGCCA-AAAACGTGATGGTTAGTACAC

            *                                           *                   *
       1722 AATTTCAGCT-AAATTTTACAAAAATTGACCCGAAAGATTTTTCTTCAAATTTTAGCCACAATAT
         64 GATTTCAGCTAAAATTTTACAAAAATTGACCCGAAAGATTTTTCCTCAAATTTTAGCCACAATAA

                   *              *                              *        
       1786 TCATAGACATATATAATTCAACATCAAAAATGATTGAAGGGCTTTTCACGCTTCTAATATCG
        129 TCATAGAAATATATAATTCAACTTCAAAAA-GATTGAAGGGCTTTTCACGCTTTTAATATCG


Statistics
Matches: 1371,  Mismatches: 133, Indels: 23
        0.90            0.09        0.02

Matches are distributed among these distances:
 330   13  0.01
 331  1146  0.84
 332  209  0.15
 333    3  0.00

ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33


Consensus pattern (328 bp):   
TCATGCAAAACTGAGTCGGACCCAGGAATGCGTTTTTAGCCAAAAACGTGATGGTTAGTACACGA
TTTCAGCTAAAATTTTACAAAAATTGACCCGAAAGATTTTTCCTCAAATTTTAGCCACAATAATC
ATAGAAATATATAATTCAACTTCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTT
ATTTTTTTCTGAATTAATTTCAAATAAAATTGAAACAAGATTCTGATGCTCGTAAAAACAAATCC
TTAAATCCACTGTGGCTGAGATTTGGTTAGATGAATATAGATTTTTCAAGGAGTCTTGGCGCCAA
AAA

Done.