Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014907.1 Corchorus olitorius cultivar O-4 contig14940, 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, 865

Length: 1442
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33


Found at i:623 original size:321 final size:321

Alignment explanation


    Indices: 1--1442  Score: 2351
    Period size: 321  Copynumber: 4.5  Consensus size: 321

                            *                *                               
          1 AATTCGATTTAACGATTTTTTTAACGAGCATCTTAATCTTGTTTCGATTTAATTAGAAATAAATT
          1 AATTCGATTTAACGATGTTTTTAACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATT

                                                  *         *   *            
         66 CGGAAAAAAATGCAAAATGATATTAGAAGTGTGAAAAGACCGTCAATCATTTGGGCGTTAAATTA
         66 CGGAAAAAAATGCAAAATGATATTAGAAGTGTGAAAAGCCCGTCAATCTTTTAGGCGTTAAATTA

                 *                                                           
        131 TATATATTTTCTGAGTATTGCT-GCAGAAAAT-AAG-AAAAAATTTTCGGGTCAGTTTTTAGCCG
        131 TATATTTTTTCTGAGTATTG-TGGCAGAAAATAAAGAAAAAAATTTTCGGGTCAGTTTTTAGCCG

                                          * *                                
        193 AAATCGTGTACTAACCATCACAGTTTTTGGCCCAAAAACGAGTTACGGGGCCCTGCCTCAGTTTT
        195 AAATCGTGTACTAACCATCACAGTTTTTGGGCAAAAAACGAGTTACGGGGCCCTGCCTCAGTTTT

                  *                                                       
        258 GCATGAGTTTTGGCGTGAAGACTCCTTGAAATGCCTATATTCATCGAACCAAATTCCAGCCA
        260 GCATGATTTTTGGCGTGAAGACTCCTTGAAATGCCTATATTCATCGAACCAAATTCCAGCCA

                                                                          *  
        320 AATTCGATTTAACGATGTTTTTAACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAACTT
          1 AATTCGATTTAACGATGTTTTTAACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATT

             *      *                   *                              *     
        385 CAGAAAAAGATGCAAAATGATATTAGAAATGTGAAAAGCCCGTCAATCTTTTAGGCGTTTAATTA
         66 CGGAAAAAAATGCAAAATGATATTAGAAGTGTGAAAAGCCCGTCAATCTTTTAGGCGTTAAATTA

                                                                             
        450 TATATTTTTTCTGAGTATTGTGGCAGAAAATAAAGAAAAAAATTTTCGGGTCAGTTTTTAGCCGA
        131 TATATTTTTTCTGAGTATTGTGGCAGAAAATAAAGAAAAAAATTTTCGGGTCAGTTTTTAGCCGA

                                            *                                
        515 AATCGTGTACTAACCATCACAGTTTTTGGGCAGAAAACGAGTTACGGGGCCCTGCCTCAGTTTTG
        196 AATCGTGTACTAACCATCACAGTTTTTGGGCAAAAAACGAGTTACGGGGCCCTGCCTCAGTTTTG

                                             *                 *   *     
        580 CATGATTTTTGGCGTGAAGACTCCTTGAAATGCGTATATTCATCGAACCAATTTCTAGCCA
        261 CATGATTTTTGGCGTGAAGACTCCTTGAAATGCCTATATTCATCGAACCAAATTCCAGCCA

                            *           *                                    
        641 AATTCGATTTAACGATTTTTTTAACGAGGATCTGAATCTTGTTTCGATTTAATTAGAAATAAATT
          1 AATTCGATTTAACGATGTTTTTAACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATT

                                                                 *           
        706 CGGGAAAAAAATGCAAAATGATATTAGAAGTGTGAAAAGCCCGTCAATCTTTTGGGCGTTAAATT
         66 C-GGAAAAAAATGCAAAATGATATTAGAAGTGTGAAAAGCCCGTCAATCTTTTAGGCGTTAAATT

                       *            *       *                            *   
        771 ATATATTTTTTATGAGTATTGTGGTAGAAAATTAAGAAAAAAATTTT-GGGTCAG-TTTTATCCG
        130 ATATATTTTTTCTGAGTATTGTGGCAGAAAATAAAGAAAAAAATTTTCGGGTCAGTTTTTAGCCG

                             *                              **               
        834 AAATCGTGTACTAACCACCACAGTTTTTGGGCAAAAAACGAAGTT-CTATGGCCCTGCCTCAGTT
        195 AAATCGTGTACTAACCATCACAGTTTTTGGGCAAAAAACG-AGTTAC-GGGGCCCTGCCTCAGTT

               *                                                            
        898 TTGTATGATTTTTGGCGTGAAGACTCCTTGAAATGCCTATATTCATCGAACCAAATTCCAGCCA
        258 TTGCATGATTTTTGGCGTGAAGACTCCTTGAAATGCCTATATTCATCGAACCAAATTCCAGCCA

                       **          *                                       * 
        962 AATTCGATTTATGGAT-TATTTTCACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAACT
          1 AATTCGATTTAACGATGT-TTTTAACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAAT

              *      *                                                   *   
       1026 TCAGAAAAAGATGCAAAATGATATTAGAAGTGTGAAAAGCCCGTCAATCTTTTAGGCGTTAGATT
         65 TCGGAAAAAAATGCAAAATGATATTAGAAGTGTGAAAAGCCCGTCAATCTTTTAGGCGTTAAATT

                          *      *                *        *                 
       1091 ATATATTTTTTCTGTGTATTGCGGCAGAAAATAAAGAAGAAAATTTTTGGGTCAGTTTTTAGCCG
        130 ATATATTTTTTCTGAGTATTGTGGCAGAAAATAAAGAAAAAAATTTTCGGGTCAGTTTTTAGCCG

                                                        *                    
       1156 AAATCGTGTACTAACCATCACAGTTTTTGGGCAAAAAACGAGTTCCGGGGCCCTGCCTCAGTTTT
        195 AAATCGTGTACTAACCATCACAGTTTTTGGGCAAAAAACGAGTTACGGGGCCCTGCCTCAGTTTT

                                                                  *   *   
       1221 GCATGATTTTTGGCGTGAAGACTCCTTGAAATGCCTATATTCATCGAACCAAATCCCAACCA
        260 GCATGATTTTTGGCGTGAAGACTCCTTGAAATGCCTATATTCATCGAACCAAATTCCAGCCA

                                             *   *               * *         
       1283 AATTCGATTTAACGATGTTTTTAACGAGCATCTCAATTTTGTTTCGATTTAATCATAAATAAATT
          1 AATTCGATTTAACGATGTTTTTAACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATT

                                                                             
       1348 CGGAAAAAAATGCAAAATGATATTAGAAGTGTGAAAAGCCCGTCAATCTTTTAGGCGTTAAATTA
         66 CGGAAAAAAATGCAAAATGATATTAGAAGTGTGAAAAGCCCGTCAATCTTTTAGGCGTTAAATTA

                                           
       1413 TATATTTTTT-TGAAGTATTGTGGCAGAAAA
        131 TATATTTTTTCTG-AGTATTGTGGCAGAAAA


Statistics
Matches: 1038,  Mismatches: 73, Indels: 22
        0.92            0.06        0.02

Matches are distributed among these distances:
 318    1  0.00
 319  148  0.14
 320  153  0.15
 321  585  0.56
 322  151  0.15

ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33


Consensus pattern (321 bp):   
AATTCGATTTAACGATGTTTTTAACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATT
CGGAAAAAAATGCAAAATGATATTAGAAGTGTGAAAAGCCCGTCAATCTTTTAGGCGTTAAATTA
TATATTTTTTCTGAGTATTGTGGCAGAAAATAAAGAAAAAAATTTTCGGGTCAGTTTTTAGCCGA
AATCGTGTACTAACCATCACAGTTTTTGGGCAAAAAACGAGTTACGGGGCCCTGCCTCAGTTTTG
CATGATTTTTGGCGTGAAGACTCCTTGAAATGCCTATATTCATCGAACCAAATTCCAGCCA

Done.