Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011752.1 Corchorus olitorius cultivar O-4 contig11785, 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, 709

Length: 1182
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22


Found at i:305 original size:154 final size:154

Alignment explanation


    Indices: 1--1182  Score: 1884
    Period size: 154  Copynumber: 7.7  Consensus size: 154

                                         *                                   
          1 ATAGGCCCAAAATAACAAGTGTTCCAAATTAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAA
          1 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAA

                            *                                                
         66 ATGAATTATAGTTAGACCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACG
         66 ATG-ATTATAGTTAG-GCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACG

                                      
        131 ATTCAATACGTCACTAATGGGCCCCG
        129 ATTCAATACGTCACTAATGGGCCCCG

                     *                   *                                   
        157 ATAGGCCCAGAATAACAAGTGTTCCAAATTAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAA
          1 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAA

                                    *                                        
        222 ATGATTATAGTTAGGCCATAAACAGTGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGAT
         66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGAT

                                    
        287 TCAATACGTCACTAATGGGCCCCG
        131 TCAATACGTCACTAATGGGCCCCG

                                *                                      * *   
        311 ATAGGCCCAAAATAACAAGTATTCCAAAGTGAGCTAAAAAGTTCACAGTGGACTAATCTAAACAA
          1 ATAGGCCCAAAATAACAAGTGTTCCAAA-TGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAA

                       *  *                 *             *       *       *  
        376 AATGATTATAGGTATGCCATAAACAATGGAAACAAAAGCATTGAGGCTTGCCAATTCGAAGAAGA
         65 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA

                                    *
        441 TTCAATACGTCACTAATGGGCCCCA
        130 TTCAATACGTCACTAATGGGCCCCG

                                         *          *                        
        466 ATAGGCCCAAAATAACAAGTGTTCCAAATTAGCTAAAAAGCTCACAGTGGACTAATCTCACCAAA
          1 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAA

                                                                             
        531 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGAT
         66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGAT

                                    
        596 TCAATACGTCACTAATGGGCCCCG
        131 TCAATACGTCACTAATGGGCCCCG

                   *            *                           *  *    *        
        620 ATAGGCCAAAAATAACAAGTTTTCCAAATGAGCTAAAAAGTTCACAGTAGAGTAATATCACCAAA
          1 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAA

              *                                   *                          
        685 ATTATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCGTTGAGGTTTGCCAAATCGAAGACGAT
         66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGAT

             *  *    *  *            
        750 TTAAAACG-GATTTAATGGGCCCCG
        131 TCAATACGTCA-CTAATGGGCCCCG

              * *                      *                     *     *         
        774 ATTGTCCCAAAATAACAAGTGTTCCAACTGAGCTAAAAAGTTCACAGTGTACTAACCTCACCAAA
          1 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAA

                           *                                             *   
        839 ATGATTATAGTTAGGTCATAAACAATGGAAAGAAAA-CATTGAGGTTTGCCAAATCGAAGAAGAT
         66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGAT

                                     
        903 T-AAGTACGTCACTAATGGGCCCCG
        131 TCAA-TACGTCACTAATGGGCCCCG

                             * *                   *    *           *        
        927 ATAGGCCCAAAATAACAGGAGTTCCAAATGAGCTAAAAACTTCATAGTGGACTAATATCACCAAA
          1 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAA

                                                                             
        992 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGAT
         66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGAT

                       *          * 
       1057 TCAATACGTCAGTAATGGGCCCTG
        131 TCAATACGTCACTAATGGGCCCCG

                                *                *      *                    
       1081 ATAGGCCCAAAATAACAAGTATTCCAAATGAGCTAAAGAGTTCATAGTGGACTAATCTCACCAAA
          1 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAA

                          *                      
       1146 ATGATTATAGTTAGACCATAAACAATGGAAAGAAAAG
         66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG


Statistics
Matches: 941,  Mismatches: 79, Indels: 14
        0.91            0.08        0.01

Matches are distributed among these distances:
 152    2  0.00
 153  133  0.14
 154  584  0.62
 155  155  0.16
 156   67  0.07

ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22


Consensus pattern (154 bp):   
ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAA
ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGAT
TCAATACGTCACTAATGGGCCCCG

Found at i:1023 original size:307 final size:308

Alignment explanation


    Indices: 1--1182  Score: 1868
    Period size: 307  Copynumber: 3.8  Consensus size: 308

                               *         *                          *        
          1 ATAGGCCCAAAATAACAAGTGTTCCAAATTAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAA
          1 ATAGGCCCAAAATAACAAGAGTTCCAAATGAGCTAAAAAGTTCACAGTGGACTAATATCACCAAA

                            *                                                
         66 ATGAATTATAGTTAGACCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACG
         66 ATG-ATTATAGTTAG-GCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACG

                                               *                   *         
        131 ATTCAATACGTCACTAATGGGCCCCGATAGGCCCAGAATAACAAGTGTTCCAAATTAGCTAAAAA
        129 ATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAA

                                                              *              
        196 GTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAGTGGAAAGAAAAGCA
        194 GTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA

                                                              
        261 TTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCG
        259 TTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCG

                                                                      * * *  
        311 ATAGGCCCAAAATAACAAGTA-TTCCAAAGTGAGCTAAAAAGTTCACAGTGGACTAATCTAAACA
          1 ATAGGCCCAAAATAACAAG-AGTTCCAAA-TGAGCTAAAAAGTTCACAGTGGACTAATATCACCA

                        *  *                 *             *       *       * 
        375 AAATGATTATAGGTATGCCATAAACAATGGAAACAAAAGCATTGAGGCTTGCCAATTCGAAGAAG
         64 AAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACG

                                     *                             *         
        440 ATTCAATACGTCACTAATGGGCCCCAATAGGCCCAAAATAACAAGTGTTCCAAATTAGCTAAAAA
        129 ATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAA

             *                                                               
        505 GCTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
        194 GTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA

                                                              
        570 TTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCG
        259 TTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCG

                   *           **                           *  *             
        620 ATAGGCCAAAAATAACAAGTTTTCCAAATGAGCTAAAAAGTTCACAGTAGAGTAATATCACCAAA
          1 ATAGGCCCAAAATAACAAGAGTTCCAAATGAGCTAAAAAGTTCACAGTGGACTAATATCACCAAA

              *                                   *                          
        685 ATTATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCGTTGAGGTTTGCCAAATCGAAGACGAT
         66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGAT

             *  *    *  *              * *                      *            
        750 TTAAAACG-GATTTAATGGGCCCCGATTGTCCCAAAATAACAAGTGTTCCAACTGAGCTAAAAAG
        131 TCAATACGTCA-CTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAG

                     *     *                        *                        
        814 TTCACAGTGTACTAACCTCACCAAAATGATTATAGTTAGGTCATAAACAATGGAAAGAAAA-CAT
        195 TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT

                                 *                            
        878 TGAGGTTTGCCAAATCGAAGAAGATT-AAGTACGTCACTAATGGGCCCCG
        260 TGAGGTTTGCCAAATCGAAGACGATTCAA-TACGTCACTAATGGGCCCCG

                             *                     *    *                    
        927 ATAGGCCCAAAATAACAGGAGTTCCAAATGAGCTAAAAACTTCATAGTGGACTAATATCACCAAA
          1 ATAGGCCCAAAATAACAAGAGTTCCAAATGAGCTAAAAAGTTCACAGTGGACTAATATCACCAAA

                                                                             
        992 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGAT
         66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGAT

                       *          *                     *                *   
       1057 TCAATACGTCAGTAATGGGCCCTGATAGGCCCAAAATAACAAGTATTCCAAATGAGCTAAAGAGT
        131 TCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAGT

               *                                  *                      
       1122 TCATAGTGGACTAATCTCACCAAAATGATTATAGTTAGACCATAAACAATGGAAAGAAAAG
        196 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG


Statistics
Matches: 796,  Mismatches: 69, Indels: 16
        0.90            0.08        0.02

Matches are distributed among these distances:
 306    2  0.00
 307  277  0.35
 308  200  0.25
 309  245  0.31
 310   35  0.04
 311   37  0.05

ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22


Consensus pattern (308 bp):   
ATAGGCCCAAAATAACAAGAGTTCCAAATGAGCTAAAAAGTTCACAGTGGACTAATATCACCAAA
ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGAT
TCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAAGT
TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT
GAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCG

Found at i:1095 original size:461 final size:463

Alignment explanation


    Indices: 1--1182  Score: 1906
    Period size: 461  Copynumber: 2.6  Consensus size: 463

                                                   *                         
          1 ATAGGCCCAAAATAACAAGTGTTCCAAATTAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAA
          1 ATAGGCCCAAAATAACAAGTGTTCCAAATTAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA

                            *                                                
         66 ATGAATTATAGTTAGACCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACG
         66 ATG-ATTATAGTTAG-GCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACG

                                               *          *        *         
        131 ATTCAATACGTCACTAATGGGCCCCGATAGGCCCAGAATAACAAGTGTTCCAAATTAGCTAAAAA
        129 ATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAA

                                                              *              
        196 GTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAGTGGAAAGAAAAGCA
        194 GTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA

                                          *                                  
        261 TTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAA
        259 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAA

                         *                           *                      *
        326 CAAGTATTCCAAAGTGAGCTAAAAAGTTCACAGTGGACTAATCTAAACAAAATGATTATAGGTAT
        324 CAAGTATTCCAAACTGAGCTAAAAAGTTCACAGTGGACTAACCTAAACAAAATGATTATAGGTAG

                                                   *                         
        391 GCCATAAACAATGGAAACAAAAGCATTGAGGCTTGCCAATTCGAAGAAGATTCAATACGTCACTA
        389 GCCATAAACAATGGAAACAAAAGCATTGAGGCTTGCCAAATCGAAGAAGATTCAATACGTCACTA

                      
        456 ATGGGCCCCA
        454 ATGGGCCCCA

                                                                             
        466 ATAGGCCCAAAATAACAAGTGTTCCAAATTAGCTAAAAAGC-TCACAGTGGACTAATCTCACCAA
          1 ATAGGCCCAAAATAACAAGTGTTCCAAATTAGCTAAAAA-CTTCACAGTGGACTAATCTCACCAA

                                                                             
        530 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA
         65 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGA

                                            *            *                   
        595 TTCAATACGTCACTAATGGGCCCCGATAGGCCAAAAATAACAAGTTTTCCAAATGAGCTAAAAAG
        130 TTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAAG

                    *  *    *          *                                   * 
        660 TTCACAGTAGAGTAATATCACCAAAATTATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCGT
        195 TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT

                                      *       *  *              * *          
        725 TGAGGTTTGCCAAATCGAAGACGATTTAAAACG-GATTTAATGGGCCCCGATTGTCCCAAAATAA
        260 TGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCA-CTAATGGGCCCCGATAGGCCCAAAATAA

                 *                             *        * *              *   
        789 CAAGTGTTCC-AACTGAGCTAAAAAGTTCACAGTGTACTAACCTCACCAAAATGATTATAGTTAG
        324 CAAGTATTCCAAACTGAGCTAAAAAGTTCACAGTGGACTAACCTAAACAAAATGATTATAGGTAG

             *               *             *                                 
        853 GTCATAAACAATGGAAAGAAAA-CATTGAGGTTTGCCAAATCGAAGAAGATT-AAGTACGTCACT
        389 GCCATAAACAATGGAAACAAAAGCATTGAGGCTTGCCAAATCGAAGAAGATTCAA-TACGTCACT

                      *
        916 AATGGGCCCCG
        453 AATGGGCCCCA

                             * *         *              *           *        
        927 ATAGGCCCAAAATAACAGGAGTTCCAAATGAGCTAAAAACTTCATAGTGGACTAATATCACCAAA
          1 ATAGGCCCAAAATAACAAGTGTTCCAAATTAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA

                                                                             
        992 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGAT
         66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGAT

                       *          *                                      *   
       1057 TCAATACGTCAGTAATGGGCCCTGATAGGCCCAAAATAACAAGTATTCCAAATGAGCTAAAGAGT
        131 TCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAAGT

               *                                  *                      
       1122 TCATAGTGGACTAATCTCACCAAAATGATTATAGTTAGACCATAAACAATGGAAAGAAAAG
        196 TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG


Statistics
Matches: 666,  Mismatches: 47, Indels: 12
        0.92            0.06        0.02

Matches are distributed among these distances:
 460    3  0.00
 461  284  0.43
 462   68  0.10
 463  234  0.35
 464   11  0.02
 465   66  0.10

ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22


Consensus pattern (463 bp):   
ATAGGCCCAAAATAACAAGTGTTCCAAATTAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGAT
TCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAAGT
TCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT
GAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACA
AGTATTCCAAACTGAGCTAAAAAGTTCACAGTGGACTAACCTAAACAAAATGATTATAGGTAGGC
CATAAACAATGGAAACAAAAGCATTGAGGCTTGCCAAATCGAAGAAGATTCAATACGTCACTAAT
GGGCCCCA
Done.