Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016337.1 Corchorus capsularis cultivar CVL-1 contig16358, 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: 3531
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34


Found at i:531 original size:35 final size:35

Alignment explanation


    Indices: 453--1880  Score: 1582
    Period size: 35  Copynumber: 40.9  Consensus size: 35

        443 CTGTGCGGTC

                  *                            
        453 TTTCAACAAGTTTTCAGAGGTCAGAG-T--TCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

                  *        *                   
        485 TTTCAAAAAGTTTTCCGAGGTCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

              * *         *        *           
        520 TTCCCAGAAGTTTTAAGAGGTCAAAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

              *    *     *        *            
        555 TTCCAAGCAGTTTACAGAGGTCCGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

              *    *                  *        
        590 TTCCAAGCAGTTTTCAGAGGTCAGAGGTGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

              *                                
        625 TTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

             **                *               
        660 TGCCAAGAAGTTTTCAGAGATCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

              *                      *  *      
        695 TTCCAAGAAGTTTTCAGAGGTCAGAATTAATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

              *           *                    
        730 TTCCAAGAAGTTTTAAGAGGTCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

             *                                 
        765 TATCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

                  *                            
        800 TTTCAAAAAGTTTTCAGAGGTCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

             *           *                     
        835 TATCAAGAAGTTTCCAGAGGTCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

                                                 
        870 TATT-AAGAAG-TTTCAAGAGGTCAGAGTTGATCTCA
          1 T-TTCAAGAAGTTTTC-AGAGGTCAGAGTTGATCTCA

              *          *      *               
        905 TTCCAAGAAGTTTCCA-ATGATCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATCTCA

                *                               
        940 TTTTAAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
          1 -TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

             *                                 
        976 TATCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

             *              *      *           
       1011 TATCAAGAAGTTTTCAAAGGTCAAAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

                            *                  
       1046 TTTCAAGAAGTTTTCAAAGGTCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

                            *                  
       1081 TTTCAAGAAGTTTTCAAAGGTCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

                      *                          
       1116 -TTCAGAGGATGTTTTCAGAGGTCAGAGTTGATCTCA
          1 TTTCA-A-GAAGTTTTCAGAGGTCAGAGTTGATCTCA

            * *             *                  
       1152 ATCCAAGAAGTTTTCAAAGGTC--AG-TGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

                               *               
       1184 TTTCAAGAAGTTTTCAGAGTTCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

                                             * 
       1219 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTTA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

              *                                
       1254 TTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

                  *        *                   
       1289 TTTCAACAAGTTTT-GGAGGTCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

             *           *    *            *   
       1323 TATCAAGAAGTTTCCAGATGTCAGAGTTGATTTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

                                                 
       1358 TATT-AAGAAG-TTTCAAGAGGTCAGAGTTGATCTCA
          1 T-TTCAAGAAGTTTTC-AGAGGTCAGAGTTGATCTCA

              *          *     **               
       1393 TTCCAAGAAGTTTCCA-ATCATCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATCTCA

                *                   *           
       1428 TTTTAAAGAAGTTTTCAGAGGTCATAGTTGATCTCA
          1 -TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

                                               
       1464 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

              *                                
       1499 TTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

              *                *               
       1534 TTCCAAGAAGTTTTCAGAGATCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

                    *            *             
       1569 TTTCAAGACGTTTTCAGAGGTAAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

              * *          *   **           **  
       1604 TTCCTAGAAG-TTTCCGATTATCAGAGTTGATGGCA
          1 TTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATCTCA

                    *             *            *  
       1639 TTTTC-AGTA-TTTTCCA-ACGATCAGAGTTGATCGCA
          1 -TTTCAAGAAGTTTT-CAGA-GGTCAGAGTTGATCTCA

                    *      *      *            *  
       1674 TTTTC-AGTA-TTCTCCA-ACGATCAGAGTTGATCGCA
          1 -TTTCAAGAAGTT-TTCAGA-GGTCAGAGTTGATCTCA

                    *     *      *            *  
       1709 TTTTC-AGTAGTTTCCA-ACGATCAGAGTTGATCGCA
          1 -TTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATCTCA

                *  *     *      *            *  
       1744 TTTCCAGTAGTTTCCA-ACGATCAGAGTTGATCGCA
          1 TTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATCTCA

                    *     *      *            *  
       1779 TTTTC-AGTAGTTTCCA-ACGATCAGAGTTGATCGCA
          1 -TTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATCTCA

                    *     *      *               
       1814 TTTCCAA-TAGTTTCCA-ACGATCAGAGTTGATCTCA
          1 TTT-CAAGAAGTTTTCAGA-GGTCAGAGTTGATCTCA

                      *    *    *            
       1849 TTTCAAGAA-ATTTCCGATGATCAGAGTTGATC
          1 TTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATC

       1881 CAGAGGAGTT


Statistics
Matches: 1243,  Mismatches: 117, Indels: 69
        0.87            0.08        0.05

Matches are distributed among these distances:
  32   50  0.04
  33    3  0.00
  34   65  0.05
  35  1016  0.82
  36  104  0.08
  37    5  0.00

ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33


Consensus pattern (35 bp):   
TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

Found at i:3187 original size:87 final size:87

Alignment explanation


    Indices: 3083--3311  Score: 413
    Period size: 87  Copynumber: 2.6  Consensus size: 87

       3073 ATTGTTAAAA

                                                                             
       3083 TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAAT
          1 TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAAT

                    *             
       3148 AAATAAATTATAAAGATTGAAC
         66 AAATAAATCATAAAGATTGAAC

                                                                             
       3170 TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAAT
          1 TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAAT

                                **
       3235 AAATAAATCATAAAGATTGAGT
         66 AAATAAATCATAAAGATTGAAC

                  *                                         *      
       3257 TAATAAAGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAGATAT
          1 TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATAT

       3312 AGAAAAGAAA


Statistics
Matches: 137,  Mismatches: 5, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  87  137  1.00

ACGTcount: A:0.42, C:0.06, G:0.17, T:0.34


Consensus pattern (87 bp):   
TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAAT
AAATAAATCATAAAGATTGAAC
Done.