Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010969.1 Corchorus olitorius cultivar O-4 contig11001, 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: 2187
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.26


Found at i:429 original size:154 final size:154

Alignment explanation


    Indices: 1--1494  Score: 2137
    Period size: 154  Copynumber: 9.7  Consensus size: 154

                                                 *             *       *     
          1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAATTGATTATAGTTAGTCCATAAAAAATGG
          1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG

                         *                             *            *        
         66 AAAGAAAAGCATTAAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGACCCGATAG
         66 AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGATAG

                                     
        131 GCCCAAAATAACAAAG-GTTCCAAA
        131 GCCCAAAATAAC-AAGTGTTCCAAA

                    *       *               *        *                       
        155 TGAGCTAAGAACTTCATAGTGGACTAATCTCATCAAAATGACTA-A--TAGGCCATAAACAACT-
          1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA-TG

            *          *          *         * *         **        *     *    
        216 TAAAGAAAAGCTTTGAGGTTTGTCAAATCGAATATGATTCAAAACAGAACTAATAGGCCCTGATA
         65 GAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGATA

            *                        
        281 CGCCCAAAATAACAAGTGTTCCAAA
        130 GGCCCAAAATAACAAGTGTTCCAAA

                                        *   *              *                 
        306 TGAGCTAAAAACTTCACAGTGGACTAATGTCAACAAAATGATTATAGATAGGCCATAAACAATGG
          1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG

             *        *     *                            **                  
        371 ATAGAAAAGCCTTGAGATTTGCCAAATCGAAGACGATTCAAAATGTCACTAATGGGCCCCGATAG
         66 AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGATAG

                             *  *   
        436 GCCCAAAATAACAAGTGATCTAAA
        131 GCCCAAAATAACAAGTGTTCCAAA

                             *                   *            *              
        460 TGAGCTAAAAACTTCACGGTGGACTAATCTCACCAAATTGATTATAGTTACGCCATAAACAATGG
          1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG

                                           *           *         *           
        525 AAAGAAAAGCATTGAGGTTTGCCAAATCGAATACGATTCAAAACGG-ACTAATAGGCCCCGATAG
         66 AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGATAG

                            *       
        589 GCCCAAAAT-ACAAGTATTCCAAA
        131 GCCCAAAATAACAAGTGTTCCAAA

                *                             *                    **        
        612 TGAGATAAAAACTTCACAGTGGACTAATCTCACATAAAATGATTATAGTTAGTG-TGTAAACCAA
          1 TGAGCTAAAAACTTCACAGTGGACTAATCTCAC-CAAAATGATTATAGTTAG-GCCATAAA-CAA

                                                  *           *       *      
        676 TGGAAAGAAAAGCATTTGAGGTTTGCCAAATCGAAG-CTATTCAAAATGGGACTAATGTGCCCCG
         63 TGGAAAGAAAAGCA-TTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCG

                                        
        740 ATAGGCCCAAAAT-ACAAGTGTTCCAAA
        127 ATAGGCCCAAAATAACAAGTGTTCCAAA

                                           *                                 
        767 TGAGCTAAAAAACTTCACAGTGGACTAAAT-GCACCAAAATGATTATAGTTAGGCCATAAACAAT
          1 TGAGCT-AAAAACTTCACAGTGGACT-AATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT

                        *              *                   **                
        831 GGAAAGAAAAGCCTTGAGGTTTGCCAATTCGAAGACGATTCAAAATGTCACTAATGGGCCCCGAT
         64 GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGAT

             *                    *   
        896 AAGCCCAAAATAACAAGTGTTCTAAA
        129 AGGCCCAAAATAACAAGTGTTCCAAA

                                        *                  *                 
        922 TGAGCTAAAAACTTCACAGTGGACTAATGTCACCAAAATGATTATAGATAGGCCATAAACAATGG
          1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG

                      *                                  **                  
        987 AAAGAAAAGCCTTGAGGTTTGCCAAATCGAAGACGATTCAAAATGTCACTAATGGGCCCCGATAG
         66 AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGATAG

                    *        *      
       1052 GCCCAAAACAACAAGTGATCCAAA
        131 GCCCAAAATAACAAGTGTTCCAAA

                             *                   *            *              
       1076 TGAGCTAAAAACTTCACGGTGGACTAATCTCACCAAATTGATTATAGTTACGCCATAAACAATGG
          1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG

             *        *                *   *           *         *           
       1141 ATAGAAAAGCTTTGAGGTTTGCCAAATTGAATACGATTCAAAACGGAACTAATAGGCCCCGATAG
         66 AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGATAG

                          * *       
       1206 GCCCAAAATAACAAATATTCCAAA
        131 GCCCAAAATAACAAGTGTTCCAAA

                *                                 *            *             
       1230 TGAGATAAAAACTTCACAGTGGACTAATCTCACCAAAAAGATTATAGTTAGTCCATAAACAATGG
          1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG

                                                                  *          
       1295 AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGTGCCCCGATAG
         66 AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGATAG

              *                     
       1360 GCTCAAAATAACAAGTGTTCCAAA
        131 GCCCAAAATAACAAGTGTTCCAAA

                                                       *     * *          *  
       1384 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTTTAGTTTGTCCATAAACAACGG
          1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG

                                                          
       1449 AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGG
         66 AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGG

       1495 GTCATTGAAT


Statistics
Matches: 1197,  Mismatches: 126, Indels: 34
        0.88            0.09        0.03

Matches are distributed among these distances:
 150    3  0.00
 151  126  0.11
 152   44  0.04
 153   70  0.06
 154  826  0.69
 155  103  0.09
 156   22  0.02
 157    3  0.00

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


Consensus pattern (154 bp):   
TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG
AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAATGGGCCCCGATAG
GCCCAAAATAACAAGTGTTCCAAA

Found at i:1711 original size:21 final size:21

Alignment explanation


    Indices: 1687--1736  Score: 73
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       1677 TGCTAGAAGT

                                 
       1687 TCATTGGAGAAGGTTCCAAAA
          1 TCATTGGAGAAGGTTCCAAAA

                           *   **
       1708 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAAA

                    
       1729 TCATTGGA
          1 TCATTGGA

       1737 ATTGCCTAAG


Statistics
Matches: 26,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   26  1.00

ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAAA
Done.