Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011602.1 Corchorus olitorius cultivar O-4 contig11635, 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: 1686
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.21


Found at i:320 original size:154 final size:154

Alignment explanation


    Indices: 1--1686  Score: 2391
    Period size: 154  Copynumber: 11.0  Consensus size: 154

                                 * *   *    *                             ***
          1 TGAGCTAAAAACTTCACAGTGAATTAACCTCATCAAAATGATTATAGTTAGGCCATAAACAACAT
          1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG

                 *    *          **                      **      *   *  *    
         66 AAAGACAA-CTTTGAGGTTT-ATAAATCGAAGACGATTCAAAACGTCACTAATTGGCACCTATAG
         66 AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAG

               *                    
        129 GCCAAAAATAACAAGTGTTCCAAA
        131 GCCCAAAATAACAAGTGTTCCAAA

                           *                                   *       *     
        153 TGAGCTAAAAACTTCGCAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAAAAAATGG
          1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG

                      *              *                                       
        218 AAAGAAAAGCTTTGAGGTTTGCCACTATCGAAGACGATTC-AAACGGAACTAATGGGCCCCGATA
         66 AAAGAAAAGCATTGAGGTTTGCCA-AATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATA

             *                       
        282 GTCCCAAAATAACAAGTGTTCCAAA
        130 GGCCCAAAATAACAAGTGTTCCAAA

                    *                       *                             *  
        307 TGAGCTAAGAACTTCACAGTGGACTAATCTCATCAAAATGATTATAGTTAGGCCATAAACAACGG
          1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG

                                   *                                  **     
        372 AAAGAAAAGCATTGAGGTTTGCCCAATCGAAGACGATTCAAAACGGAACTAATGGGCCATGATAG
         66 AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAG

             * *                    
        437 GGCGAAAATAACAAGTGTTCCAAA
        131 GCCCAAAATAACAAGTGTTCCAAA

             *              *                *                               
        461 TAAGCTAAAAACTTCAAAGTGGACTAATCTCACAAAAATGATTATAGTTAGGCCATAAACAATGG
          1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG

                                  *                     *              *     
        526 AAAGAAAAGCATTGAGGTTTGCGAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCTGATAG
         66 AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAG

             * *         *          
        591 GGCGAAAATAACATGTGTTCCAAA
        131 GCCCAAAATAACAAGTGTTCCAAA

             *                                                 *             
        615 TAAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCATAATA-AATG
          1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAA-ACAATG

                       *          *                   *   **             *   
        679 GAAAGAAAAGCTTTGAGGTTTGTCAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCTATA
         65 GAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATA

                                     
        744 GGCCCAAAATAACAAGTGTTCCAAA
        130 GGCCCAAAATAACAAGTGTTCCAAA

                                *      *                  *                  
        769 TGAGCTAAAAACTTCACAGTAGACTAAACTCACCAAAATGATTATAATTAGGCC--AAACAATGG
          1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG

                                 **         **               *     *         
        832 AAAGAAAAGCATTGAGGTTTGAAAAATCGAAGGGGATTCAAAACGGAACAAATGGCCCCCGATAG
         66 AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAG

                    *               
        897 GCCCAAAACAACAAGTGTTCCAAA
        131 GCCCAAAATAACAAGTGTTCCAAA

                                   *                                        *
        921 TGAGCTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGA
          1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG

                      *       *           * **   *       **       **      *  
        986 AAAGAAAAGCTTTGAGGTCTGCCAAATCGATGGGGATCCAAAACGTCACTAATGACCCCCGAAAG
         66 AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAG

                  *                *
       1051 GCCCAAGATAACAAGTGTTCCAAC
        131 GCCCAAAATAACAAGTGTTCCAAA

                *            *                                               
       1075 TGAGATAAAAACTTCACGGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG
          1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG

                                        *         *       **                 
       1140 AAAGAAAAGCAATT-AGGTTTGCCAAATAGAAGACGATCCAAAACGTCACTAAT-GGCCCCGATA
         66 AAAGAAAAGC-ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATA

                                     
       1203 GGCCCAAAATAACAAGTGTTCCAAA
        130 GGCCCAAAATAACAAGTGTTCCAAA

             *                  *                                            
       1228 TAAGCTAAAAACTTCACAGTAGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG
          1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG

                       *          *    *         *       ***          *      
       1293 AAAGAAAAGCAATGAGGTTTGCTAAATAGAAGACGATCCAAAACGTCTCTAATGGGCCTCGATAG
         66 AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAG

                                    
       1358 GCCCAAAATAACAAGTGTTCCAAA
        131 GCCCAAAATAACAAGTGTTCCAAA

             *                  *                                            
       1382 TAAGCTAAAAACTTCACAGTAGACTAATCTCACCAAAAATGATTATAGTTAGGCCATAAACAATG
          1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACC-AAAATGATTATAGTTAGGCCATAAACAATG

                    *             *                               *          
       1447 GAAAG-AATGCATTGAGGTTTGTCAAATCGAAGACGATTCAAAACGGAACTAATCGGCCCCGATA
         65 GAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATA

              *                      
       1511 GGGCCAAAATAACAAGTGTTCCAAA
        130 GGCCCAAAATAACAAGTGTTCCAAA

               *                                     *                       
       1536 TGAACTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAATATAGTTAGGCCATAAACAATGG
          1 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG

                                                                 *           
       1601 AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATCGGCCCCGATAG
         66 AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAG

                                 
       1666 GCCCAAAATAACAAGTGTTCC
        131 GCCCAAAATAACAAGTGTTCC


Statistics
Matches: 1382,  Mismatches: 139, Indels: 24
        0.89            0.09        0.02

Matches are distributed among these distances:
 151    1  0.00
 152  198  0.14
 153  197  0.14
 154  934  0.68
 155   52  0.04

ACGTcount: A:0.41, C:0.19, G:0.18, T:0.21


Consensus pattern (154 bp):   
TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG
AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAG
GCCCAAAATAACAAGTGTTCCAAA

Done.