Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011856.1 Corchorus olitorius cultivar O-4 contig11889, 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: 2356
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29


Found at i:873 original size:154 final size:154

Alignment explanation


    Indices: 595--1562  Score: 1548
    Period size: 154  Copynumber: 6.3  Consensus size: 154

        585 ATTCGTATCA

                         *                                      *            
        595 GAACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTG
          1 GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG

                       *                                *      *   *         
        660 GACTAATCTCATCAAAATGATTATAGTTAGGCCATAAACAACT-TAAAGAATAGCTTTGAGGTTT
         66 GACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCATTGAGGTTT

                   *                 
        724 GCCAAATTGAAGACGATTCAAAACG
        130 GCCAAATCGAAGACGATTCAAAACG

                                                                             
        749 GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
          1 GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG

                                          *                                  
        814 GACTAATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTG
         66 GACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTG

                             *      
        879 CCAAATCGAAGACGATTAAAAACG
        131 CCAAATCGAAGACGATTCAAAACG

            **           *  *                                   *            
        903 TCACTAATGGGCCGCGGTAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTG
          1 GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG

                            *          *                                     
        968 GACTAATCTCACCAAATTGATTATAGTAAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTG
         66 GACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTG

                                  * 
       1033 CCAAATCGAAGACGATTCAAAATG
        131 CCAAATCGAAGACGATTCAAAACG

            **           *                                      *            
       1057 TCACTAATGGGCCGCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAGAACTTCACAGTG
          1 GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG

            *          *                                      *        *     
       1122 AACTAATCTCATCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAATAGCATTGACGTTTG
         66 GACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTG

                                    
       1187 CCAAATCGAAGACGATTCAAAACG
        131 CCAAATCGAAGACGATTCAAAACG

                                                         *    *              
       1211 GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATAAGCTCAAAACTTCACAGTG
          1 GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG

                       *    *            *                                   
       1276 GACTAATCTCATCAAATTGATTATAGTTACGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTG
         66 GACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTG

                                    
       1341 CCAAATCGAAGACGATTCAAAACG
        131 CCAAATCGAAGACGATTCAAAACG

                                                                         *   
       1365 GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACTGTG
          1 GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG

                            *            *                       *           
       1430 GACTAATCTCACCAAATTGATTATAGTTACGCCATAAACAATGGAAAGAAAAGAATTGAGGTTTG
         66 GACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTG

                      *             
       1495 CCAAATCGAACACGATTCAAAACG
        131 CCAAATCGAAGACGATTCAAAACG

             *                                      *      
       1519 TCAA-TATAT-GG-CCCGATAGGCCCAAAATAACAAGTGTCCCAAAT
          1 -GAACTA-ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAAT

       1563 ATATTAAAAA


Statistics
Matches: 765,  Mismatches: 46, Indels: 7
        0.94            0.06        0.01

Matches are distributed among these distances:
 153   33  0.04
 154  728  0.95
 155    4  0.01

ACGTcount: A:0.40, C:0.20, G:0.19, T:0.22


Consensus pattern (154 bp):   
GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
GACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTG
CCAAATCGAAGACGATTCAAAACG

Found at i:1710 original size:21 final size:21

Alignment explanation


    Indices: 1684--1817  Score: 200
    Period size: 21  Copynumber: 6.4  Consensus size: 21

       1674 TGCTAGAAGT

                                  
       1684 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                  
       1705 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                *
       1726 TCATTGGAGAAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                *
       1747 TCATTGGAGAAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                *
       1768 TCATTGGAGAAGGTTCCAAGA
          1 TCATTGGAGAAGGTTCCAAGC

                           *     
       1789 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
       1810 TCATTGGA
          1 TCATTGGA

       1818 ATTGCCTAAG


Statistics
Matches: 108,  Mismatches: 4, Indels: 2
        0.95            0.04        0.02

Matches are distributed among these distances:
  20    2  0.02
  21  106  0.98

ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Done.