Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010504.1 Corchorus olitorius cultivar O-4 contig10536, 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, 666

Length: 1110
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30


Found at i:870 original size:336 final size:331

Alignment explanation


    Indices: 5--1110  Score: 1464
    Period size: 336  Copynumber: 3.3  Consensus size: 331

          1 AAAT

                        * *                     *                            
          5 TGAGCTGGGGCCTCGGAACGCGTTTTTAGCTAAAAAGCGTGAT-G---GTACACGATTTCGGCTA
          1 TGAGCTGGGGCCCCAGAACGCGTTTTTAGCTAAAAACCGTGATGGTTAGTACACGATTTCGGCTA

               *                                        *                    
         66 AAAATTTGC-AAAAAATGACCCAAAAAATTTTTCCTCAATTTTTAACCACAATACTTAAAAAAAT
         66 AAATTTTGCAAAAAAATGACCCAAAAAATTTTTCCTCAATTTTTGACCACAATACTTAAAAAAAT

                  *     **                                    **   *         
        130 ATATAACTCAACATCAAAAAGATTGAAGGGCTTTTCAAGCATCTAATATCACTTTACCTATTTTT
        131 ATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCAAGCATCTAATATCGTTTTTCC-ATTTTT

                  *        *      *    *  *    * *                   **   *  
        195 TCTGAACTAATTTCTGATTAAATCGAAACATGATTTAGATGCTCGTAAAAACAAATTATTAAATC
        195 TCTGAATTAATTTCTAATTAAAACGAACCAAGATTCAAATGCTCGTAAAAACAAATTCCTAAGTC

               *     *               *      *  *   *       *                 
        260 CAATGTAGCCGAGATTCGGTTAGATGAATATAGATATTTGAAGGAGTCTGGGCGCC-AAAATCAA
        260 CAACGTAGCTGAGATTCGGTTAGATAAATATATATGTTTCAAGGAGTTTGGGCGCCAAAAATCAA

                   
        324 GCAAAAC
        325 GCAAAAC

                  **    **    *                                         **   
        331 TGAG-TCAGGCCATAGAATGC-TTTCTTAG-TCAAAAACCGTGATGGTTAGTACACGATTAAGGC
          1 TGAGCTGGGGCCCCAGAACGCGTTT-TTAGCT-AAAAACCGTGATGGTTAGTACACGATTTCGGC

                                      *                         *   *  * *   
        393 TAAAATTTTGCAAAAAAAATGACCCAGAAAATTTTTCCTCAATTTTTGACCATAATTCTCATAAA
         64 TAAAATTTTGC-AAAAAAATGACCCAAAAAATTTTTCCTCAATTTTTGACCACAATACTTAAAAA

                           *                                                 
        458 AATATATGCAATTCAGCGCCAAAAAGATTGAAGGGCTTTTCAAGCATCTAATATCGTTTTTCCAT
        128 AATATAT--AATTCAACGCCAAAAAGATTGAAGGGCTTTTCAAGCATCTAATATCGTTTTTCCAT

                                                                             
        523 TTTTTCTGAATTAATTTCTAATTAAAACGAACCAAGATTCAAATGCTCGTAAAAACAAATTCCTA
        191 TTTTTCTGAATTAATTTCTAATTAAAACGAACCAAGATTCAAATGCTCGTAAAAACAAATTCCTA

                                *                        *                   
        588 AGTCCAACGTAGCTGAGATTGGGTTAGATAAATATATATGTTTCAGGGAGTTTGGGCGCCAAAAA
        256 AGTCCAACGTAGCTGAGATTCGGTTAGATAAATATATATGTTTCAAGGAGTTTGGGCGCCAAAAA

                      *
        653 TCAAGCAAAAT
        321 TCAAGCAAAAC

                                                               *             
        664 TGAGCTGGGGCCCCAGAACGCGTTTTTAGCTAAAAACCGTGATGGTTAGTAAACGATTTCGGCTA
          1 TGAGCTGGGGCCCCAGAACGCGTTTTTAGCTAAAAACCGTGATGGTTAGTACACGATTTCGGCTA

                                           *                  *              
        729 AAATTTTGCAAAAAAAAATGACCCGAAAAATTTTTTTCCTCAATTTTTTGGCCACAATACTTAAA
         66 AAATTTTGC--AAAAAAATGACCC-AAAAA-ATTTTTCCTCAA-TTTTTGACCACAATACTTAAA

                                                     *    *                  
        794 AAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCGAGCAACTAATATCGTTTTTCCAT
        126 AAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCAAGCATCTAATATCGTTTTTCCAT

                *                                 *                          
        859 TTTTCCTGAATTAATTTCTAATTAAAACGAACCAAGATCCAAATGCTCGTAAAAACAAA-TCCTT
        191 TTTTTCTGAATTAATTTCTAATTAAAACGAACCAAGATTCAAATGCTCGTAAAAACAAATTCC-T

                                  *                          *               
        923 AAGTCCAACGT-GTCTGAGATTTGGTTA-ATTAAATATATATGTTTCAACGAGTTTGGGCGCCAA
        255 AAGTCCAACGTAG-CTGAGATTCGGTTAGA-TAAATATATATGTTTCAAGGAGTTTGGGCGCCAA

                          
        986 AAATCAAGCAAAAC
        318 AAATCAAGCAAAAC

             *           **                                 *                
       1000 TAAGCTGGGGCCCTGGAACGCGTTTTTAGCTAAAAACCGTGATGGTTATTACACGATTTCGGCTA
          1 TGAGCTGGGGCCCCAGAACGCGTTTTTAGCTAAAAACCGTGATGGTTAGTACACGATTTCGGCTA

                             *  *                          
       1065 AAATTTTG-AAAAAAATTACTCAAAAAATTTTTCCTCAATTTTTGAC
         66 AAATTTTGCAAAAAAATGACCCAAAAAATTTTTCCTCAATTTTTGAC


Statistics
Matches: 683,  Mismatches: 76, Indels: 38
        0.86            0.10        0.05

Matches are distributed among these distances:
 324    4  0.01
 325   25  0.04
 326    5  0.01
 329   23  0.03
 330    7  0.01
 331   64  0.09
 332  113  0.17
 333   76  0.11
 334   55  0.08
 335   23  0.03
 336  252  0.37
 337   11  0.02
 338   25  0.04

ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30


Consensus pattern (331 bp):   
TGAGCTGGGGCCCCAGAACGCGTTTTTAGCTAAAAACCGTGATGGTTAGTACACGATTTCGGCTA
AAATTTTGCAAAAAAATGACCCAAAAAATTTTTCCTCAATTTTTGACCACAATACTTAAAAAAAT
ATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCAAGCATCTAATATCGTTTTTCCATTTTTT
CTGAATTAATTTCTAATTAAAACGAACCAAGATTCAAATGCTCGTAAAAACAAATTCCTAAGTCC
AACGTAGCTGAGATTCGGTTAGATAAATATATATGTTTCAAGGAGTTTGGGCGCCAAAAATCAAG
CAAAAC
Done.