Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011641.1 Corchorus olitorius cultivar O-4 contig11674, 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, 702

Length: 1170
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22


Found at i:296 original size:154 final size:154

Alignment explanation


    Indices: 1--1062  Score: 1651
    Period size: 154  Copynumber: 6.9  Consensus size: 154

                            *  * *          *                           *    
          1 AAATCGAAAGACGATTTAAAATGTCACTAATGTGCCCCGATAGGCCCAAAAT-ACAAGTGATCCA
          1 AAATCG-AAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCA

                                                                             
         65 AATGAAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
         65 AATG-AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA

             *                        
        130 TTGAAAGAAAAGCATTGAGGTTTGCC
        129 TGGAAAGAAAAGCATTGAGGTTTGCC

                *                                                         *  
        156 AAATAGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCTAA
          1 AAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA

            *                *             * *              *                
        221 TTGAGCTAAAAACTTCAAAGTGGACTAATCTAAACAAAATGATTATAGGTAGGCCATAAACAATG
         66 ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG

                **            *     
        286 GAAACCAAAGCATTGAGGCTTGCC
        131 GAAAGAAAAGCATTGAGGTTTGCC

            * *       *            *                 *                       
        310 GATTCGAAGAAGATTCAATACGTTACTAATGGGCCCCGATAAGCCCAAAATAACAAGTGTTCCAA
          1 AAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA

                               *                    *                        
        375 ATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATCATTATAGTTAGGCCATAAACAATG
         66 ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG

                                   *
        440 GAAAGAAAAGCATTGAGGTTTGCT
        131 GAAAGAAAAGCATTGAGGTTTGCC

                             *                                 *      *      
        464 AAATCGAAGACGATTCAGTACGTCACTAATGGGCCCCGATAGGCCCAAAATTACAAGTATTCCAA
          1 AAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA

                                               *    *           *      *    *
        529 ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCGAAATTATTATAGTTAGACCATAACCAATT
         66 ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG

                                    
        594 GAAAGAAAAGCATTGAGGTTTGCC
        131 GAAAGAAAAGCATTGAGGTTTGCC

                              *                  *                           
        618 AAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCAATAGGCCCAAAATAACAAGTGTTCCAA
          1 AAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA

            *           *           *                            *           
        683 CTGAGCTAAAAAGTTCACAGTGGATTAATCTCACCAAAATGATTATAGTTAGGTCATAAA-AATG
         66 ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG

                      *             
        747 GAAAGAAAAGAATTGAGGTTTGCC
        131 GAAAGAAAAGCATTGAGGTTTGCC

                              *   **       *                               * 
        771 AAATCGAAGACGATTCAAAACGGAACTAATGAGCCCCGATAGGCCCAAAATAACAAGTGTTCCGA
          1 AAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA

                          *                                                 *
        836 ATGAGCTAAAAACTACACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATT
         66 ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG

              *                    *
        901 GATAGAAAAGCATTGAGGTTTGCT
        131 GAAAGAAAAGCATTGAGGTTTGCC

                                                                             
        925 AAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA
          1 AAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA

                                   *                                         
        990 ATGAGCTAAAAACTTCACAGTGGCCTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG
         66 ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG

                    
       1055 GAAAGAAA
        131 GAAAGAAA

       1063 TAATGGGCCC


Statistics
Matches: 818,  Mismatches: 87, Indels: 5
        0.90            0.10        0.01

Matches are distributed among these distances:
 153  141  0.17
 154  659  0.81
 155   18  0.02

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


Consensus pattern (154 bp):   
AAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA
ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG
GAAAGAAAAGCATTGAGGTTTGCC

Found at i:1148 original size:112 final size:112

Alignment explanation


    Indices: 951--1169  Score: 420
    Period size: 112  Copynumber: 2.0  Consensus size: 112

        941 AATACGTCAC

                                                                *         *  
        951 TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGCCT
          1 TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACT

                                                           
       1016 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
         66 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA

                                                                             
       1063 TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACT
          1 TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACT

                                                      
       1128 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
         66 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA

       1170 T


Statistics
Matches: 105,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 112  105  1.00

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


Consensus pattern (112 bp):   
TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACT
AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
Done.