Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016868.1 Corchorus olitorius cultivar O-4 contig16901, 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: 5413
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29


Found at i:401 original size:28 final size:28

Alignment explanation


    Indices: 369--493  Score: 153
    Period size: 28  Copynumber: 4.5  Consensus size: 28

        359 GCACTTGAAG

                          * *   *  *    
        369 TGACCAAAATGCCCCTAGATGTGTAAAA
          1 TGACCAAAATGCCCTTGGATATGCAAAA

                                        
        397 TGACCAAAATGCCCTTGGATATGCAAAA
          1 TGACCAAAATGCCCTTGGATATGCAAAA

                                   *    
        425 TGACCAAAATGCCCTTGGATATGGAAAA
          1 TGACCAAAATGCCCTTGGATATGCAAAA

                     **        *       *
        453 TGACCAAAACACCCTTGGACATGC-AAG
          1 TGACCAAAATGCCCTTGGATATGCAAAA

                  *       
        480 TGACCAGAATGCCC
          1 TGACCAAAATGCCC

        494 CCTTAAGTGA


Statistics
Matches: 84,  Mismatches: 13, Indels: 1
        0.86            0.13        0.01

Matches are distributed among these distances:
  27   13  0.15
  28   71  0.85

ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19


Consensus pattern (28 bp):   
TGACCAAAATGCCCTTGGATATGCAAAA

Found at i:848 original size:48 final size:48

Alignment explanation


    Indices: 796--893  Score: 169
    Period size: 48  Copynumber: 2.0  Consensus size: 48

        786 AAGATCATGG

                  *                                         
        796 ATATTGTGCACAACATGTTTCAAGCACCAAGGAGTTGCCAAAGATGCC
          1 ATATTGCGCACAACATGTTTCAAGCACCAAGGAGTTGCCAAAGATGCC

                                          **                
        844 ATATTGCGCACAACATGTTTCAAGCACCAATTAGTTGCCAAAGATGCC
          1 ATATTGCGCACAACATGTTTCAAGCACCAAGGAGTTGCCAAAGATGCC

              
        892 AT
          1 AT

        894 TTGATCCATT


Statistics
Matches: 47,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  48   47  1.00

ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24


Consensus pattern (48 bp):   
ATATTGCGCACAACATGTTTCAAGCACCAAGGAGTTGCCAAAGATGCC

Found at i:4954 original size:40 final size:40

Alignment explanation


    Indices: 4911--5278  Score: 479
    Period size: 40  Copynumber: 9.2  Consensus size: 40

       4901 AGGAATAGGA

                          *  *                  *   *
       4911 ACAACACC-TCCTGATGAGGAAGGGCAAACTGGGAACTTAA
          1 ACAACACCTTCC-GGTGGGGAAGGGCAAACTGGGAATTTAG

                   *   *      *  *          *        
       4951 ACAACACTTTCTGGTGGGAAAAGGCAAACTTGAGAATTTAG
          1 ACAACACCTTCCGGTGGGGAAGGGCAAAC-TGGGAATTTAG

                  *                        *        
       4992 ACAACAACTTCCGGTGGGGAAGGGCAAACTGAGAATTTAG
          1 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTAG

                                      *             
       5032 ACAACACCTTCCGGTGGGGAAGGGCAGACTGGGAATTTAG
          1 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTAG

                                                   *
       5072 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTAA
          1 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTAG

                        *               *           *
       5112 ACAACACCTTCCAGTGGGGAAGGGCAAAATGGGTAA-TTAA
          1 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGG-AATTTAG

                                             *    * 
       5152 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTTG
          1 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTAG

                                          *         
       5192 ACAACACCTTCCGGTGGGGAAGGGCAAACTAGGAATTTAG
          1 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTAG

                       * *              * *     *   
       5232 ACAACACCTTCTGATGGGGAAGGGCAAATTTGGAATCTAG
          1 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTAG

                   
       5272 ACAACAC
          1 ACAACAC

       5279 TGATCCTTCG


Statistics
Matches: 290,  Mismatches: 34, Indels: 8
        0.87            0.10        0.02

Matches are distributed among these distances:
  39    1  0.00
  40  253  0.87
  41   36  0.12

ACGTcount: A:0.33, C:0.19, G:0.29, T:0.19


Consensus pattern (40 bp):   
ACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTAG

Done.