Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016832.1 Corchorus olitorius cultivar O-4 contig16865, 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: 5869
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30


Found at i:4761 original size:58 final size:58

Alignment explanation


    Indices: 4614--5232  Score: 932
    Period size: 58  Copynumber: 10.8  Consensus size: 58

       4604 TTTAAATCAA

                               *                  *        *          
       4614 ATCATCTTGTTTTAAAATCATGTTCGAGGTCTCTGTTAAAGAGTTTTTAATTC--AA-
          1 ATCATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT

                               *                                      
       4669 ATCATCTTGTTTTAAAATCATGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT
          1 ATCATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT

               *               *                                      
       4727 ATCTTCTTGTTTTAAAATCATGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT
          1 ATCATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT

               *                                                      
       4785 ATCTTCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT
          1 ATCATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT

                                                                      
       4843 ATCATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTC---AT
          1 ATCATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT

                                                                      
       4898 ATCATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTC--AA-
          1 ATCATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT

                     *         *                                      
       4953 ATCATCTTGGTTTAAAATCTTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT
          1 ATCATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT

                        *                                      *      *
       5011 ATCATCTTGTTTCAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTTCAACTCAAAAC
          1 ATCATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAG-TTTTCAATTCAAAAT

            * *         *  *           *                              
       5070 CTTATCTTGTTTCAAGATCCTGTTCGACGTCTCTGTTAGAGAGTTTTCAATTCAAAAT
          1 ATCATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT

               *                                             *   **   
       5128 ATCTTCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAGTTCGCAAT
          1 ATCATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT

            * *         *                   *              
       5186 CTTATCTTGTTTCAAAATCCTGTTCGAGGTCTTTGTTAAGAGAGTTT
          1 ATCATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTT-AGAGAGTTT

       5233 ATATTTCAGA


Statistics
Matches: 523,  Mismatches: 32, Indels: 14
        0.92            0.06        0.02

Matches are distributed among these distances:
  55  157  0.30
  56    1  0.00
  57    4  0.01
  58  300  0.57
  59   61  0.12

ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42


Consensus pattern (58 bp):   
ATCATCTTGTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAAT

Found at i:5530 original size:29 final size:30

Alignment explanation


    Indices: 5491--5630  Score: 135
    Period size: 29  Copynumber: 4.8  Consensus size: 30

       5481 TATTTTGGTC

                         * *            * 
       5491 ATCCAAGGGCATTATAGTCATTTCTACATA
          1 ATCCAAGGGCATTTTGGTCATTTCTACACA

                 *                 *     *
       5521 ATCC-GGGGCATTTTGGTCATTTTTAC-CC
          1 ATCCAAGGGCATTTTGGTCATTTCTACACA

                         *         * *    
       5549 ATCCAAGGGCATTATGGTCATTTTTGCAC-
          1 ATCCAAGGGCATTTTGGTCATTTCTACACA

                  *         *         *    
       5578 ATCCAGGGGGCATTTTAGTCATTTCTGCACA
          1 ATCCA-AGGGCATTTTGGTCATTTCTACACA

                                   
       5609 ATCCAA-GGCATTTTGGTCATTT
          1 ATCCAAGGGCATTTTGGTCATTT

       5631 TGGTTTTATT


Statistics
Matches: 91,  Mismatches: 15, Indels: 9
        0.79            0.13        0.08

Matches are distributed among these distances:
  28    4  0.04
  29   57  0.63
  30   25  0.27
  31    5  0.05

ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36


Consensus pattern (30 bp):   
ATCCAAGGGCATTTTGGTCATTTCTACACA

Found at i:5619 original size:59 final size:58

Alignment explanation


    Indices: 5491--5631  Score: 160
    Period size: 59  Copynumber: 2.4  Consensus size: 58

       5481 TATTTTGGTC

                           *       *                    *       *    *
       5491 ATCCAAGGGCATTATAGTCATTTCTACATAATCCGGGGCATTTTGGTCATTTTTACCC
          1 ATCCAAGGGCATTATGGTCATTTTTACATAATCCGGGGCATTTTAGTCATTTCTACCA

                                     *   *                          *    
       5549 ATCCAAGGGCATTATGGTCATTTTTGCA-CATCCAGGGGGCATTTTAGTCATTTCTGCACA
          1 ATCCAAGGGCATTATGGTCATTTTTACATAATCC--GGGGCATTTTAGTCATTTCTAC-CA

                         *          
       5609 ATCCAA-GGCATTTTGGTCATTTT
          1 ATCCAAGGGCATTATGGTCATTTT

       5632 GGTTTTATTT


Statistics
Matches: 71,  Mismatches: 9, Indels: 5
        0.84            0.11        0.06

Matches are distributed among these distances:
  57    4  0.06
  58   25  0.35
  59   35  0.49
  60    7  0.10

ACGTcount: A:0.23, C:0.21, G:0.19, T:0.36


Consensus pattern (58 bp):   
ATCCAAGGGCATTATGGTCATTTTTACATAATCCGGGGCATTTTAGTCATTTCTACCA
Done.