Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007118.1 Corchorus olitorius cultivar O-4 contig07143, 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, 775

Length: 1292
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44


Found at i:151 original size:35 final size:35

Alignment explanation


    Indices: 5--179  Score: 174
    Period size: 35  Copynumber: 5.0  Consensus size: 35

          1 TTTA

                  *      *                     
          5 CTTCAAGTTATTTTAGTTGATCCAGGGCGATCTTT
          1 CTTCAATTTATTTCAGTTGATCCAGGGCGATCTTT

                          *  *   *      * *     
         40 CCTTCAATTTATTTTAGCTGACCCAGGGTGGTCTTT
          1 -CTTCAATTTATTTCAGTTGATCCAGGGCGATCTTT

                 *       *      *        *     
         76 CTTCAGTTTATTTTAGTTGACCCAGGGCGGTCTTT
          1 CTTCAATTTATTTCAGTTGATCCAGGGCGATCTTT

                    *      *                    
        111 CTTCAATTCATTTCAATTGATCCAGGGCGATCTTAT
          1 CTTCAATTTATTTCAGTTGATCCAGGGCGATCTT-T

                  **       *                   
        147 -TTCAAGATA-TTCATTTGATCCAGGGCGATCTTT
          1 CTTCAATTTATTTCAGTTGATCCAGGGCGATCTTT

        180 TCTCCAGTTT


Statistics
Matches: 120,  Mismatches: 18, Indels: 5
        0.84            0.13        0.03

Matches are distributed among these distances:
  33    1  0.01
  34   22  0.18
  35   66  0.55
  36   31  0.26

ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41


Consensus pattern (35 bp):   
CTTCAATTTATTTCAGTTGATCCAGGGCGATCTTT

Found at i:467 original size:30 final size:30

Alignment explanation


    Indices: 426--910  Score: 670
    Period size: 30  Copynumber: 16.3  Consensus size: 30

        416 ACTATTCTAC

                                          
        426 ATCATTGCTTTATTTTAATCCTGGTTGAGG
          1 ATCATTGCTTTATTTTAATCCTGGTTGAGG

                  *                       
        456 ATCATTACTTTATTTTAATCCTGGTTGAGG
          1 ATCATTGCTTTATTTTAATCCTGGTTGAGG

                                          
        486 ATCATTGCTTTATTTTAATCCTGGTTGAGG
          1 ATCATTGCTTTATTTTAATCCTGGTTGAGG

               *    *  *        * **      
        516 ATCGTTGCGTTGTTTTAATCTTATTTGAGG
          1 ATCATTGCTTTATTTTAATCCTGGTTGAGG

               *      *                   
        546 ATCGTTGCTTCATTTTAATCCTGGTTGAGG
          1 ATCATTGCTTTATTTTAATCCTGGTTGAGG

               * *                        
        576 ATCGTCGCTTTATTTTAATCCTGGTTGAGG
          1 ATCATTGCTTTATTTTAATCCTGGTTGAGG

                  * *              *      
        606 ATCATTACCTTATTTTAATCCTGTTTGAGG
          1 ATCATTGCTTTATTTTAATCCTGGTTGAGG

               *    *              *      
        636 ATCGTTGCCTTATTTTAATCCTGTTTGAGG
          1 ATCATTGCTTTATTTTAATCCTGGTTGAGG

               *                      *   
        666 ATCGTTGCTTTATTTTAATCCTGGTTAAGG
          1 ATCATTGCTTTATTTTAATCCTGGTTGAGG

               *                   *      
        696 ATCTTTGCTTTATTTTAATCCTGTTTGAGG
          1 ATCATTGCTTTATTTTAATCCTGGTTGAGG

                      * *                 
        726 ATCATTGCTTCAATTTAATCCTGGTTGAGG
          1 ATCATTGCTTTATTTTAATCCTGGTTGAGG

                  *                       
        756 ATCATTACTTTATTTTAATCCTGGTTGAGG
          1 ATCATTGCTTTATTTTAATCCTGGTTGAGG

                *                         
        786 ATCACTGCTTTATTTTAATCCTGGTTGAGG
          1 ATCATTGCTTTATTTTAATCCTGGTTGAGG

                                *  *      
        816 ATCATTGCTTTATTTTAATCTTGTTTGAGG
          1 ATCATTGCTTTATTTTAATCCTGGTTGAGG

                           *      *   *   
        846 ATCATTGCTTTATTTCAATCCTAGTTTAGG
          1 ATCATTGCTTTATTTTAATCCTGGTTGAGG

                                      *   
        876 ATCATTG--TT-TTTTAATCCTGGTTTAGG
          1 ATCATTGCTTTATTTTAATCCTGGTTGAGG

                    
        903 ATCATTGC
          1 ATCATTGC

        911 CTCATCAGAT


Statistics
Matches: 406,  Mismatches: 48, Indels: 4
        0.89            0.10        0.01

Matches are distributed among these distances:
  27   23  0.06
  28    2  0.00
  30  381  0.94

ACGTcount: A:0.20, C:0.14, G:0.19, T:0.47


Consensus pattern (30 bp):   
ATCATTGCTTTATTTTAATCCTGGTTGAGG

Done.