Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001336.1 Kokia drynarioides strain JFW-HI SEQ_112779, 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, 905

Length: 1509
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34


Found at i:694 original size:29 final size:29

Alignment explanation


    Indices: 654--1100  Score: 354
    Period size: 29  Copynumber: 15.2  Consensus size: 29

        644 CCCCGGAGGT

                                          
        654 CCCT-AAACCTTCCAAAAATTACCATTTTA
          1 CCCTCAAA-CTTCCAAAAATTACCATTTTA

                 *              *          
        683 CCCTCGAACTTCCAAAAA-TCCCATTTTTTA
          1 CCCTCAAACTTCCAAAAATTACCA--TTTTA

                                          
        713 CCCT-AAACCTTCCAAAAATTACCATTTTA
          1 CCCTCAAA-CTTCCAAAAATTACCATTTTA

               *    *                     
        742 CCCCCAAATTTCCAAAAA-T-CCATTTTTA
          1 CCCTCAAACTTCCAAAAATTACCA-TTTTA

                     *                   * 
        770 GCCC-CGAACCTTCCAAAAATTACCATTTCA
          1 -CCCTC-AAACTTCCAAAAATTACCATTTTA

                 *              *          
        800 CCCTCGAACTTCCAAAAA-TCCCAATTTTAA
          1 CCCTCAAACTTCCAAAAATTACC-ATTTT-A

                                  *     * 
        830 CCCT-AAACCTTCCAAAAATTAACATTTCA
          1 CCCTCAAA-CTTCCAAAAATTACCATTTTA

                                *          
        859 CCCTCAAACTTCCAAAAA-TCCCATTTTCGA
          1 CCCTCAAACTTCCAAAAATTACCATTTT--A

                    *                     
        889 CCC-CGAATCTTCCAAAAATTACCATTTTA
          1 CCCTC-AAACTTCCAAAAATTACCATTTTA

               *     *   *                 
        918 CCCCCAAACATCCTAAAATT-CCATTTTTGA
          1 CCCTCAAACTTCCAAAAATTACCA-TTTT-A

                            *             
        948 CCC-CAAATCTTCCAAGAATTACCATTTTA
          1 CCCTCAAA-CTTCCAAAAATTACCATTTTA

                                 *          *
        977 CCC-CTAAACTTCCAAAAA-TCCCATTTTTGGT
          1 CCCTC-AAACTTCCAAAAATTACCA-TTTT--A

                                          
       1008 CCCT-AAACCTTCCAAAAATTACCATTTTA
          1 CCCTCAAA-CTTCCAAAAATTACCATTTTA

               *                *         
       1037 CCCCCAAACTTCCAAAAA-TCCCATTTTTA
          1 CCCTCAAACTTCCAAAAATTACCA-TTTTA

            *                               
       1066 ACCTCAAAAC-TCTC-AAAATTACCATTTTTA
          1 CCCTC-AAACTTC-CAAAAATTACCA-TTTTA

                 
       1096 CCCTC
          1 CCCTC

       1101 GAACATTTTA


Statistics
Matches: 341,  Mismatches: 39, Indels: 75
        0.75            0.09        0.16

Matches are distributed among these distances:
  27    3  0.01
  28   31  0.09
  29  152  0.45
  30  114  0.33
  31   37  0.11
  32    4  0.01

ACGTcount: A:0.35, C:0.33, G:0.02, T:0.30


Consensus pattern (29 bp):   
CCCTCAAACTTCCAAAAATTACCATTTTA

Found at i:755 original size:59 final size:59

Alignment explanation


    Indices: 654--1098  Score: 542
    Period size: 59  Copynumber: 7.5  Consensus size: 59

        644 CCCCGGAGGT

                                            * *                        
        654 CCCTAAACCTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTA
          1 CCCTAAACCTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTTA

                                                 *                     
        713 CCCTAAACCTTCCAAAAATTACCATTTTACCCCCAAATTTCCAAAAAT-CCA-TTTTTA
          1 CCCTAAACCTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTTA

                **                      *    * *                 *    * 
        770 GCCCCGAACCTTCCAAAAATTACCATTTCACCCTCGAACTTCCAAAAATCCCAATTTTAA
          1 -CCCTAAACCTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTTA

                                 *     *    *                       ** 
        830 CCCTAAACCTTCCAAAAATTAACATTTCACCCTCAAACTTCCAAAAATCCCATTTTCGA
          1 CCCTAAACCTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTTA

               **  *                              *   *     *        * 
        889 CCCCGAATCTTCCAAAAATTACCATTTTACCCCCAAACATCCTAAAATTCCATTTTTGA
          1 CCCTAAACCTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTTA

               *   *       *                 *                           
        948 CCCCAAATCTTCCAAGAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGGT-
          1 CCCTAAACCTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTT--TA

                                                                       
       1008 CCCTAAACCTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCA-TTTTTA
          1 CCCTAAACCTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTTA

            *       *                          
       1066 ACCTCAAAAC-TCTC-AAAATTACCATTTTTACCC
          1 CCCT-AAACCTTC-CAAAAATTACCA-TTTTACCC

       1099 TCGAACATTT


Statistics
Matches: 337,  Mismatches: 40, Indels: 18
        0.85            0.10        0.05

Matches are distributed among these distances:
  57    7  0.02
  58   60  0.18
  59  217  0.64
  60   53  0.16

ACGTcount: A:0.35, C:0.33, G:0.02, T:0.30


Consensus pattern (59 bp):   
CCCTAAACCTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTTA

Done.