Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013707.1 Kokia drynarioides strain JFW-HI SEQ_128735, 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: 7447
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26


Found at i:673 original size:59 final size:59

Alignment explanation


    Indices: 581--933  Score: 414
    Period size: 59  Copynumber: 6.0  Consensus size: 59

        571 GGAGGTCCCT

                                  *   * *                *             
        581 AACTTCCAAAAATCCCATTTTTGACCTCGAAACTTTCAAAAATTCTATTTTTACCCCCG
          1 AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTTCAAAAATTCCATTTTTACCCCCG

                 *                     *       *      *    *           
        640 AACTTGCAAAAATCCCATTTTTAACCCAAAAACTTCCAAAAAATCCAATTTTACCCCCG
          1 AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTTCAAAAATTCCATTTTTACCCCCG

                                  *     *                            * 
        699 AACTTCCAAAAATCCCA-TTTTGACCCCGAAACTTTCAAAAATTCCA-TTTTACCCCAG
          1 AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTTCAAAAATTCCATTTTTACCCCCG

                                       *          *                     
        756 AACTTCCAAAAATCCCATTTTTAACCCTAAAAC-TTCTGAAAATTCCATTTTTACCCCCG
          1 AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTTC-AAAAATTCCATTTTTACCCCCG

                         *        *                       *             **
        815 AACTTCCAAAAATACCA-TTTTGACCCCAAAAC-TTCTAAAAATTCTATTTTTTTACCCCTA
          1 AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTTC-AAAAATTCCA--TTTTTACCCCCG

                                                  *          *           
        875 AACTTCCAAAAATCCCATTTTTAACCCCAAAA-TTTCCCAAAATTACC-CTTTTACCCCCG
          1 AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTT-CAAAAATT-CCATTTTTACCCCCG

        934 GGTATCCGAA


Statistics
Matches: 250,  Mismatches: 35, Indels: 18
        0.83            0.12        0.06

Matches are distributed among these distances:
  57   30  0.12
  58   70  0.28
  59  101  0.40
  60   26  0.10
  61   21  0.08
  62    2  0.01

ACGTcount: A:0.35, C:0.31, G:0.03, T:0.31


Consensus pattern (59 bp):   
AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTTCAAAAATTCCATTTTTACCCCCG

Found at i:902 original size:30 final size:29

Alignment explanation


    Indices: 581--917  Score: 318
    Period size: 29  Copynumber: 11.4  Consensus size: 29

        571 GGAGGTCCCT

                                      * * 
        581 AACTTCCAAAAATCCCATTTTTGACCTCGA
          1 AACTTCCAAAAATCCCATTTTT-ACCCCAA

                 *       * *           **
        611 AACTTTCAAAAATTCTATTTTTACCCCCG
          1 AACTTCCAAAAATCCCATTTTTACCCCAA

                 *                     *  
        640 AACTTGCAAAAATCCCATTTTTAACCCAAA
          1 AACTTCCAAAAATCCCATTTTT-ACCCCAA

                              *         **
        670 AACTTCCAAAAAAT-CCAATTTTACCCCCG
          1 AACTTCC-AAAAATCCCATTTTTACCCCAA

                                 *     * 
        699 AACTTCCAAAAATCCCATTTTGACCCCGA
          1 AACTTCCAAAAATCCCATTTTTACCCCAA

                 *       *              *
        728 AACTTTCAAAAATTCCA-TTTTACCCCAG
          1 AACTTCCAAAAATCCCATTTTTACCCCAA

                                       *  
        756 AACTTCCAAAAATCCCATTTTTAACCCTAA
          1 AACTTCCAAAAATCCCATTTTT-ACCCCAA

                  **     *             **
        786 AACTTCTGAAAATTCCATTTTTACCCCCG
          1 AACTTCCAAAAATCCCATTTTTACCCCAA

                         *       *       
        815 AACTTCCAAAAATACCATTTTGACCCCAA
          1 AACTTCCAAAAATCCCATTTTTACCCCAA

                  *      * *             * 
        844 AACTTCTAAAAATTCTATTTTTTTACCCCTA
          1 AACTTCCAAAAATCCCA--TTTTTACCCCAA

                                          
        875 AACTTCCAAAAATCCCATTTTTAACCCCAA
          1 AACTTCCAAAAATCCCATTTTT-ACCCCAA

              *    *     
        905 AATTTCCCAAAAT
          1 AACTTCCAAAAAT

        918 TACCCTTTTA


Statistics
Matches: 246,  Mismatches: 53, Indels: 16
        0.78            0.17        0.05

Matches are distributed among these distances:
  28   29  0.12
  29  110  0.45
  30   77  0.31
  31   30  0.12

ACGTcount: A:0.36, C:0.30, G:0.03, T:0.31


Consensus pattern (29 bp):   
AACTTCCAAAAATCCCATTTTTACCCCAA
Done.