Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000015.1 Kokia drynarioides strain JFW-HI SEQ_18217, 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, 711

Length: 1186
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.39


Found at i:635 original size:29 final size:29

Alignment explanation


    Indices: 601--953  Score: 291
    Period size: 29  Copynumber: 12.0  Consensus size: 29

        591 CCGAAAATCT

                                         
        601 CATTTTTACCCCCGAACTTCCAAAAATTC
          1 CATTTTTACCCCCGAACTTCCAAAAATTC

                  *    *       *         
        630 CATTTTGACCCACGAACTTTCAAAAATTC
          1 CATTTTTACCCCCGAACTTCCAAAAATTC

                         **      *      * 
        659 CATTTTTGACCCCAAAACTTCTAAAAATGC
          1 CATTTTT-ACCCCCGAACTTCCAAAAATTC

                               *         
        689 CATTTTTACCCCCGAACTTTCAAAAATTC
          1 CATTTTTACCCCCGAACTTCCAAAAATTC

                       * **       *       
        718 CATTTTTGACCTCAAAACTTCCCAAAATTC
          1 CATTTTT-ACCCCCGAACTTCCAAAAATTC

            *          *   *    *        
        748 TATTTTTACCCTCGATCTTCTAAAAATTC
          1 CATTTTTACCCCCGAACTTCCAAAAATTC

                  * *                    *
        777 CATTTTCAACCCCGAAACTTCCAAAAATTA
          1 CATTTTTACCCCCG-AACTTCCAAAAATTC

                         **     **         
        807 CATTTTTTACCCCTAAACTTTTAAAAATTAC
          1 CA-TTTTTACCCCCGAACTTCCAAAAATT-C

                                       *  
        838 CA-TTTTACCCCCGAA-TGTCCAAAAACTC
          1 CATTTTTACCCCCGAACT-TCCAAAAATTC

            *     * *  *    *             
        866 TATTTTCAACCTC-AAATCTCCAAAAATTC
          1 CATTTTTACCCCCGAACT-TCCAAAAATTC

                                 *        
        895 CATTTTTACCCCCGAA-TATCTAAAAATTC
          1 CATTTTTACCCCCGAACT-TCCAAAAATTC

                     *  *          *      
        924 CATCTTTTAACCTCGAACTTTCCCAAAATT
          1 CAT-TTTTACCCCCGAAC-TTCCAAAAATT

        954 ACTATCTTGC


Statistics
Matches: 249,  Mismatches: 63, Indels: 22
        0.75            0.19        0.07

Matches are distributed among these distances:
  28    5  0.02
  29  140  0.56
  30   85  0.34
  31   18  0.07
  32    1  0.00

ACGTcount: A:0.34, C:0.29, G:0.04, T:0.34


Consensus pattern (29 bp):   
CATTTTTACCCCCGAACTTCCAAAAATTC

Found at i:685 original size:59 final size:58

Alignment explanation


    Indices: 601--945  Score: 274
    Period size: 59  Copynumber: 5.9  Consensus size: 58

        591 CCGAAAATCT

                         **                     *                      
        601 CATTTTT-ACCCCCGAACTTCCAAAAATTCCATTTTGACCCACGAACTTTCAAAAATTC
          1 CATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCC-CGAACTTTCAAAAATTC

                                 *      *                              
        659 CATTTTTGACCCCAAAACTTCTAAAAATGCCATTTTTACCCCCGAACTTTCAAAAATTC
          1 CATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTA-CCCCGAACTTTCAAAAATTC

                       *          *       *              *              
        718 CATTTTTGACCTCAAAACTTCCCAAAATTCTATTTTTACCCTCGATC-TTCTAAAAATTC
          1 CATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCC-CGAACTTTC-AAAAATTC

                  **     *               *              *      *         
        777 CATTTTCAACCCCGAAACTTCCAAAAATTACATTTTTTACCCCTAAACTTTTAAAAATTAC
          1 CATTTTTGACCCCAAAACTTCCAAAAATTCCA-TTTTTACCCC-GAACTTTCAAAAATT-C

                         **             *  *      *   *    *   *         
        838 CA-TTTT-ACCCCCGAA-TGTCCAAAAACTCTATTTTCAACCTC-AAATCTCCAAAAATTC
          1 CATTTTTGACCCCAAAACT-TCCAAAAATTCCATTTT-TACCCCGAACT-TTCAAAAATTC

                         **       *                    *         
        895 CATTTTT-ACCCCCGAA-TATCTAAAAATTCCATCTTTTAACCTCGAACTTTC
          1 CATTTTTGACCCCAAAACT-TCCAAAAATTCCAT-TTTT-ACCCCGAACTTTC

        946 CCAAAATTAC


Statistics
Matches: 233,  Mismatches: 39, Indels: 29
        0.77            0.13        0.10

Matches are distributed among these distances:
  57    6  0.03
  58   51  0.22
  59  144  0.62
  60   27  0.12
  61    5  0.02

ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34


Consensus pattern (58 bp):   
CATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCGAACTTTCAAAAATTC
Done.