Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012707.1 Kokia drynarioides strain JFW-HI SEQ_127718, 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: 5650
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:170 original size:30 final size:30

Alignment explanation


    Indices: 129--447  Score: 266
    Period size: 30  Copynumber: 10.7  Consensus size: 30

        119 GAGGTTCCTA

                                  *        
        129 AACTATCCAAAAATTCCATTTTCACCCCTCG
          1 AACT-TCCAAAAATTCCATTTTTACCCCTCG

                                          **
        160 AACTTCCAAAAA-TCTCATTTTTAACCCC-AA
          1 AACTTCCAAAAATTC-CATTTTT-ACCCCTCG

                  * *    *              **
        190 AACTTCTATAAATCCCATTTTTA-CCCTTA
          1 AACTTCCAAAAATTCCATTTTTACCCCTCG

                         *         **     
        219 AACTTCCAAAAATCCCATTTTTAATCCT-G
          1 AACTTCCAAAAATTCCATTTTTACCCCTCG

                                            
        248 AAACTTCCAAAAA-TCTCATTTTTACCCC-CG
          1 -AACTTCCAAAAATTC-CATTTTTACCCCTCG

             *                      *     
        278 AGCTTCCAAAAATTCCATTTTTA-ACCTCG
          1 AACTTCCAAAAATTCCATTTTTACCCCTCG

                                  *        
        307 AAGCTTCCAAAAATTCCATTTTCACCCCT-G
          1 AA-CTTCCAAAAATTCCATTTTTACCCCTCG

                         *        *      **
        337 AACTTCCAAAAATCCCATTTTCGACCCC-AA
          1 AACTTCCAAAAATTCCATTTT-TACCCCTCG

                                     *   **
        367 AACTTCCAAAAATTCCATTTTTGA-TCCTAA
          1 AACTTCCAAAAATTCCATTTTT-ACCCCTCG

                           *              
        397 AACTTCCAAAAATTCTATTTTTACCCC-C-
          1 AACTTCCAAAAATTCCATTTTTACCCCTCG

                                   
        425 ATACTTCCAAAAATCTCCATTTT
          1 A-ACTTCCAAAAAT-TCCATTTT

        448 GGACCTTAAA


Statistics
Matches: 240,  Mismatches: 29, Indels: 39
        0.78            0.09        0.13

Matches are distributed among these distances:
  28    6  0.03
  29   81  0.34
  30  140  0.58
  31   13  0.05

ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33


Consensus pattern (30 bp):   
AACTTCCAAAAATTCCATTTTTACCCCTCG

Found at i:225 original size:59 final size:59

Alignment explanation


    Indices: 128--447  Score: 306
    Period size: 59  Copynumber: 5.4  Consensus size: 59

        118 GGAGGTTCCT

                           *       *       *                             
        128 AAACTATCCAAAAATTCCATTTTCACCCCTCGAACTTCCAAAAATCTCATTTTTAACCCCA
          1 AAACT-TCCAAAAATCCCATTTTTACCCCT-AAACTTCCAAAAATCTCATTTTTAACCCCA

                   * *                 *                *         *  **
        189 AAACTTCTATAAATCCCATTTTTACCCTTAAACTTCCAAAAATCCCATTTTTAATCCTG
          1 AAACTTCCAAAAATCCCATTTTTACCCCTAAACTTCCAAAAATCTCATTTTTAACCCCA

                           *            ** *                         * *
        248 AAACTTCCAAAAATCTCATTTTTACCCCCGAGCTTCCAAAAAT-TCCATTTTTAACCTCG
          1 AAACTTCCAAAAATCCCATTTTTACCCCTAAACTTCCAAAAATCT-CATTTTTAACCCCA

              *           *       *      *              *      **      
        307 AAGCTTCCAAAAATTCCATTTTCACCCCTGAACTTCCAAAAATCCCATTTTCGACCCCA
          1 AAACTTCCAAAAATCCCATTTTTACCCCTAAACTTCCAAAAATCTCATTTTTAACCCCA

                          *           *                                  *
        366 AAACTTCCAAAAATTCCATTTTTGA-TCCTAAAACTTCCAAAAAT-TCTATTTTT-ACCCCC
          1 AAACTTCCAAAAATCCCATTTTT-ACCCCT-AAACTTCCAAAAATCTC-ATTTTTAACCCCA

             *                     
        425 ATACTTCCAAAAATCTCCATTTT
          1 AAACTTCCAAAAATC-CCATTTT

        448 GGACCTTAAA


Statistics
Matches: 212,  Mismatches: 41, Indels: 13
        0.80            0.15        0.05

Matches are distributed among these distances:
  59  162  0.76
  60   45  0.21
  61    5  0.02

ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33


Consensus pattern (59 bp):   
AAACTTCCAAAAATCCCATTTTTACCCCTAAACTTCCAAAAATCTCATTTTTAACCCCA

Found at i:469 original size:89 final size:86

Alignment explanation


    Indices: 124--448  Score: 355
    Period size: 89  Copynumber: 3.7  Consensus size: 86

        114 CCTTGGAGGT

                                                                      *      
        124 TCCTAAACTATCCAAAAATTCCATTTTCACCCCTCGAACTTCCAAAAATCTCATTTTTAACCCCA
          1 TCCTAAACT-TCCAAAAATTCCATTTTCACCCCTC-AACTTCCAAAAATCTCA-TTTTGACCCCA

                   * *    *         
        189 AAACTTCTATAAATCCCATTTTTA
         63 AAACTTCCAAAAATTCCATTTTTA

            *                  *       * **    *                     *     **
        213 CCCTTAAACTTCCAAAAATCCCATTTTTAATCCTGAAACTTCCAAAAATCTCATTTTTACCCCCG
          1 TCC-TAAACTTCCAAAAATTCCATTTTCACCCCT-CAACTTCCAAAAATCTCATTTTGACCCCAA

             *                     
        278 AGCTTCCAAAAATTCCATTTTTA
         64 AACTTCCAAAAATTCCATTTTTA

            *       *                          *              *              
        301 ACCTCGAAGCTTCCAAAAATTCCATTTTCACCCCTGAACTTCCAAAAATCCCATTTTCGACCCCA
          1 TCCT--AAACTTCCAAAAATTCCATTTTCACCCCTCAACTTCCAAAAATCTCATTTT-GACCCCA

                                     
        366 AAACTTCCAAAAATTCCATTTTTGA
         63 AAACTTCCAAAAATTCCATTTTT-A

                                 *     *                               
        391 TCCTAAAACTTCCAAAAATTCTATTTTTACCCC-CATACTTCCAAAAATCTCCATTTTG
          1 TCCT-AAACTTCCAAAAATTCCATTTTCACCCCTCA-ACTTCCAAAAATCT-CATTTTG

        449 GACCTTAAAA


Statistics
Matches: 196,  Mismatches: 32, Indels: 16
        0.80            0.13        0.07

Matches are distributed among these distances:
  87    1  0.01
  88   51  0.26
  89  128  0.65
  90   16  0.08

ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33


Consensus pattern (86 bp):   
TCCTAAACTTCCAAAAATTCCATTTTCACCCCTCAACTTCCAAAAATCTCATTTTGACCCCAAAA
CTTCCAAAAATTCCATTTTTA
Done.