Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010442.1 Kokia drynarioides strain JFW-HI SEQ_125333, 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: 4359
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29

Warning! 10 characters in sequence are not A, C, G, or T


Found at i:643 original size:30 final size:30

Alignment explanation


    Indices: 554--876  Score: 178
    Period size: 29  Copynumber: 10.9  Consensus size: 30

        544 CCCCAAAGGT

                *                      *  
        554 CCCCGAACTTCCAAAAATCCCATTTTTGAC
          1 CCCCAAACTTCCAAAAATCCCATTTTTTAC

               *  *   * *     **   *      
        584 CCCGAACCTTTCGAAAATTAC-TATTTTAC
          1 CCCCAAACTTCCAAAAATCCCATTTTTTAC

                                          
        613 CCCCAAACTTCCAAAAATCCCATTTTTTAC
          1 CCCCAAACTTCCAAAAATCCCATTTTTTAC

               *  *   *       **   *      
        643 CCCGAACCTTTCAAAAATTAC-TATTTTAC
          1 CCCCAAACTTCCAAAAATCCCATTTTTTAC

                *   *          *       *  
        672 CCCCGAACATCC-AAAATCTCATTTTTGAC
          1 CCCCAAACTTCCAAAAATCCCATTTTTTAC

             * *  *   *        *           
        701 CTCGAACCTTTCAAAAATTACCA--TTTTAC
          1 CCCCAAACTTCCAAAAA-TCCCATTTTTTAC

                *      *      *        *  
        730 CCCCGAACTTCTAAAAATTCCATTTTTGAC
          1 CCCCAAACTTCCAAAAATCCCATTTTTTAC

                *  *    *       *           
        760 CCTCGAACCTTCTAAAAATTACCA--TTTTAC
          1 CC-CCAAACTTCCAAAAA-TCCCATTTTTTAC

                *                      *  
        790 CCCCGAACTTCCAAAAATCCCATTTTTAAC
          1 CCCCAAACTTCCAAAAATCCCATTTTTTAC

               *  *   *        *           
        820 CCCGAACCTTTCAAAAATTACCA--TTTTAC
          1 CCCCAAACTTCCAAAAA-TCCCATTTTTTAC

              * *               *       
        849 CCTCGAACTTCCAAAAATCCTATTTTTT
          1 CCCCAAACTTCCAAAAATCCCATTTTTT

        877 TACTCTGAAC


Statistics
Matches: 208,  Mismatches: 72, Indels: 26
        0.68            0.24        0.08

Matches are distributed among these distances:
  28   17  0.08
  29   91  0.44
  30   77  0.37
  31   19  0.09
  32    4  0.02

ACGTcount: A:0.32, C:0.32, G:0.04, T:0.32


Consensus pattern (30 bp):   
CCCCAAACTTCCAAAAATCCCATTTTTTAC

Found at i:905 original size:59 final size:59

Alignment explanation


    Indices: 554--875  Score: 495
    Period size: 59  Copynumber: 5.5  Consensus size: 59

        544 CCCCAAAGGT

                                                      *        *       
        554 CCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTCGAAAATTACTATTTTAC
          1 CCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAAATTACCATTTTAC

                *                      *                       *       
        613 CCCCAAACTTCCAAAAATCCCATTTTTTACCCCGAACCTTTCAAAAATTACTATTTTAC
          1 CCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAAATTACCATTTTAC

                    *          *           *                           
        672 CCCCGAACATCC-AAAATCTCATTTTTGACCTCGAACCTTTCAAAAATTACCATTTTAC
          1 CCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAAATTACCATTTTAC

                       *      *                                          
        730 CCCCGAACTTCTAAAAATTCCATTTTTGACCCTCGAACC-TTCTAAAAATTACCATTTTAC
          1 CCCCGAACTTCCAAAAATCCCATTTTTGACCC-CGAACCTTTC-AAAAATTACCATTTTAC

                                       *                               
        790 CCCCGAACTTCCAAAAATCCCATTTTTAACCCCGAACCTTTCAAAAATTACCATTTTAC
          1 CCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAAATTACCATTTTAC

              *                 *      
        849 CCTCGAACTTCCAAAAATCCTATTTTT
          1 CCCCGAACTTCCAAAAATCCCATTTTT

        876 TTACTCTGAA


Statistics
Matches: 240,  Mismatches: 19, Indels: 8
        0.90            0.07        0.03

Matches are distributed among these distances:
  58   52  0.22
  59  133  0.55
  60   55  0.23

ACGTcount: A:0.32, C:0.32, G:0.04, T:0.32


Consensus pattern (59 bp):   
CCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTTCAAAAATTACCATTTTAC

Found at i:1298 original size:96 final size:96

Alignment explanation


    Indices: 1133--1314  Score: 210
    Period size: 96  Copynumber: 1.9  Consensus size: 96

       1123 TTTTTTTTAA

                                                     *                    ***
       1133 AATCGAGGCAATATTCCTTTATTTCGAGTTTCGAAAATTTGTGCCTTAACTCACTAGGTGCATTT
          1 AATCGAGGCAATATTCCTTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTCACTAGGTGCAACC

                                           
       1198 TTTCTTCAAATCGAAATAATCAAACACCGTT
         66 TTTCTTCAAATCGAAATAATCAAACACCGTT

                         *                                         * *       
       1229 AATCGAGGCAATGTTTCC-TTATCTTCGA--TTCTG-AAATATTGCGCCTTAACTTATTAGGTGC
          1 AATCGAGGCAAT-ATTCCTTTAT-TTCGAGTTTC-GAAAAT-TTGCGCCTTAACTCACTAGGTGC

                      **      *      
       1290 AACCTTTCTTTGAATCGAGATAATC
         62 AACCTTTCTTCAAATCGAAATAATC

       1315 GAATATCCTT


Statistics
Matches: 72,  Mismatches: 10, Indels: 8
        0.80            0.11        0.09

Matches are distributed among these distances:
  95    7  0.10
  96   56  0.78
  97    9  0.12

ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37


Consensus pattern (96 bp):   
AATCGAGGCAATATTCCTTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTCACTAGGTGCAACC
TTTCTTCAAATCGAAATAATCAAACACCGTT
Done.