Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000584.1 Kokia drynarioides strain JFW-HI SEQ_111513, 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: 2690
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32


Found at i:1806 original size:30 final size:30

Alignment explanation


    Indices: 1701--2289  Score: 650
    Period size: 30  Copynumber: 19.9  Consensus size: 30

       1691 CCTTGGAGGT

                *       *       *         
       1701 CCCCGAAACTTCCAAAAATCTCATTTTT-A
          1 CCCCAAAACTTCTAAAAATCCCATTTTTAA

                *                         
       1730 CCCCTAAACTTCTAAAAATCCCATTTTT-A
          1 CCCCAAAACTTCTAAAAATCCCATTTTTAA

                *      *        *         
       1759 CCCCCAAACTTTTAAAAATCACATTTTTAA
          1 CCCCAAAACTTCTAAAAATCCCATTTTTAA

            *           *                *
       1789 TCCCAAAACTTCAAAAAATCCCATTTTTAC
          1 CCCCAAAACTTCTAAAAATCCCATTTTTAA

                *       *                 
       1819 CCCCGAAACTTCCAAAAATCCCATTTTT-A
          1 CCCCAAAACTTCTAAAAATCCCATTTTTAA

                  *           *            
       1848 CCCTC-GAACTTCTAAAATTCCCATTTTTAA
          1 CCC-CAAAACTTCTAAAAATCCCATTTTTAA

                *       *       *      *  
       1878 CCCCGAAACTTCAAAAAATCTCATTTTAAA
          1 CCCCAAAACTTCTAAAAATCCCATTTTTAA

                    *   *                *
       1908 CCCCAAAATTTCAAAAAATCCCATTTTTAC
          1 CCCCAAAACTTCTAAAAATCCCATTTTTAA

                                           
       1938 CCCCAAAACTT-TGAAAAATCCCATTTTTAA
          1 CCCCAAAACTTCT-AAAAATCCCATTTTTAA

               *                          
       1968 CCCTAAAACTTCTAAAAATCCCATTTTTAA
          1 CCCCAAAACTTCTAAAAATCCCATTTTTAA

              **                          
       1998 CCTTAAAACTTCTAAAAATCCCATTTTT-A
          1 CCCCAAAACTTCTAAAAATCCCATTTTTAA

                       *                  
       2027 CCCC-AAACTTTTAAAAATCCCA-TTTTAA
          1 CCCCAAAACTTCTAAAAATCCCATTTTTAA

                        *              *  
       2055 CCCCAAAACTTCAAAAAATCCCATTTTAAA
          1 CCCCAAAACTTCTAAAAATCCCATTTTTAA

              *         *                 
       2085 CCTCAAAACTTCCAAAAATCCCA-TTTTAA
          1 CCCCAAAACTTCTAAAAATCCCATTTTTAA

                         *                 
       2114 CCCCCAAAACTTCAAAAAATCCCA-TTTTAA
          1 -CCCCAAAACTTCTAAAAATCCCATTTTTAA

                        *                  
       2144 GCCCCAAAACTTATAAAAATCCCATTTTT-A
          1 -CCCCAAAACTTCTAAAAATCCCATTTTTAA

                        *  *               
       2174 CCCTC-AAACTTTTATAAATCCCATTTTT-A
          1 CCC-CAAAACTTCTAAAAATCCCATTTTTAA

                *                         
       2203 CCCCCAAACTTCTAAAAATCCCATTTTTAA
          1 CCCCAAAACTTCTAAAAATCCCATTTTTAA

              *               * *          
       2233 CCTCAAAACTT-TCAAAAGTTCCATTTTT-A
          1 CCCCAAAACTTCT-AAAAATCCCATTTTTAA

                **    *     *           
       2262 CCCCCGAACTCCTAAAGATCCCATTTTT
          1 CCCCAAAACTTCTAAAAATCCCATTTTT

       2290 TTACCTCGAA


Statistics
Matches: 481,  Mismatches: 63, Indels: 32
        0.84            0.11        0.06

Matches are distributed among these distances:
  27    4  0.01
  28   23  0.05
  29  169  0.35
  30  280  0.58
  31    5  0.01

ACGTcount: A:0.38, C:0.30, G:0.02, T:0.31


Consensus pattern (30 bp):   
CCCCAAAACTTCTAAAAATCCCATTTTTAA

Found at i:2257 original size:59 final size:59

Alignment explanation


    Indices: 1701--2289  Score: 633
    Period size: 59  Copynumber: 10.0  Consensus size: 59

       1691 CCTTGGAGGT

                *      *        *            *                         
       1701 CCCCGAAACTTCCAAAAATCTCATTTTTACCCCTAAACTTCTAAAAATCCCATTTTT-A
          1 CCCCAAAACTTTCAAAAATCCCATTTTTACCCCAAAACTTCTAAAAATCCCATTTTTAA

                *       *       *         *           *                *
       1759 CCCCCAAACTTTTAAAAATCACATTTTTAATCCCAAAACTTCAAAAAATCCCATTTTTAC
          1 CCCCAAAACTTTCAAAAATCCCATTTTT-ACCCCAAAACTTCTAAAAATCCCATTTTTAA

                *      *                       *           *            
       1819 CCCCGAAACTTCCAAAAATCCCATTTTTACCCTC-GAACTTCTAAAATTCCCATTTTTAA
          1 CCCCAAAACTTTCAAAAATCCCATTTTTACCC-CAAAACTTCTAAAAATCCCATTTTTAA

                *                *       *         *   *                *
       1878 CCCCGAAAC-TTCAAAAAATCTCATTTTAAACCCCAAAATTTCAAAAAATCCCATTTTTAC
          1 CCCCAAAACTTTC-AAAAATCCCATTTT-TACCCCAAAACTTCTAAAAATCCCATTTTTAA

                        *                    *                          
       1938 CCCCAAAACTTTGAAAAATCCCATTTTTAACCCTAAAACTTCTAAAAATCCCATTTTTAA
          1 CCCCAAAACTTTCAAAAATCCCATTTTT-ACCCCAAAACTTCTAAAAATCCCATTTTTAA

              **                                     *                  
       1998 CCTTAAAAC-TTCTAAAAATCCCATTTTTACCCC-AAACTTTTAAAAATCCCA-TTTTAA
          1 CCCCAAAACTTTC-AAAAATCCCATTTTTACCCCAAAACTTCTAAAAATCCCATTTTTAA

                                         *   *         *                 
       2055 CCCCAAAAC-TTCAAAAAATCCCATTTTAAACCTCAAAACTTCCAAAAATCCCA-TTTTAA
          1 CCCCAAAACTTTC-AAAAATCCCATTTT-TACCCCAAAACTTCTAAAAATCCCATTTTTAA

                                         *             *                  
       2114 CCCCCAAAAC-TTCAAAAAATCCCATTTTAAGCCCCAAAACTTATAAAAATCCCATTTTT-A
          1 -CCCCAAAACTTTC-AAAAATCCCATTTTTA-CCCCAAAACTTCTAAAAATCCCATTTTTAA

                         * *                  *                         
       2174 CCCTC-AAACTTTTATAAATCCCATTTTTACCCCCAAACTTCTAAAAATCCCATTTTTAA
          1 CCC-CAAAACTTTCAAAAATCCCATTTTTACCCCAAAACTTCTAAAAATCCCATTTTTAA

              *              * *             **    *     *           
       2233 CCTCAAAACTTTCAAAAGTTCCATTTTTACCCCCGAACTCCTAAAGATCCCATTTTT
          1 CCCCAAAACTTTCAAAAATCCCATTTTTACCCCAAAACTTCTAAAAATCCCATTTTT

       2290 TTACCTCGAA


Statistics
Matches: 452,  Mismatches: 61, Indels: 35
        0.82            0.11        0.06

Matches are distributed among these distances:
  57   30  0.07
  58   74  0.16
  59  172  0.38
  60  170  0.38
  61    6  0.01

ACGTcount: A:0.38, C:0.30, G:0.02, T:0.31


Consensus pattern (59 bp):   
CCCCAAAACTTTCAAAAATCCCATTTTTACCCCAAAACTTCTAAAAATCCCATTTTTAA

Done.