Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006139.1 Kokia drynarioides strain JFW-HI SEQ_120673, 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: 3062
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.33


Found at i:917 original size:17 final size:16

Alignment explanation


    Indices: 842--907  Score: 60
    Period size: 17  Copynumber: 3.9  Consensus size: 16

        832 CCCAGTAAAC

                     **      
        842 TTAAATTTATTTTTATT
          1 TTAAATTTAAATTTA-T

                           * 
        859 TTAAATTTAAATTTGGT
          1 TTAAATTTAAATTT-AT

             *        *     
        876 TGAAATTTAAGTTTAT
          1 TTAAATTTAAATTTAT

                            
        892 TATAAATTTAAATTTA
          1 T-TAAATTTAAATTTA

        908 AAGTTTATTT


Statistics
Matches: 39,  Mismatches: 8, Indels: 4
        0.76            0.16        0.08

Matches are distributed among these distances:
  16    2  0.05
  17   37  0.95

ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56


Consensus pattern (16 bp):   
TTAAATTTAAATTTAT

Found at i:2690 original size:29 final size:29

Alignment explanation


    Indices: 2658--2867  Score: 173
    Period size: 29  Copynumber: 7.1  Consensus size: 29

       2648 AAAATTATCA

                    *                    
       2658 TTTTACCCCCGAACTTCCAAAAATCCCAT
          1 TTTTACCCTCGAACTTCCAAAAATCCCAT

                               *       *    
       2687 TTTTGA-CCTCGAACCTTCTAAAAATTACCA-
          1 TTTT-ACCCTCGAA-CTTCCAAAAA-TCCCAT

                  *                      
       2717 TTTTACTCTCGAACTTCCAAAAATCCCAT
          1 TTTTACCCTCGAACTTCCAAAAATCCCAT

                                *       *    
       2746 TTTTGACCC-C-ATACCTTCTAAAAATTACC-T
          1 TTTT-ACCCTCGA-A-CTTCCAAAAA-TCCCAT

                                     *   
       2776 TTTTACCCTCGAACTTCCAAAAATCTCAT
          1 TTTTACCCTCGAACTTCCAAAAATCCCAT

                      *         *    * *    
       2805 TTTTGA-CCTTGAACCTTTCGAAAATTACCA-
          1 TTTT-ACCCTCGAA-C-TTCCAAAAATCCCAT

                      *                  
       2835 TTTTACCCTCAAACTTCCAAAAATCCCAT
          1 TTTTACCCTCGAACTTCCAAAAATCCCAT

                
       2864 TTTT
          1 TTTT

       2868 TGACTCCGAA


Statistics
Matches: 142,  Mismatches: 22, Indels: 34
        0.72            0.11        0.17

Matches are distributed among these distances:
  28   18  0.13
  29   56  0.39
  30   50  0.35
  31   18  0.13

ACGTcount: A:0.31, C:0.30, G:0.04, T:0.35


Consensus pattern (29 bp):   
TTTTACCCTCGAACTTCCAAAAATCCCAT

Found at i:2739 original size:59 final size:59

Alignment explanation


    Indices: 2647--2897  Score: 339
    Period size: 59  Copynumber: 4.3  Consensus size: 59

       2637 TAAACTTTTC

                    *          *                                       
       2647 AAAAATTATCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCT
          1 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCT

                             *                                *         
       2706 AAAAATTACCATTTTACTCTCGAACTTCCAAAAATCCCATTTTTGACC-CCATACCTTCT
          1 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCGA-ACCTTCT

                      *                         *            *         
       2765 AAAAATTACCTTTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCTTGAACCTT-T
          1 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCT

             *                    *                                       
       2823 CGAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTTGA-CTCCGAACCTTC-
          1 -AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCA-TTTTTGACCT-CGAACCTTCT

            *    *         
       2883 CAAAACTACCATTTT
          1 AAAAATTACCATTTT

       2898 GCCCCCGTGC


Statistics
Matches: 170,  Mismatches: 16, Indels: 12
        0.86            0.08        0.06

Matches are distributed among these distances:
  58    3  0.02
  59  152  0.89
  60   15  0.09

ACGTcount: A:0.32, C:0.29, G:0.04, T:0.34


Consensus pattern (59 bp):   
AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCT

Found at i:2927 original size:118 final size:118

Alignment explanation


    Indices: 2647--2928  Score: 320
    Period size: 118  Copynumber: 2.4  Consensus size: 118

       2637 TAAACTTTTC

                 *  *                *          *  *                         
       2647 AAAAATTATCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCTAAAAAT
          1 AAAAACTACCATTTTACCCCCGAACATCCAAAAATCTCAGTTTTGACCTCGAACCTTCTAAAAAT

                       *   *                                     
       2712 TACCATTTTACTCTCGAACTTCCAAAAATCCCATTTTTGACCCCATACCTTCT
         66 TACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCATACCTTCT

                 *    *        *     *             *         *          *    
       2765 AAAAATTACCTTTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCTTGAACCTT-TCGAAAA
          1 AAAAACTACCATTTTACCCCCGAACATCCAAAAATCTCAGTTTTGACCTCGAACCTTCT-AAAAA

                                                          *         
       2829 TTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTTGACTCCGA-ACCTTC-
         65 TTACCATTTTACCCTCAAACTTCCAAAAATCCCA-TTTTTGAC-CCCATACCTTCT

            *              *      **          *            
       2883 CAAAACTACCATTTTGCCCCCGTGCATCCGAAAAGTCTC-GTTTTGA
          1 AAAAACTACCATTTTACCCCCGAACATCC-AAAAATCTCAGTTTTGA

       2929 ACTCCGATTA


Statistics
Matches: 141,  Mismatches: 19, Indels: 8
        0.84            0.11        0.05

Matches are distributed among these distances:
 117    1  0.01
 118  115  0.82
 119   22  0.16
 120    3  0.02

ACGTcount: A:0.31, C:0.30, G:0.06, T:0.33


Consensus pattern (118 bp):   
AAAAACTACCATTTTACCCCCGAACATCCAAAAATCTCAGTTTTGACCTCGAACCTTCTAAAAAT
TACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCATACCTTCT
Done.