Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003446.1 Kokia drynarioides strain JFW-HI SEQ_116234, 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: 2987
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34


Found at i:44 original size:30 final size:29

Alignment explanation


    Indices: 8--146  Score: 111
    Period size: 30  Copynumber: 4.7  Consensus size: 29

          1 AACTATC

                     *                    
          8 CAAAAATCATATTTTGATCCCTAAACTTTT
          1 CAAAAATCACATTTTGA-CCCTAAACTTTT

                   **     *     *    *    
         38 CAAAAATTGCATTTGGACCTTTAAAATTTT
          1 CAAAAATCACATTTTGACC-CTAAACTTTT

                           *            * 
         68 CAAAAATCACATTTTTACCCCTAAACTTCT
          1 CAAAAATCACATTTTGA-CCCTAAACTTTT

               *   *       *             
         98 -AAGAATTACATTTTAACCCTAAA-TTTT
          1 CAAAAATCACATTTTGACCCTAAACTTTT

                    *       *     
        125 CCAAAAATTACATTTTAACCCT
          1 -CAAAAATCACATTTTGACCCT

        147 CGAATGTCTA


Statistics
Matches: 87,  Mismatches: 18, Indels: 9
        0.76            0.16        0.08

Matches are distributed among these distances:
  27    3  0.03
  28    7  0.08
  29   34  0.39
  30   41  0.47
  31    2  0.02

ACGTcount: A:0.38, C:0.21, G:0.04, T:0.37


Consensus pattern (29 bp):   
CAAAAATCACATTTTGACCCTAAACTTTT

Found at i:140 original size:29 final size:29

Alignment explanation


    Indices: 6--146  Score: 108
    Period size: 29  Copynumber: 4.8  Consensus size: 29

          1 AACTA

                     * *       *           
          6 TCCAAAAATCATATTTTGATCCCTAAACTTT
          1 TCCAAAAATTACATTTT-AACCCTAAA-TTT

                      *     **    *        
         37 T-CAAAAATTGCATTTGGACCTTTAAAATTT
          1 TCCAAAAATTACATTTTAACC-CT-AAATTT

                     *         *        * 
         67 T-CAAAAATCACATTTTTACCCCTAAA-CT
          1 TCCAAAAATTACA-TTTTAACCCTAAATTT

              *  *                       
         95 TCTAAGAATTACATTTTAACCCTAAATTT
          1 TCCAAAAATTACATTTTAACCCTAAATTT

                                   
        124 TCCAAAAATTACATTTTAACCCT
          1 TCCAAAAATTACATTTTAACCCT

        147 CGAATGTCTA


Statistics
Matches: 84,  Mismatches: 21, Indels: 12
        0.72            0.18        0.10

Matches are distributed among these distances:
  28   14  0.17
  29   35  0.42
  30   26  0.31
  31    9  0.11

ACGTcount: A:0.38, C:0.21, G:0.04, T:0.38


Consensus pattern (29 bp):   
TCCAAAAATTACATTTTAACCCTAAATTT

Found at i:157 original size:58 final size:57

Alignment explanation


    Indices: 8--223  Score: 143
    Period size: 58  Copynumber: 3.7  Consensus size: 57

          1 AACTATC

                     *     * *          *         *     **    *         
          8 CAAAAATCATATTTTGATCCCTAAACTTTTCAAAAATTGCATTTGGACCTTTAAAATTTT
          1 CAAAAATCACATTTTAACCCCTAAACTTCT-AAAAATTACATTTTAACC-CT-AAATTTT

                           *                *                        
         68 CAAAAATCACATTTTTACCCCTAAACTTCTAAGAATTACATTTTAACCCTAAATTTT
          1 CAAAAATCACATTTTAACCCCTAAACTTCTAAAAATTACATTTTAACCCTAAATTTT

                    *               *               *           * *  *  * 
        125 CCAAAAATTACATTTTAA-CCCTCGAA-TGTCTAAAAATTCCATTTTTGAACTCGAACTTCT
          1 -CAAAAATCACATTTTAACCCCT-AAACT-TCTAAAAATTACA-TTTT-AACCCTAAATTTT

                     *             *                 
        185 -AAAAATCATATTTTTAACCCC-GAACTTTCTAAAAATTAC
          1 CAAAAATCACA-TTTTAACCCCTAAAC-TTCTAAAAATTAC

        224 CATGTCCAGG


Statistics
Matches: 126,  Mismatches: 21, Indels: 19
        0.76            0.13        0.11

Matches are distributed among these distances:
  57   12  0.10
  58   40  0.32
  59   35  0.28
  60   39  0.31

ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37


Consensus pattern (57 bp):   
CAAAAATCACATTTTAACCCCTAAACTTCTAAAAATTACATTTTAACCCTAAATTTT

Found at i:159 original size:29 final size:31

Alignment explanation


    Indices: 65--223  Score: 133
    Period size: 29  Copynumber: 5.5  Consensus size: 31

         55 CCTTTAAAAT

                       *         *     *   
         65 TTTC-AAAAATCACATTTTTACCCCT-AAAC
          1 TTTCTAAAAATTACATTTTTAACCCTCGAAC

                   *                   *  *
         94 -TTCTAAGAATTACA-TTTTAACCCT-AAAT
          1 TTTCTAAAAATTACATTTTTAACCCTCGAAC

                *                          
        122 TTTCCAAAAATTACA-TTTTAACCCTCGAA-
          1 TTTCTAAAAATTACATTTTTAACCCTCGAAC

             *          *                   
        151 TGTCTAAAAATTCCATTTTTGAA--CTCGAAC
          1 TTTCTAAAAATTACATTTTT-AACCCTCGAAC

                       * *                 
        181 -TTCTAAAAATCATATTTTTAACCC-CGAAC
          1 TTTCTAAAAATTACATTTTTAACCCTCGAAC

                          
        210 TTTCTAAAAATTAC
          1 TTTCTAAAAATTAC

        224 CATGTCCAGG


Statistics
Matches: 105,  Mismatches: 16, Indels: 17
        0.76            0.12        0.12

Matches are distributed among these distances:
  28   17  0.16
  29   68  0.65
  30   18  0.17
  31    2  0.02

ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36


Consensus pattern (31 bp):   
TTTCTAAAAATTACATTTTTAACCCTCGAAC
Done.