Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001783.1 Kokia drynarioides strain JFW-HI SEQ_113512, 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: 6678
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33


Found at i:2599 original size:41 final size:41

Alignment explanation


    Indices: 2547--2831  Score: 291
    Period size: 41  Copynumber: 6.9  Consensus size: 41

       2537 CTTTAGTGAT

                *        *                           
       2547 GCTTGCTCATAAGTGCCGCTAATGCTCTGACCTTTAGCGGC
          1 GCTTCCTCATAAGCGCCGCTAATGCTCTGACCTTTAGCGGC

                  *        * **              *       
       2588 GCTTCCACATAAGCGTCATTAATGCTCTGACCTGTAGCGGC
          1 GCTTCCTCATAAGCGCCGCTAATGCTCTGACCTTTAGCGGC

                  *                                  *
       2629 GCTTCCACATAAGCGCCGCTAAATGCTCTGACCTTTAGCGGT
          1 GCTTCCTCATAAGCGCCGCT-AATGCTCTGACCTTTAGCGGC

                     *    **  *        **  *       * 
       2671 GCTTCCTCAAAAGCATCGTTAATGCTCCAACTTTTAGCGAC
          1 GCTTCCTCATAAGCGCCGCTAATGCTCTGACCTTTAGCGGC

            *   *       *              *   *         
       2712 ACTTTCTCATAAACGCCGCTAATGCTCCGACTTTTAGCGGC
          1 GCTTCCTCATAAGCGCCGCTAATGCTCTGACCTTTAGCGGC

                           * *         *   *         
       2753 GCTTCCTCATAAGCGTCTCTAATGCTCCGACTTTTAGCGGC
          1 GCTTCCTCATAAGCGCCGCTAATGCTCTGACCTTTAGCGGC

                          *  **             *     
       2794 GCTTCCTCATAAGCACCATTAATGCTCTGACCATTAGC
          1 GCTTCCTCATAAGCGCCGCTAATGCTCTGACCTTTAGC

       2832 AGCGTTTTAT


Statistics
Matches: 200,  Mismatches: 43, Indels: 2
        0.82            0.18        0.01

Matches are distributed among these distances:
  41  166  0.83
  42   34  0.17

ACGTcount: A:0.22, C:0.31, G:0.19, T:0.29


Consensus pattern (41 bp):   
GCTTCCTCATAAGCGCCGCTAATGCTCTGACCTTTAGCGGC

Found at i:2776 original size:82 final size:82

Alignment explanation


    Indices: 2547--2831  Score: 347
    Period size: 82  Copynumber: 3.5  Consensus size: 82

       2537 CTTTAGTGAT

                *        *                                 *                 
       2547 GCTTGCTCATAAGTGCCGCTAATGCTCTGACCTTTAGCGGCGCTTCCACATAAGCGTCATTAATG
          1 GCTTCCTCATAAGCGCCGCTAATGCTCTGACCTTTAGCGGCGCTTCCTCATAAGCGTCATTAATG

               *   * *       
       2612 CTCTGACCTGTAGCGGC
         66 CTCCGACTTTTAGCGGC

                  *                                  *         *    *  *     
       2629 GCTTCCACATAAGCGCCGCTAAATGCTCTGACCTTTAGCGGTGCTTCCTCAAAAGCATCGTTAAT
          1 GCTTCCTCATAAGCGCCGCT-AATGCTCTGACCTTTAGCGGCGCTTCCTCATAAGCGTCATTAAT

                 *          * 
       2694 GCTCCAACTTTTAGCGAC
         65 GCTCCGACTTTTAGCGGC

            *   *       *              *   *                                 
       2712 ACTTTCTCATAAACGCCGCTAATGCTCCGACTTTTAGCGGCGCTTCCTCATAAGCGTC-TCTAAT
          1 GCTTCCTCATAAGCGCCGCTAATGCTCTGACCTTTAGCGGCGCTTCCTCATAAGCGTCAT-TAAT

                              
       2776 GCTCCGACTTTTAGCGGC
         65 GCTCCGACTTTTAGCGGC

                          *  **             *     
       2794 GCTTCCTCATAAGCACCATTAATGCTCTGACCATTAGC
          1 GCTTCCTCATAAGCGCCGCTAATGCTCTGACCTTTAGC

       2832 AGCGTTTTAT


Statistics
Matches: 168,  Mismatches: 33, Indels: 4
        0.82            0.16        0.02

Matches are distributed among these distances:
  81    1  0.01
  82   99  0.59
  83   68  0.40

ACGTcount: A:0.22, C:0.31, G:0.19, T:0.29


Consensus pattern (82 bp):   
GCTTCCTCATAAGCGCCGCTAATGCTCTGACCTTTAGCGGCGCTTCCTCATAAGCGTCATTAATG
CTCCGACTTTTAGCGGC

Found at i:2896 original size:40 final size:40

Alignment explanation


    Indices: 2837--2955  Score: 157
    Period size: 40  Copynumber: 3.0  Consensus size: 40

       2827 TTAGCAGCGT

                          *       *           *     
       2837 TTTATGGAAAAATGTCGCTATTACTTTACCTTTTACGGTA
          1 TTTATGGAAAAATGCCGCTATTGCTTTACCTTTTGCGGTA

                                                 ***
       2877 TTTATGGAAAAATGCCGCTATTGCTTTACCTTTTGCGACG
          1 TTTATGGAAAAATGCCGCTATTGCTTTACCTTTTGCGGTA

                        *    *           *         
       2917 TTTATGGAAAAACGCCGTTATTGCTTTACTTTTTGCGGT
          1 TTTATGGAAAAATGCCGCTATTGCTTTACCTTTTGCGGT

       2956 GTTTTCTATC


Statistics
Matches: 68,  Mismatches: 11, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  40   68  1.00

ACGTcount: A:0.24, C:0.17, G:0.18, T:0.41


Consensus pattern (40 bp):   
TTTATGGAAAAATGCCGCTATTGCTTTACCTTTTGCGGTA

Found at i:4784 original size:2 final size:2

Alignment explanation


    Indices: 4771--4806  Score: 63
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       4761 CGAGTGCAAA

                   *                                             
       4771 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       4807 CTGCTACAAC


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Done.