Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004417.1 Kokia drynarioides strain JFW-HI SEQ_117798, 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: 3157
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32


Found at i:948 original size:17 final size:16

Alignment explanation


    Indices: 921--977  Score: 62
    Period size: 17  Copynumber: 3.4  Consensus size: 16

        911 AATAAATAAA

                *           
        921 AATACATGAATAAAAT
          1 AATAAATGAATAAAAT

                            * 
        937 AATTAAATGAATACAATT
          1 AA-TAAATGAATA-AAAT

                             
        955 AATAACAT-AATAAAAT
          1 AATAA-ATGAATAAAAT

                   
        971 AATAAAT
          1 AATAAAT

        978 AGAAGTAACT


Statistics
Matches: 35,  Mismatches: 3, Indels: 7
        0.78            0.07        0.16

Matches are distributed among these distances:
  15    2  0.06
  16   10  0.29
  17   16  0.46
  18    7  0.20

ACGTcount: A:0.63, C:0.05, G:0.04, T:0.28


Consensus pattern (16 bp):   
AATAAATGAATAAAAT

Found at i:2540 original size:45 final size:45

Alignment explanation


    Indices: 2354--2934  Score: 565
    Period size: 45  Copynumber: 12.6  Consensus size: 45

       2344 CATCAATTTA

                           *     *               *           
       2354 CCCCTCTAGATTTAATGGGTATAAGATTGGATGTGTTAGCTTCAATCTG
          1 CCCCTCTAGA-TT-AGGGGTAAAAGATTGGATG-G-TGGCTTCAATCTG

            *                   *               *           
       2403 TCCCTCTAGATTTAGGGGTATAAGATTGGATGTGGTAGCTTCAATCTG
          1 CCCCTCTAGA-TTAGGGGTAAAAGATTGGA--TGGTGGCTTCAATCTG

              *  * *                        *      *     *
       2451 CCTCTATGGATTTAGGGGTAAAAGATTGGATGATGGCTTTAATCTA
          1 CCCCTCTAGA-TTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTG

                         *   *                *          
       2497 CCCCTCTAGATTAAGGGCAAAAGATTGGATGGTGACTTCAATCTG
          1 CCCCTCTAGATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTG

                   *     *                   *           
       2542 CCCCTCTGGATTAAGGGTAAAAGATTGGATGGTAGCTTCAATCTG
          1 CCCCTCTAGATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTG

                          *                *          *  
       2587 CCCCTCTAGATTAGAGGTAAAAGATTGGATGATGGCTTCAATTTG
          1 CCCCTCTAGATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTG

                       *                  *  *         *  
       2632 CCCCTCT-GAAGTAGGGGTAAAAGATTGGACGGAGGCTTCAATTTG
          1 CCCCTCTAG-ATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTG

               * * *         *      *              **    *
       2677 CCCTTTTGGATTTAGGGATAAAAGGTTGGATGGTGGCTTTGATCTA
          1 CCCCTCTAGA-TTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTG

              *                          *              *  
       2723 CCTCT-TCAGATTTAGGGGTAAAAGATTGAATGGTGGCTTCAATTTG
          1 CCCCTCT-AGA-TTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTG

              *     *                         *         *
       2769 CCTCTCTAAATTAGGGGTAAAAGATTGGATGGTGACTTCAATCTA
          1 CCCCTCTAGATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTG

            *  *                                 *  *      
       2814 TCCTTCT-GTATTTAGGGGTAAAAGATTGGATGGTGGTTTAAATCTG
          1 CCCCTCTAG-A-TTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTG

                   *                    *        *         
       2860 CCCCTCTGGATTTAGGGAGTAAAAGATTAGATGGTGGTTTCAATCTG
          1 CCCCTCTAGA-TTAGGG-GTAAAAGATTGGATGGTGGCTTCAATCTG

              *                         
       2907 CCTCTCTAGATTAGGGGTAAAAGATTGG
          1 CCCCTCTAGATTAGGGGTAAAAGATTGG

       2935 GTGTTACAGC


Statistics
Matches: 445,  Mismatches: 76, Indels: 26
        0.81            0.14        0.05

Matches are distributed among these distances:
  44    1  0.00
  45  201  0.45
  46  137  0.31
  47   37  0.08
  48   54  0.12
  49   13  0.03
  50    2  0.00

ACGTcount: A:0.26, C:0.15, G:0.27, T:0.33


Consensus pattern (45 bp):   
CCCCTCTAGATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTG

Done.