Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000475.1 Kokia drynarioides strain JFW-HI SEQ_111349, 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, 971

Length: 1619
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34


Found at i:533 original size:36 final size:36

Alignment explanation


    Indices: 432--533  Score: 152
    Period size: 36  Copynumber: 2.8  Consensus size: 36

        422 ATTCGTGAGA

                     *                   *      
        432 TAAGCACTTCCTTAGAATTACGCTCTAACCAAGACG
          1 TAAGCACTTTCTTAGAATTACGCTCTAACTAAGACG

                           *                    
        468 TAAGCACTTTCTTAGCATTACGCTCTAACTAAGACG
          1 TAAGCACTTTCTTAGAATTACGCTCTAACTAAGACG

                              *            
        504 TAAGCACTTT-TATAGAAATACGCTCTAACT
          1 TAAGCACTTTCT-TAGAATTACGCTCTAACT

        534 GAGATGTATG


Statistics
Matches: 60,  Mismatches: 5, Indels: 2
        0.90            0.07        0.03

Matches are distributed among these distances:
  35    1  0.02
  36   59  0.98

ACGTcount: A:0.33, C:0.25, G:0.13, T:0.29


Consensus pattern (36 bp):   
TAAGCACTTTCTTAGAATTACGCTCTAACTAAGACG

Found at i:611 original size:108 final size:108

Alignment explanation


    Indices: 448--681  Score: 285
    Period size: 108  Copynumber: 2.2  Consensus size: 108

        438 CTTCCTTAGA

                          *   *    *                 *       *               
        448 ATTACGCTCTAACCAAGACGTAAGCACTTTCTTAGCATTACGCTCTAACTAAGACGTAAGCACTT
          1 ATTACGCTCTAACCGAGAAGTAACCACTTTCTTAGCATTACACTCTAACCAAGACGTAAGCA-TT

              *                  **         *         * 
        513 T-TATAGAAATACGCTCTAACTGAGATGTATGTAATCACACAGC
         65 TCCATAGAAATACGCTCTAACCAAGATGTATGCAATCACACAAC

                 *                                              *            
        556 ATTACACTCTAACCGAGAAGTAACCA-TTTCCTTTA-CATTACACTCTAACCGAGACGTAAGCAT
          1 ATTACGCTCTAACCGAGAAGTAACCACTTT-C-TTAGCATTACACTCTAACCAAGACGTAAGCAT

                    *    *                               
        619 TTCCATAGCAATATGCTCTAACCAAGATGTATGCAATCACACAAC
         64 TTCCATAGAAATACGCTCTAACCAAGATGTATGCAATCACACAAC

                *             
        664 ATTATGCTCTAACCGAGA
          1 ATTACGCTCTAACCGAGA

        682 TATAAACTCT


Statistics
Matches: 107,  Mismatches: 16, Indels: 6
        0.83            0.12        0.05

Matches are distributed among these distances:
 107    6  0.06
 108   98  0.92
 109    3  0.03

ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27


Consensus pattern (108 bp):   
ATTACGCTCTAACCGAGAAGTAACCACTTTCTTAGCATTACACTCTAACCAAGACGTAAGCATTT
CCATAGAAATACGCTCTAACCAAGATGTATGCAATCACACAAC

Found at i:638 original size:36 final size:36

Alignment explanation


    Indices: 432--681  Score: 150
    Period size: 36  Copynumber: 6.9  Consensus size: 36

        422 ATTCGTGAGA

                  *    *   *              *     
        432 TAAGCACTTCCTTAGAATTACGCTCTAACCAAGACG
          1 TAAGCATTTCCATAGCATTACGCTCTAACCGAGACG

                        *                 **     
        468 TAAGCACTTT-CTTAGCATTACGCTCTAACTAAGACG
          1 TAAGCA-TTTCCATAGCATTACGCTCTAACCGAGACG

                       *    * *           *    * 
        504 TAAGCACTTT-TATAGAAATACGCTCTAACTGAGATG
          1 TAAGCA-TTTCCATAGCATTACGCTCTAACCGAGACG

              * *  *     *        *            * 
        540 TATGTA-ATCACACAGCATTACACTCTAACCGAGAAG
          1 TAAGCATTTC-CATAGCATTACGCTCTAACCGAGACG

               *        *         *              
        576 TAACCATTTCCTTTA-CATTACACTCTAACCGAGACG
          1 TAAGCATTTCC-ATAGCATTACGCTCTAACCGAGACG

                             *  *         *   * 
        612 TAAGCATTTCCATAGCAATATGCTCTAACCAAGATG
          1 TAAGCATTTCCATAGCATTACGCTCTAACCGAGACG

              *    *     * *     *             
        648 TATGCA-ATCACACAACATTATGCTCTAACCGAGA
          1 TAAGCATTTC-CATAGCATTACGCTCTAACCGAGA

        682 TATAAACTCT


Statistics
Matches: 168,  Mismatches: 39, Indels: 14
        0.76            0.18        0.06

Matches are distributed among these distances:
  34    1  0.01
  35    4  0.02
  36  158  0.94
  37    5  0.03

ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27


Consensus pattern (36 bp):   
TAAGCATTTCCATAGCATTACGCTCTAACCGAGACG
Done.