Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000476.1 Kokia drynarioides strain JFW-HI SEQ_111350, 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, 959

Length: 1599
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35


Found at i:533 original size:36 final size:35

Alignment explanation


    Indices: 432--533  Score: 150
    Period size: 36  Copynumber: 2.8  Consensus size: 35

        422 ATTCGTGAGA

                                         *      
        432 TAAGCACTTCTTTAGAATTACGCTCTAACCAAGACG
          1 TAAGCACTT-TTTAGAATTACGCTCTAACTAAGACG

                           *                    
        468 TAAGCACTTTCTTAGCATTACGCTCTAACTAAGACG
          1 TAAGCACTTT-TTAGAATTACGCTCTAACTAAGACG

                             *            
        504 TAAGCACTTTTATAGAAATACGCTCTAACT
          1 TAAGCACTTTT-TAGAATTACGCTCTAACT

        534 GAGATGTATG


Statistics
Matches: 60,  Mismatches: 4, Indels: 4
        0.88            0.06        0.06

Matches are distributed among these distances:
  35    2  0.03
  36   58  0.97

ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30


Consensus pattern (35 bp):   
TAAGCACTTTTTAGAATTACGCTCTAACTAAGACG

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 CTTCTTTAGA

                          *   *       *              *       *               
        448 ATTACGCTCTAACCAAGACGTAAGCACTTTCTTAGCATTACGCTCTAACTAAGACGTAAGCACTT
          1 ATTACGCTCTAACCGAGAAGTAAGCAATTTCTTAGCATTACACTCTAACCAAGACGTAAGCA-TT

              *                  **         *         * 
        513 T-TATAGAAATACGCTCTAACTGAGATGTATGTAATCACACAGC
         65 TCCATAGAAATACGCTCTAACCAAGATGTATGCAATCACACAAC

                 *                                              *            
        556 ATTACACTCTAACCGAGAAGTAAG-AATTTCCTTTA-CATTACACTCTAACCGAGACGTAAGCAT
          1 ATTACGCTCTAACCGAGAAGTAAGCAATTT-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    7  0.07
 108   97  0.91
 109    3  0.03

ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27


Consensus pattern (108 bp):   
ATTACGCTCTAACCGAGAAGTAAGCAATTTCTTAGCATTACACTCTAACCAAGACGTAAGCATTT
CCATAGAAATACGCTCTAACCAAGATGTATGCAATCACACAAC

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

Alignment explanation


    Indices: 448--681  Score: 145
    Period size: 36  Copynumber: 6.5  Consensus size: 36

        438 CTTCTTTAGA

                          *                 *    
        448 ATTACGCTCTAACCAAGACGTAAGCACTTT-CTTAGC
          1 ATTACGCTCTAACCGAGACGTAAGCA-TTTCCATAGC

                         **                *    *
        484 ATTACGCTCTAACTAAGACGTAAGCACTTT-TATAGA
          1 ATTACGCTCTAACCGAGACGTAAGCA-TTTCCATAGC

             *           *    *   * *  *     *   
        520 AATACGCTCTAACTGAGATGTATGTA-ATCACACAGC
          1 ATTACGCTCTAACCGAGACGTAAGCATTTC-CATAGC

                 *            *     *       *    
        556 ATTACACTCTAACCGAGAAGTAAGAATTTCCTTTA-C
          1 ATTACGCTCTAACCGAGACGTAAGCATTTCC-ATAGC

                 *                              
        592 ATTACACTCTAACCGAGACGTAAGCATTTCCATAGC
          1 ATTACGCTCTAACCGAGACGTAAGCATTTCCATAGC

             *  *         *   *   *    *     * * 
        628 AATATGCTCTAACCAAGATGTATGCA-ATCACACAAC
          1 ATTACGCTCTAACCGAGACGTAAGCATTTC-CATAGC

                *             
        664 ATTATGCTCTAACCGAGA
          1 ATTACGCTCTAACCGAGA

        682 TATAAACTCT


Statistics
Matches: 156,  Mismatches: 36, Indels: 12
        0.76            0.18        0.06

Matches are distributed among these distances:
  34    1  0.01
  35    4  0.03
  36  148  0.95
  37    3  0.02

ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27


Consensus pattern (36 bp):   
ATTACGCTCTAACCGAGACGTAAGCATTTCCATAGC
Done.