Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004134.1 Kokia drynarioides strain JFW-HI SEQ_117329, 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: 17625
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33


Found at i:3668 original size:53 final size:52

Alignment explanation


    Indices: 3603--3891  Score: 307
    Period size: 53  Copynumber: 5.5  Consensus size: 52

       3593 GAAAATGTCC

                   *         *                                   
       3603 GATGACTTTGTGTCATCGTGAGTTATATGAATCCTATCACGAATTAAAGGTCT
          1 GATGACTCTGTGTCATCATGAGTTATATGAATCCTATCA-GAATTAAAGGTCT

                                             *       *           
       3656 GATGACTCTGTGTCATCATGAGTTATATGAATCTTATCACGGATTAAAGGT-T
          1 GATGACTCTGTGTCATCATGAGTTATATGAATCCTATCA-GAATTAAAGGTCT

                     *        *                     *             
       3708 AGATGACTCAGTGTCATCGTGAGTTATATGAATCCTATCATAGATTAAAGGTCT
          1 -GATGACTCTGTGTCATCATGAGTTATATGAATCCTATCAGA-ATTAAAGGTCT

                    *        *                   *         *    *
       3762 GATGACTCAGTGTCATCGTGAGTTATATGAATCCTATTAGAAATTAAGGGTCC
          1 GATGACTCTGTGTCATCATGAGTTATATGAATCCTATCAG-AATTAAAGGTCT

                          *          *        *       *       *  *
       3815 GATGA--CTGTGTCCTCATGAGTTACA-GAAATCTTATCATGGATTAAAGCTCC
          1 GATGACTCTGTGTCATCATGAGTTATATG-AATCCTATCA-GAATTAAAGGTCT

                   *      *           
       3866 GATGACTTTGTGTCGTCATGAGTTAT
          1 GATGACTCTGTGTCATCATGAGTTAT

       3892 CACATGTGAA


Statistics
Matches: 203,  Mismatches: 25, Indels: 16
        0.83            0.10        0.07

Matches are distributed among these distances:
  50    1  0.00
  51   38  0.19
  52    2  0.01
  53  160  0.79
  54    2  0.01

ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35


Consensus pattern (52 bp):   
GATGACTCTGTGTCATCATGAGTTATATGAATCCTATCAGAATTAAAGGTCT

Found at i:3738 original size:25 final size:25

Alignment explanation


    Indices: 3705--3791  Score: 59
    Period size: 25  Copynumber: 3.4  Consensus size: 25

       3695 CGGATTAAAG

                *                    
       3705 GTTAGATGACTCAGTGTCATCGTGA
          1 GTTATATGACTCAGTGTCATCGTGA

                     *   * *    *     * 
       3730 GTTATATGAATC-CTATCATAGATTAAA
          1 GTTATATGACTCAGTGTCATCG--T-GA

             * *                      
       3757 GGTCTGATGACTCAGTGTCATCGTGA
          1 GTTAT-ATGACTCAGTGTCATCGTGA

                     
       3783 GTTATATGA
          1 GTTATATGA

       3792 ATCCTATTAG


Statistics
Matches: 42,  Mismatches: 15, Indels: 10
        0.63            0.22        0.15

Matches are distributed among these distances:
  24    6  0.14
  25   14  0.33
  26    5  0.12
  27    5  0.12
  28    6  0.14
  29    6  0.14

ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34


Consensus pattern (25 bp):   
GTTATATGACTCAGTGTCATCGTGA

Found at i:3872 original size:157 final size:158

Alignment explanation


    Indices: 3603--3891  Score: 395
    Period size: 157  Copynumber: 1.8  Consensus size: 158

       3593 GAAAATGTCC

                   **                                           *            
       3603 GATGACTTTGTGTCATCGTGAGTTATATGAATCCTATCACGAATTAAAGGTCTGATGACTCTGTG
          1 GATGACTCAGTGTCATCGTGAGTTATATGAATCCTATCACGAATTAAAGGTCCGATGAC-CTGTG

                         *                       * *                  *      
       3668 TCATCATGAGTTATATGAATCTTATCACGGATTAAAGGTTAGATGACTCAGTGTCATCGTGAGTT
         65 TCATCATGAGTTACATGAATCTTATCACGGATTAAAGCTCAGATGACTCAGTGTCATCATGAGTT

                                         
       3733 ATATGAATCCTATCATAGATTAAAGGTCT
        130 ATATGAATCCTATCATAGATTAAAGGTCT

                                                 *          *                
       3762 GATGACTCAGTGTCATCGTGAGTTATATGAATCCTATTA-GAAATTAAGGGTCCGATGA-CTGTG
          1 GATGACTCAGTGTCATCGTGAGTTATATGAATCCTATCACG-AATTAAAGGTCCGATGACCTGTG

              *                         *            *       **     *        
       3825 TCCTCATGAGTTACA-GAAATCTTATCATGGATTAAAGCTCCGATGACTTTGTGTCGTCATGAGT
         65 TCATCATGAGTTACATG-AATCTTATCACGGATTAAAGCTCAGATGACTCAGTGTCATCATGAGT

               
       3889 TAT
        129 TAT

       3892 CACATGTGAA


Statistics
Matches: 113,  Mismatches: 15, Indels: 6
        0.84            0.11        0.04

Matches are distributed among these distances:
 156    1  0.01
 157   60  0.53
 158    1  0.01
 159   51  0.45

ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35


Consensus pattern (158 bp):   
GATGACTCAGTGTCATCGTGAGTTATATGAATCCTATCACGAATTAAAGGTCCGATGACCTGTGT
CATCATGAGTTACATGAATCTTATCACGGATTAAAGCTCAGATGACTCAGTGTCATCATGAGTTA
TATGAATCCTATCATAGATTAAAGGTCT

Found at i:4452 original size:24 final size:25

Alignment explanation


    Indices: 4425--4472  Score: 71
    Period size: 24  Copynumber: 2.0  Consensus size: 25

       4415 GTTGATTAGT

                    *                
       4425 AAGTATCGGTAG-TTCTGTACTTGA
          1 AAGTATCGATAGATTCTGTACTTGA

                           *        
       4449 AAGTATCGATAGATTTTGTACTTG
          1 AAGTATCGATAGATTCTGTACTTG

       4473 TATCGGTAGA


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  24   11  0.52
  25   10  0.48

ACGTcount: A:0.27, C:0.10, G:0.23, T:0.40


Consensus pattern (25 bp):   
AAGTATCGATAGATTCTGTACTTGA

Found at i:6461 original size:18 final size:17

Alignment explanation


    Indices: 6438--6471  Score: 50
    Period size: 18  Copynumber: 1.9  Consensus size: 17

       6428 AAAATGAGTG

                              
       6438 CAGTGAAAATATAAAATC
          1 CAGTGAAAATA-AAAATC

                  *         
       6456 CAGTGACAATAAAAAT
          1 CAGTGAAAATAAAAAT

       6472 GCAAAAACTA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    5  0.33
  18   10  0.67

ACGTcount: A:0.56, C:0.12, G:0.12, T:0.21


Consensus pattern (17 bp):   
CAGTGAAAATAAAAATC
Done.