Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009444.1 Kokia drynarioides strain JFW-HI SEQ_124151, 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: 12671
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25


Found at i:11377 original size:160 final size:155

Alignment explanation


    Indices: 10993--11473  Score: 478
    Period size: 156  Copynumber: 3.1  Consensus size: 155

      10983 CATCTTCCTT

                              *                    *                *        
      10993 ATGAGATACTGAGAAGAATACCAAACCAAACCCACGCTCAATGTGAGCAAGTCTTCAAATCCCAG
          1 ATGAGATACTGAGAAGAAAACCAAACCAAACCCACGCTCGATGTGAGCAAGTCTTCGAA-CCCAG

                       *                  *                                  
      11058 CTTCCTGATGATACACCGAGAAGCAGATCGGAGCAATAAACGATTAGCTTCCTGAGGAGATACGG
         65 CTTCCTGATGACACACCGAGAAGCAGATCGAAGCAATAAACGATTAGCTTCCTGAGGAGATACGG

                      *       *   *  *
      11123 AGAAGTAGGCCAAATTCATCTTCCTG
        130 AGAAGTAGGCAAAATTCAGCTTACTA

                             **                                          *   
      11149 ATGAGATACTGAGAAGATGACCAAACCAAACCCACGCTCGATGTGAGCAAGTCTTCGAATCTCAG
          1 ATGAGATACTGAGAAGAAAACCAAACCAAACCCACGCTCGATGTGAGCAAGTCTTCGAA-CCCAG

                           *                         * *            *       *
      11214 CTTCCTGATGACACATCGAGAAGCAGATCGAAGCAATAAAGTGGTTAGCTTCCTGATGAGATACT
         65 CTTCCTGATGACACACCGAGAAGCAGATCGAAGCAATAAA-CGATTAGCTTCCTGAGGAGATACG

                       *                    
      11279 GAGAAGCGT-GTCGAAGTAATT-AGCTTACTA
        129 GAGAA--GTAGGC-AA--AATTCAGCTTACTA

                      *             ***       *      *        *              
      11309 ATGAGATACTAAGAAGAAAACCAAGTAAAACCCATGCTCGACGTGAGCAAATCTTCGAACCACAG
          1 ATGAGATACTGAGAAGAAAACCAAACCAAACCCACGCTCGATGTGAGCAAGTCTTCGAACC-CAG

                       * *  *                                       *        
      11374 CTTCCTGATGAGATACTGAGAAG-AGTATCGAAG---T-AAC---TAGCTTCCTGATGAGATACG
         65 CTTCCTGATGACACACCGAGAAGCAG-ATCGAAGCAATAAACGATTAGCTTCCTGAGGAGATACG

                     * *       *   *  *
      11431 GAGAAGTAGACCAAATTCATCTTCCTG
        129 GAGAAGTAGGCAAAATTCAGCTTACTA

                *    *      
      11458 ATGAAATACGGAGAAG
          1 ATGAGATACTGAGAAG

      11474 CAGTTTGAAA


Statistics
Matches: 274,  Mismatches: 41, Indels: 27
        0.80            0.12        0.08

Matches are distributed among these distances:
 148    4  0.01
 149   19  0.07
 150    3  0.01
 151    2  0.01
 152   24  0.09
 156   99  0.36
 157   26  0.09
 158    2  0.01
 159    6  0.02
 160   85  0.31
 161    4  0.01

ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21


Consensus pattern (155 bp):   
ATGAGATACTGAGAAGAAAACCAAACCAAACCCACGCTCGATGTGAGCAAGTCTTCGAACCCAGC
TTCCTGATGACACACCGAGAAGCAGATCGAAGCAATAAACGATTAGCTTCCTGAGGAGATACGGA
GAAGTAGGCAAAATTCAGCTTACTA

Found at i:12101 original size:18 final size:17

Alignment explanation


    Indices: 12048--12116  Score: 102
    Period size: 17  Copynumber: 4.0  Consensus size: 17

      12038 GTCTAAAAAA

                             
      12048 TTAAATTTATTTTAAAT
          1 TTAAATTTATTTTAAAT

                *            
      12065 TTAACTTTATTTTAAAT
          1 TTAAATTTATTTTAAAT

                              
      12082 TTAAATTTATTTTCAAAT
          1 TTAAATTTATTTT-AAAT

                 *      *    
      12100 TTAAAATTATTTAAAAT
          1 TTAAATTTATTTTAAAT

      12117 AAATAAATAA


Statistics
Matches: 47,  Mismatches: 4, Indels: 2
        0.89            0.08        0.04

Matches are distributed among these distances:
  17   32  0.68
  18   15  0.32

ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55


Consensus pattern (17 bp):   
TTAAATTTATTTTAAAT

Found at i:12113 original size:34 final size:34

Alignment explanation


    Indices: 12048--12116  Score: 102
    Period size: 35  Copynumber: 2.0  Consensus size: 34

      12038 GTCTAAAAAA

                                 **           
      12048 TTAAATTTATTTTAAATTTAACTTTATTTTAAAT
          1 TTAAATTTATTTTAAATTTAAAATTATTTTAAAT

                                          *    
      12082 TTAAATTTATTTTCAAATTTAAAATTATTTAAAAT
          1 TTAAATTTATTTT-AAATTTAAAATTATTTTAAAT

      12117 AAATAAATAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 1
        0.89            0.09        0.03

Matches are distributed among these distances:
  34   13  0.42
  35   18  0.58

ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55


Consensus pattern (34 bp):   
TTAAATTTATTTTAAATTTAAAATTATTTTAAAT
Done.