Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007820.1 Kokia drynarioides strain JFW-HI SEQ_122456, 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: 2938
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36


Found at i:154 original size:39 final size:38

Alignment explanation


    Indices: 111--254  Score: 114
    Period size: 39  Copynumber: 3.7  Consensus size: 38

        101 GATGACTACA

                     *                      *      
        111 ATCTGCCCCTGGCTCGGGGTAAGAGATTGGTTGATGGTG
          1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGG-TAATGGTG

                       *   *      *     *           *
        150 ATCTGCCCCAGACTCAGGGTAAAAGA-TCG-AATGGCTACC
          1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGTAATGG-T--G

                               *                *   
        189 ATCTGCCCC-GAGCTCGGGATAAGAGATTGGCTAATAGTG
          1 ATCTGCCCCAG-GCTCGGGGTAAGAGATTGG-TAATGGTG

                   *  *                
        228 ATCTGCCTCAAGCTCGGGGTAAGAGAT
          1 ATCTGCCCCAGGCTCGGGGTAAGAGAT

        255 CGGAATCTTC


Statistics
Matches: 80,  Mismatches: 17, Indels: 16
        0.71            0.15        0.14

Matches are distributed among these distances:
  36    4  0.05
  37    1  0.01
  38    3  0.04
  39   65  0.81
  40    2  0.03
  41    1  0.01
  42    4  0.05

ACGTcount: A:0.24, C:0.22, G:0.31, T:0.23


Consensus pattern (38 bp):   
ATCTGCCCCAGGCTCGGGGTAAGAGATTGGTAATGGTG

Found at i:159 original size:78 final size:77

Alignment explanation


    Indices: 28--256  Score: 216
    Period size: 78  Copynumber: 2.9  Consensus size: 77

         18 TGCTTCGATA

                               *                   * *        *     * * **   
         28 ACTACAATCTGCCCCAT-GATC-GGGTAAGAGATTGGATGGCTGTGATCTACCCCATAGTTGGGG
          1 ACTACAATCTGCCCC-TGGCTCGGGGTAAGAGATTGG-TTGATGTGATCTGCCCCAGACTCAGGG

                           
         91 TAAAAGATC-AGATG
         64 TAAAAGATCGA-ATG

                                                                             
        105 ACTACAATCTGCCCCTGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAGACTCAGGGT
          1 ACTACAATCTGCCCCTGGCTCGGGGTAAGAGATTGGTTGAT-GTGATCTGCCCCAGACTCAGGGT

                         
        170 AAAAGATCGAATG
         65 AAAAGATCGAATG

            *    *                   *           * *             *        *  
        183 GCTACCATCTGCCCC-GAGCTCGGGATAAGAGATTGGCTAATAGTGATCTGCCTCA-AGCTCGGG
          1 ACTACAATCTGCCCCTG-GCTCGGGGTAAGAGATTGGTTGAT-GTGATCTGCCCCAGA-CTCAGG

                *      
        246 GTAAGAGATCG
         63 GTAAAAGATCG

        257 GAATCTTCAA


Statistics
Matches: 129,  Mismatches: 17, Indels: 11
        0.82            0.11        0.07

Matches are distributed among these distances:
  76    1  0.01
  77   23  0.18
  78  104  0.81
  79    1  0.01

ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23


Consensus pattern (77 bp):   
ACTACAATCTGCCCCTGGCTCGGGGTAAGAGATTGGTTGATGTGATCTGCCCCAGACTCAGGGTA
AAAGATCGAATG

Found at i:1728 original size:18 final size:18

Alignment explanation


    Indices: 1677--1739  Score: 60
    Period size: 18  Copynumber: 3.5  Consensus size: 18

       1667 CAACCTCTCC

                     *        
       1677 TTTTT-TTCATTTTTTC-
          1 TTTTTCTTCTTTTTTTCA

                                 
       1693 TATTTTCTAT-TTTCTTTTCA
          1 T-TTTTCT-TCTTT-TTTTCA

                            * 
       1713 TTTTTCTTCTTTTTTTTA
          1 TTTTTCTTCTTTTTTTCA

                     
       1731 TTTTTCTTC
          1 TTTTTCTTC

       1740 ATTGAATCCG


Statistics
Matches: 39,  Mismatches: 2, Indels: 10
        0.76            0.04        0.20

Matches are distributed among these distances:
  16    1  0.03
  17    4  0.10
  18   18  0.46
  19   15  0.38
  20    1  0.03

ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78


Consensus pattern (18 bp):   
TTTTTCTTCTTTTTTTCA
Done.