Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010907.1 Kokia drynarioides strain JFW-HI SEQ_125875, 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: 2195
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31


Found at i:198 original size:20 final size:20

Alignment explanation


    Indices: 145--201  Score: 64
    Period size: 20  Copynumber: 3.0  Consensus size: 20

        135 AAATCGATAT

                                
        145 GCTAATGAGATAGAAAT-AC
          1 GCTAATGAGATAGAAATAAC

              *     *  *       *
        164 G-AAATGAAATTGAAATAAG
          1 GCTAATGAGATAGAAATAAC

                               
        183 GCTAATGAGATAGAAATAA
          1 GCTAATGAGATAGAAATAA

        202 AGAATTATAA


Statistics
Matches: 29,  Mismatches: 7, Indels: 3
        0.74            0.18        0.08

Matches are distributed among these distances:
  18   12  0.41
  19    3  0.10
  20   14  0.48

ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21


Consensus pattern (20 bp):   
GCTAATGAGATAGAAATAAC

Found at i:1721 original size:30 final size:32

Alignment explanation


    Indices: 1652--1731  Score: 112
    Period size: 30  Copynumber: 2.6  Consensus size: 32

       1642 TTTTTTGGTC

                    *   *                   
       1652 CAAGTTGGCACTCAAACTTGACACTTTTTCTT
          1 CAAGTTGGTACTTAAACTTGACACTTTTTCTT

               *                            
       1684 -AATTTGGTACTTAAACTTGACA-TTTTT-TT
          1 CAAGTTGGTACTTAAACTTGACACTTTTTCTT

                               
       1713 CAAGTTGGTACTTAAACTT
          1 CAAGTTGGTACTTAAACTT

       1732 TTTAGGGTCC


Statistics
Matches: 43,  Mismatches: 4, Indels: 4
        0.84            0.08        0.08

Matches are distributed among these distances:
  29    2  0.05
  30   22  0.51
  31   19  0.44

ACGTcount: A:0.28, C:0.17, G:0.12, T:0.42


Consensus pattern (32 bp):   
CAAGTTGGTACTTAAACTTGACACTTTTTCTT

Found at i:2058 original size:60 final size:62

Alignment explanation


    Indices: 1937--2058  Score: 160
    Period size: 62  Copynumber: 2.0  Consensus size: 62

       1927 ATAAATTTAG

                           *                     *             *    *     
       1937 GTACCAAATTGAATCTAAAAAAAGCTAAAGTAGCAAATTAAGAAAAAAAATGTCAAGTTCAA
          1 GTACCAAATTGAATCCAAAAAAAGCTAAAGTAGCAAAGTAAGAAAAAAAATATCAACTTCAA

                       *                     *                             
       1999 GTACCAAATTGGATCCAAAAAAAGCT-AAGATATCAAAGT-A-AAAAAAAATATCAACTTCAA
          1 GTACCAAATTGAATCCAAAAAAAGCTAAAG-TAGCAAAGTAAGAAAAAAAATATCAACTTCAA

       2059 AGATTAAATT


Statistics
Matches: 53,  Mismatches: 6, Indels: 4
        0.84            0.10        0.06

Matches are distributed among these distances:
  60   18  0.34
  61    4  0.08
  62   31  0.58

ACGTcount: A:0.55, C:0.13, G:0.11, T:0.20


Consensus pattern (62 bp):   
GTACCAAATTGAATCCAAAAAAAGCTAAAGTAGCAAAGTAAGAAAAAAAATATCAACTTCAA

Found at i:2068 original size:60 final size:62

Alignment explanation


    Indices: 1937--2080  Score: 154
    Period size: 62  Copynumber: 2.4  Consensus size: 62

       1927 ATAAATTTAG

                       *   *                     *             *    *     
       1937 GTACCAAATTGAATCTAAAAAAAGCTAAAGTAGCAAATTAAGAAAAAAAATGTCAAGTTCAA
          1 GTACCAAATTGGATCAAAAAAAAGCTAAAGTAGCAAAGTAAGAAAAAAAATATCAACTTCAA

                           *                 *                              
       1999 GTACCAAATTGGATCCAAAAAAAGCT-AAGATATCAAAGT-A-AAAAAAAATATCAACTTCAAA
          1 GTACCAAATTGGATCAAAAAAAAGCTAAAG-TAGCAAAGTAAGAAAAAAAATATCAACTTC-AA

               **                  
       2060 G-ATTAAATTGGAT-AAAAAAAA
          1 GTACCAAATTGGATCAAAAAAAA

       2081 TTTAGATATC


Statistics
Matches: 71,  Mismatches: 9, Indels: 7
        0.82            0.10        0.08

Matches are distributed among these distances:
  59    7  0.10
  60   26  0.37
  61    7  0.10
  62   31  0.44

ACGTcount: A:0.56, C:0.11, G:0.12, T:0.21


Consensus pattern (62 bp):   
GTACCAAATTGGATCAAAAAAAAGCTAAAGTAGCAAAGTAAGAAAAAAAATATCAACTTCAA
Done.