Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013100.1 Kokia drynarioides strain JFW-HI SEQ_128118, 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: 8014
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33


Found at i:2012 original size:41 final size:41

Alignment explanation


    Indices: 1958--2039  Score: 155
    Period size: 41  Copynumber: 2.0  Consensus size: 41

       1948 GTAAAGTATA

                                                     
       1958 ATTCTCAAGCTATTTATACTTCCAATACTTTACTTTTTAGT
          1 ATTCTCAAGCTATTTATACTTCCAATACTTTACTTTTTAGT

                                  *                  
       1999 ATTCTCAAGCTATTTATACTTCTAATACTTTACTTTTTAGT
          1 ATTCTCAAGCTATTTATACTTCCAATACTTTACTTTTTAGT

       2040 TTAGAAAAAT


Statistics
Matches: 40,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  41   40  1.00

ACGTcount: A:0.27, C:0.18, G:0.05, T:0.50


Consensus pattern (41 bp):   
ATTCTCAAGCTATTTATACTTCCAATACTTTACTTTTTAGT

Found at i:2293 original size:56 final size:57

Alignment explanation


    Indices: 2159--2313  Score: 186
    Period size: 56  Copynumber: 2.7  Consensus size: 57

       2149 TATATTATGT

                         *                *           * *              
       2159 TTTTTTATTAAATCATATTTTAATAATAATTATATTAAGAATGTTATTAAATGATATAC
          1 TTTTTTATTAAATTATA-TTTAATAATAATCATATTAA-AATATGATTAAATGATATAC

             *            *                 *             *   *  *   
       2218 TATTTTATTAAATTGTATTTAATAATAATCATGTTAAAATATGATTTAATTATTTA-
          1 TTTTTTATTAAATTATATTTAATAATAATCATATTAAAATATGATTAAATGATATAC

                                          *         
       2274 TTTTTTATTAAATTATATTTAATAATAATCTTATTAAAAT
          1 TTTTTTATTAAATTATATTTAATAATAATCATATTAAAAT

       2314 TTAATAACAA


Statistics
Matches: 82,  Mismatches: 14, Indels: 3
        0.83            0.14        0.03

Matches are distributed among these distances:
  56   36  0.44
  57   14  0.17
  58   18  0.22
  59   14  0.17

ACGTcount: A:0.42, C:0.03, G:0.04, T:0.52


Consensus pattern (57 bp):   
TTTTTTATTAAATTATATTTAATAATAATCATATTAAAATATGATTAAATGATATAC

Found at i:6406 original size:20 final size:20

Alignment explanation


    Indices: 6376--6437  Score: 83
    Period size: 20  Copynumber: 3.1  Consensus size: 20

       6366 TGAAAAGCAA

                             *  
       6376 TTTGA-TTAGTTAAAATGAT
          1 TTTGACTTAGTTAAAATCAT

                *               
       6395 TTTGCCTTAGTTAAAATCAT
          1 TTTGACTTAGTTAAAATCAT

                                 
       6415 TTTGACTT-GATTAAAATCAT
          1 TTTGACTTAG-TTAAAATCAT

               
       6435 TTT
          1 TTT

       6438 AATTTGATTT


Statistics
Matches: 38,  Mismatches: 3, Indels: 3
        0.86            0.07        0.07

Matches are distributed among these distances:
  19    5  0.13
  20   33  0.87

ACGTcount: A:0.32, C:0.08, G:0.11, T:0.48


Consensus pattern (20 bp):   
TTTGACTTAGTTAAAATCAT

Found at i:6444 original size:20 final size:20

Alignment explanation


    Indices: 6405--6446  Score: 66
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       6395 TTTGCCTTAG

                         *      
       6405 TTAAAATCATTTTGACTTGA
          1 TTAAAATCATTTTAACTTGA

                           *    
       6425 TTAAAATCATTTTAATTTGA
          1 TTAAAATCATTTTAACTTGA

              
       6445 TT
          1 TT

       6447 TTAAAGTTGT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50


Consensus pattern (20 bp):   
TTAAAATCATTTTAACTTGA
Done.