Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001859.1 Kokia drynarioides strain JFW-HI SEQ_113620, 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: 2327
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34


Found at i:62 original size:29 final size:29

Alignment explanation


    Indices: 3--64  Score: 72
    Period size: 30  Copynumber: 2.1  Consensus size: 29

          1 AT

                    *              *      
          3 TACAAAAATTTTGATTCAATGTGCAATTTA
          1 TACAAAAACTTTGATT-AATGTGAAATTTA

                             *            
         33 TACAAAAACTTTGATT-TTGTGAAATTTTA
          1 TACAAAAACTTTGATTAATGTGAAA-TTTA

               
         62 TAC
          1 TAC

         65 CTGATATTTT


Statistics
Matches: 28,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  28    6  0.21
  29    7  0.25
  30   15  0.54

ACGTcount: A:0.39, C:0.10, G:0.10, T:0.42


Consensus pattern (29 bp):   
TACAAAAACTTTGATTAATGTGAAATTTA

Found at i:306 original size:39 final size:39

Alignment explanation


    Indices: 263--343  Score: 135
    Period size: 39  Copynumber: 2.1  Consensus size: 39

        253 AATCAAACTT

                 *                          *      
        263 TTTGTGTTAAATTAAAATTAAATCACAATTTATATATAA
          1 TTTGTATTAAATTAAAATTAAATCACAATTTAAATATAA

                                     *             
        302 TTTGTATTAAATTAAAATTAAATCATAATTTAAATATAA
          1 TTTGTATTAAATTAAAATTAAATCACAATTTAAATATAA

               
        341 TTT
          1 TTT

        344 TGATAGTTAT


Statistics
Matches: 39,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  39   39  1.00

ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46


Consensus pattern (39 bp):   
TTTGTATTAAATTAAAATTAAATCACAATTTAAATATAA

Found at i:682 original size:34 final size:34

Alignment explanation


    Indices: 597--687  Score: 105
    Period size: 34  Copynumber: 2.6  Consensus size: 34

        587 TAGTGTTGAC

                                *              
        597 TTGGTTTTATTAATGGAAAACTTAGGTCTTCATTT
          1 TTGGTTTTATTAATGG-AAATTTAGGTCTTCATTT

              *        *                   *    
        632 TTCGTTTTATTCATGGAAATTTA-GTCCTTTGA-TT
          1 TTGGTTTTATTAATGGAAATTTAGGT-C-TTCATTT

                                  
        666 TTGGTTTTATTAATGGAAATTT
          1 TTGGTTTTATTAATGGAAATTT

        688 TAAATCTTCA


Statistics
Matches: 48,  Mismatches: 6, Indels: 5
        0.81            0.10        0.08

Matches are distributed among these distances:
  33    2  0.04
  34   29  0.60
  35   17  0.35

ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52


Consensus pattern (34 bp):   
TTGGTTTTATTAATGGAAATTTAGGTCTTCATTT

Found at i:708 original size:34 final size:33

Alignment explanation


    Indices: 601--710  Score: 89
    Period size: 34  Copynumber: 3.2  Consensus size: 33

        591 GTTGACTTGG

                            *   *       *     
        601 TTTTATTAATGGAAAACTTAGGTCTTCATTTTTC
          1 TTTTATTAATGG-AAATTTAAGTCTTCAGTTTTC

                    *                   *       *
        635 GTTTTATTCATGGAAATTT-AGTCCTT-TGATTTTGG
          1 -TTTTATTAATGGAAATTTAAGT-CTTCAG-TTTT-C

                                 *            
        670 TTTTATTAATGGAAATTTTAAATCTTCAGTTTTC
          1 TTTTATTAATGGAAA-TTTAAGTCTTCAGTTTTC

                   
        704 TTTTATT
          1 TTTTATT

        711 CTTGGTTTTG


Statistics
Matches: 59,  Mismatches: 10, Indels: 13
        0.72            0.12        0.16

Matches are distributed among these distances:
  33    2  0.03
  34   33  0.56
  35   21  0.36
  36    3  0.05

ACGTcount: A:0.25, C:0.09, G:0.13, T:0.54


Consensus pattern (33 bp):   
TTTTATTAATGGAAATTTAAGTCTTCAGTTTTC
Done.