Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009835.1 Kokia drynarioides strain JFW-HI SEQ_124556, 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: 2054
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35


Found at i:419 original size:59 final size:59

Alignment explanation


    Indices: 321--454  Score: 162
    Period size: 59  Copynumber: 2.3  Consensus size: 59

        311 AAATTTAACA

                         *                 * **           * *           
        321 TTTTTTTTAATTTCGTATTTAAATATTTTTTGATTCAATTTGATATTTGAACTTGATACT
          1 TTTTTTTTAATTTGGTATTTAAATATTTTTTAACCCAATTTGATATCTAAACTTGATA-T

                                 *                                 *   
        381 TTTTTTTTAATTTGGTATTTATAT-TTTTTTAACCCAATTTGATATCTAAACTTGGTAT
          1 TTTTTTTTAATTTGGTATTTAAATATTTTTTAACCCAATTTGATATCTAAACTTGATAT

                   *        
        439 TTTTTTCCTAATTTGG
          1 TTTTTT-TTAATTTGG

        455 CACCTAAGCT


Statistics
Matches: 64,  Mismatches: 9, Indels: 3
        0.84            0.12        0.04

Matches are distributed among these distances:
  58    7  0.11
  59   35  0.55
  60   22  0.34

ACGTcount: A:0.25, C:0.08, G:0.09, T:0.58


Consensus pattern (59 bp):   
TTTTTTTTAATTTGGTATTTAAATATTTTTTAACCCAATTTGATATCTAAACTTGATAT

Found at i:697 original size:31 final size:31

Alignment explanation


    Indices: 660--832  Score: 151
    Period size: 31  Copynumber: 5.5  Consensus size: 31

        650 GGACTCCAAA

                           *               
        660 AAGTTTAAGTACCAACTTAAAAAAAAGTGTC
          1 AAGTTTAAGTACCAAATTAAAAAAAAGTGTC

                   *   *                  *    
        691 AAGTTTAGGTATCAAATTAGGAAAAAAAAAATGTC
          1 AAGTTTAAGTACCAAATT----AAAAAAAAGTGTC

                   *          *            
        726 AAGTTTAGGTACCAAATTGAAAAAAAGTGTC
          1 AAGTTTAAGTACCAAATTAAAAAAAAGTGTC

                                             
        757 AAGTTTAAGTACCAAATTGAACAAAAAA-----
          1 AAGTTTAAGTACCAAATT-AA-AAAAAAGTGTC

              *    *                  * *  
        785 AAATTTAGGTACCAAATTAAAAAAAAATATC
          1 AAGTTTAAGTACCAAATTAAAAAAAAGTGTC

                              
        816 AAGTTT-AGATACCAAAT
          1 AAGTTTAAG-TACCAAAT

        833 ATTATATAAA


Statistics
Matches: 117,  Mismatches: 13, Indels: 24
        0.76            0.08        0.16

Matches are distributed among these distances:
  26    6  0.05
  27    2  0.02
  28   16  0.14
  30    1  0.01
  31   56  0.48
  32    1  0.01
  33    6  0.05
  35   29  0.25

ACGTcount: A:0.51, C:0.10, G:0.13, T:0.25


Consensus pattern (31 bp):   
AAGTTTAAGTACCAAATTAAAAAAAAGTGTC

Found at i:726 original size:35 final size:34

Alignment explanation


    Indices: 678--832  Score: 154
    Period size: 31  Copynumber: 4.9  Consensus size: 34

        668 GTACCAACTT

                    *               *          
        678 AAAAAAAAGTGTCAAGTTTAGGTATCAAATTAGGA
          1 AAAAAAAAATGTCAAGTTTAGGTACCAAATT-GGA

                                              
        713 AAAAAAAAATGTCAAGTTTAGGTACCAAATT-G-
          1 AAAAAAAAATGTCAAGTTTAGGTACCAAATTGGA

                    *           *             
        745 -AAAAAAAGTGTCAAGTTTAAGTACCAAATT-GA
          1 AAAAAAAAATGTCAAGTTTAGGTACCAAATTGGA

             *                                
        777 ACAAAAAAA----AA-TTTAGGTACCAAATT---
          1 AAAAAAAAATGTCAAGTTTAGGTACCAAATTGGA

                      *          *        
        803 AAAAAAAAATATCAAGTTTAGATACCAAAT
          1 AAAAAAAAATGTCAAGTTTAGGTACCAAAT

        833 ATTATATAAA


Statistics
Matches: 104,  Mismatches: 9, Indels: 18
        0.79            0.07        0.14

Matches are distributed among these distances:
  26    8  0.08
  28   14  0.13
  29    2  0.02
  30    2  0.02
  31   42  0.40
  33    7  0.07
  35   29  0.28

ACGTcount: A:0.53, C:0.09, G:0.14, T:0.25


Consensus pattern (34 bp):   
AAAAAAAAATGTCAAGTTTAGGTACCAAATTGGA

Found at i:773 original size:66 final size:60

Alignment explanation


    Indices: 657--832  Score: 203
    Period size: 66  Copynumber: 2.9  Consensus size: 60

        647 ATTGGACTCC

                      *       *                      *   *                
        657 AAAAAGTTTAAGTACCAACTTAAAAAAAAGTGTCAAGTTTAGGTATCAAATTAGGAAAAAAA
          1 AAAAAGTTTAGGTACCAAATTAAAAAAAAGTGTCAAGTTTAAGTACCAAATT--GAAAAAAA

                                     *                                 *    
        719 AAATGTCAAGTTTAGGTACCAAATTGAAAAAAAGTGTCAAGTTTAAGTACCAAATTGAACAAAA
          1 AAA----AAGTTTAGGTACCAAATTAAAAAAAAGTGTCAAGTTTAAGTACCAAATTGAAAAAAA

                                         * *                    
        783 AAAAA-TTTAGGTACCAAATTAAAAAAAAATATCAAGTTT-AGATACCAAAT
          1 AAAAAGTTTAGGTACCAAATTAAAAAAAAGTGTCAAGTTTAAG-TACCAAAT

        833 ATTATATAAA


Statistics
Matches: 100,  Mismatches: 9, Indels: 13
        0.82            0.07        0.11

Matches are distributed among these distances:
  58    2  0.02
  59   39  0.39
  60    2  0.02
  62    3  0.03
  64   10  0.10
  66   44  0.44

ACGTcount: A:0.52, C:0.10, G:0.13, T:0.25


Consensus pattern (60 bp):   
AAAAAGTTTAGGTACCAAATTAAAAAAAAGTGTCAAGTTTAAGTACCAAATTGAAAAAAA

Done.