Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008457.1 Kokia drynarioides strain JFW-HI SEQ_123132, 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: 2011
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35


Found at i:103 original size:59 final size:59

Alignment explanation


    Indices: 1--204  Score: 218
    Period size: 59  Copynumber: 3.4  Consensus size: 59

                 *             *     *         *                 *       
          1 AAAATGTAATTTTTGAGAAATTTA-TGGTCAAATACGTAA-TTTTGGAAAGTTAAAGGGT-
          1 AAAATATAATTTTTG-GAAGTTTAGGGGTCAAA-ATGTAATTTTTGGAAAGTTTAAGGGTC

                                                  *               *     
         59 AAAATTATAATTTTTGGAAGTTTAGGGGTCAAAATGTATTTTTTGGAAAGTTTAGGGGTC
          1 AAAA-TATAATTTTTGGAAGTTTAGGGGTCAAAATGTAATTTTTGGAAAGTTTAAGGGTC

                 *               * *    *                        *      
        119 AAAATGTAATTTTTGGAAGTTCAAGGGTGAAAATGTAATTTTT-GAGAAGTTTGAGGGTC
          1 AAAATATAATTTTTGGAAGTTTAGGGGTCAAAATGTAATTTTTGGA-AAGTTTAAGGGTC

                   *                   
        178 AAAATATGATTTTTGGATAGTTTAGGG
          1 AAAATATAATTTTTGGA-AGTTTAGGG

        205 ACCTTTTAGG


Statistics
Matches: 122,  Mismatches: 18, Indels: 10
        0.81            0.12        0.07

Matches are distributed among these distances:
  58   17  0.14
  59   94  0.77
  60   11  0.09

ACGTcount: A:0.35, C:0.03, G:0.25, T:0.38


Consensus pattern (59 bp):   
AAAATATAATTTTTGGAAGTTTAGGGGTCAAAATGTAATTTTTGGAAAGTTTAAGGGTC

Found at i:190 original size:29 final size:28

Alignment explanation


    Indices: 1--204  Score: 196
    Period size: 30  Copynumber: 6.9  Consensus size: 28

                               *    *    
          1 AAAATGTAATTTTTGAGAAATTTATGGTC
          1 AAAATGTAATTTTTG-GAAGTTTAGGGTC

                 *                  *      
         30 AAATACGTAA-TTTTGGAAAGTTAAAGGGT-
          1 AAA-ATGTAATTTTTGG-AAGTT-TAGGGTC

                  *                       
         59 AAAATTATAATTTTTGGAAGTTTAGGGGTC
          1 AAAA-TGTAATTTTTGGAAGTTTA-GGGTC

                    *                     
         89 AAAATGTATTTTTTGGAAAGTTTAGGGGTC
          1 AAAATGTAATTTTTGG-AAGTTTA-GGGTC

                                  *     *
        119 AAAATGTAATTTTTGGAAGTTCAAGGGTG
          1 AAAATGTAATTTTTGGAAGTT-TAGGGTC

                                          
        148 AAAATGTAATTTTTGAGAAGTTTGAGGGTC
          1 AAAATGTAATTTTTG-GAAGTTT-AGGGTC

                 * *                   
        178 AAAATATGATTTTTGGATAGTTTAGGG
          1 AAAATGTAATTTTTGGA-AGTTTAGGG

        205 ACCTTTTAGG


Statistics
Matches: 147,  Mismatches: 16, Indels: 24
        0.79            0.09        0.13

Matches are distributed among these distances:
  28    3  0.02
  29   67  0.46
  30   77  0.52

ACGTcount: A:0.35, C:0.03, G:0.25, T:0.38


Consensus pattern (28 bp):   
AAAATGTAATTTTTGGAAGTTTAGGGTC

Found at i:1004 original size:20 final size:20

Alignment explanation


    Indices: 976--1016  Score: 64
    Period size: 20  Copynumber: 2.0  Consensus size: 20

        966 TTTCCTTTCC

                            *   
        976 GAAAAATCCAGATCTAGAAT
          1 GAAAAATCCAGATCTAAAAT

                *               
        996 GAAAGATCCAGATCTAAAAT
          1 GAAAAATCCAGATCTAAAAT

             
       1016 G
          1 G

       1017 TTTTGAAAAC


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.49, C:0.15, G:0.17, T:0.20


Consensus pattern (20 bp):   
GAAAAATCCAGATCTAAAAT

Found at i:1992 original size:19 final size:20

Alignment explanation


    Indices: 1953--1992  Score: 64
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       1943 ATGAACTTGA

                                
       1953 TTTGTAACTGGACATTTATG
          1 TTTGTAACTGGACATTTATG

                   *            
       1973 TTTGTAATTGGACA-TTATG
          1 TTTGTAACTGGACATTTATG

             
       1992 T
          1 T

       1993 AAATAAATTT


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  19    6  0.32
  20   13  0.68

ACGTcount: A:0.25, C:0.07, G:0.20, T:0.47


Consensus pattern (20 bp):   
TTTGTAACTGGACATTTATG
Done.