Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008581.1 Kokia drynarioides strain JFW-HI SEQ_123259, 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: 1848
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36


Found at i:178 original size:59 final size:60

Alignment explanation


    Indices: 60--251  Score: 219
    Period size: 60  Copynumber: 3.2  Consensus size: 60

         50 TAATAAATTT

                            * *                                            
         60 AGGTACCAAATTGAATCTTAAAAAAAA-TTTAGATACCAAATTAGGAAAAAAATGTCAAGTTC
          1 AGGTACCAAATTG-A-GTAAAAAAAAAGTTTAGATACCAAATTAGG-AAAAAATGTCAAGTTC

                     *        **            *          *      *        * 
        122 AGGTACCAATTTG-G-ATCCAAAAAAGTTTAGGTACCAAATTAAGAAAAAGTGTCAAGTCC
          1 AGGTACCAAATTGAGTA-AAAAAAAAGTTTAGATACCAAATTAGGAAAAAATGTCAAGTTC

             **                                                        *
        181 AATTACCAAATTGAGTAAAAAAAAAGTTTAGATACCAAATTAGGAAAAAATGTCAAGTTT
          1 AGGTACCAAATTGAGTAAAAAAAAAGTTTAGATACCAAATTAGGAAAAAATGTCAAGTTC

                       
        241 AGGTACCAAAT
          1 AGGTACCAAAT

        252 GTTACATTTA


Statistics
Matches: 105,  Mismatches: 21, Indels: 10
        0.77            0.15        0.07

Matches are distributed among these distances:
  59   30  0.29
  60   62  0.59
  61    1  0.01
  62   12  0.11

ACGTcount: A:0.48, C:0.12, G:0.15, T:0.25


Consensus pattern (60 bp):   
AGGTACCAAATTGAGTAAAAAAAAAGTTTAGATACCAAATTAGGAAAAAATGTCAAGTTC

Found at i:242 original size:31 final size:31

Alignment explanation


    Indices: 87--251  Score: 114
    Period size: 31  Copynumber: 5.5  Consensus size: 31

         77 TTAAAAAAAA

                                            
         87 TTTAGATACCAAATTAGGAAAAAAATGTCAAG
          1 TTTAGATACCAAATTAGG-AAAAAATGTCAAG

              *  *         *     *           
        119 TTCAGGTACC-AATTTGGATCCAAAA----AAG
          1 TTTAGATACCAAATTAGGA--AAAAATGTCAAG

                 *          *      *       
        147 TTTAGGTACCAAATTAAGAAAAAGTGTCAAG
          1 TTTAGATACCAAATTAGGAAAAAATGTCAAG

             **                *         *   
        178 TCCA-ATTACCAAATTGAGTAAAAAA---AAAG
          1 TTTAGA-TACCAAATT-AGGAAAAAATGTCAAG

                                           
        207 TTTAGATACCAAATTAGGAAAAAATGTCAAG
          1 TTTAGATACCAAATTAGGAAAAAATGTCAAG

                 *        
        238 TTTAGGTACCAAAT
          1 TTTAGATACCAAAT

        252 GTTACATTTA


Statistics
Matches: 99,  Mismatches: 21, Indels: 27
        0.67            0.14        0.18

Matches are distributed among these distances:
  27    3  0.03
  28   20  0.20
  29   20  0.20
  30    2  0.02
  31   36  0.36
  32   18  0.18

ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25


Consensus pattern (31 bp):   
TTTAGATACCAAATTAGGAAAAAATGTCAAG
Done.