Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000307.1 Kokia drynarioides strain JFW-HI SEQ_111068, 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: 9353
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37


Found at i:8279 original size:18 final size:17

Alignment explanation


    Indices: 8256--8313  Score: 55
    Period size: 18  Copynumber: 3.4  Consensus size: 17

       8246 AAATTTAAGG

                  *           
       8256 ATTTTAGACAACAATAAA
          1 ATTTTAAACAAC-ATAAA

                   *   *   *  
       8274 ATTTTATCACATCATTAA
          1 ATTTTA-AACAACATAAA

                             
       8292 ATTTTAAAC-ACATAAA
          1 ATTTTAAACAACATAAA

                  
       8308 ATTTTA
          1 ATTTTA

       8314 TTATACACTC


Statistics
Matches: 33,  Mismatches: 6, Indels: 4
        0.77            0.14        0.09

Matches are distributed among these distances:
  16   11  0.33
  17    2  0.06
  18   16  0.48
  19    4  0.12

ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38


Consensus pattern (17 bp):   
ATTTTAAACAACATAAA

Found at i:8311 original size:16 final size:17

Alignment explanation


    Indices: 8265--8314  Score: 59
    Period size: 16  Copynumber: 3.0  Consensus size: 17

       8255 GATTTTAGAC

                             
       8265 AACA-ATAAAATTTTAT
          1 AACACATAAAATTTTAT

            *       *         
       8281 CACATCATTAAATTTTA-
          1 AACA-CATAAAATTTTAT

                             
       8298 AACACATAAAATTTTAT
          1 AACACATAAAATTTTAT

       8315 TATACACTCG


Statistics
Matches: 27,  Mismatches: 4, Indels: 5
        0.75            0.11        0.14

Matches are distributed among these distances:
  16   14  0.52
  17    3  0.11
  18   10  0.37

ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38


Consensus pattern (17 bp):   
AACACATAAAATTTTAT

Found at i:8644 original size:20 final size:21

Alignment explanation


    Indices: 8598--8645  Score: 55
    Period size: 20  Copynumber: 2.4  Consensus size: 21

       8588 AACTTTAAAC

                    *     *      
       8598 TCAAACCCTAAACTTAAACAT
          1 TCAAACCCCAAACTCAAACAT

              *                  
       8619 T-GAACCCCAAACTCAAA-AT
          1 TCAAACCCCAAACTCAAACAT

                    
       8638 TCAAACCC
          1 TCAAACCC

       8646 GAATCTTGAA


Statistics
Matches: 22,  Mismatches: 4, Indels: 3
        0.76            0.14        0.10

Matches are distributed among these distances:
  19    3  0.14
  20   18  0.82
  21    1  0.05

ACGTcount: A:0.46, C:0.33, G:0.02, T:0.19


Consensus pattern (21 bp):   
TCAAACCCCAAACTCAAACAT
Done.