Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002187.1 Kokia drynarioides strain JFW-HI SEQ_114158, 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: 2715
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.40


Found at i:242 original size:30 final size:30

Alignment explanation


    Indices: 174--244  Score: 81
    Period size: 30  Copynumber: 2.3  Consensus size: 30

        164 TGAATAGTTT

                      *         *  *       
        174 ATATATTTATAATTTTTAAATAATTAAATTA
          1 ATAT-TTTATTATTTTTAAAAAACTAAATTA

              *                           
        205 ATTTTTTATTATTTTTAAAAAACTAAATT-
          1 ATATTTTATTATTTTTAAAAAACTAAATTA

                       
        234 ATAATTTTATT
          1 AT-ATTTTATT

        245 TTTACTAATT


Statistics
Matches: 34,  Mismatches: 5, Indels: 3
        0.81            0.12        0.07

Matches are distributed among these distances:
  29    2  0.06
  30   29  0.85
  31    3  0.09

ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55


Consensus pattern (30 bp):   
ATATTTTATTATTTTTAAAAAACTAAATTA

Found at i:2199 original size:16 final size:16

Alignment explanation


    Indices: 2180--2229  Score: 52
    Period size: 16  Copynumber: 3.2  Consensus size: 16

       2170 TGATTATATA

                            
       2180 TAAAATATAATAAATT
          1 TAAAATATAATAAATT

                            
       2196 TAAAATAT--TAAATT
          1 TAAAATATAATAAATT

              *               
       2210 CTTAAAT-TAATAATATT
          1 -TAAAATATAATAA-ATT

               
       2227 TAA
          1 TAA

       2230 TTTTTTATTA


Statistics
Matches: 28,  Mismatches: 2, Indels: 8
        0.74            0.05        0.21

Matches are distributed among these distances:
  14    7  0.25
  15    5  0.18
  16   13  0.46
  17    3  0.11

ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42


Consensus pattern (16 bp):   
TAAAATATAATAAATT

Found at i:2224 original size:22 final size:22

Alignment explanation


    Indices: 2190--2231  Score: 59
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       2180 TAAAATATAA

                                  
       2190 TAAATTTAAAATATTAAATTCT
          1 TAAATTTAAAATATTAAATTCT

                            *    
       2212 TAAA-TTAATAATATTTAATT
          1 TAAATTTAA-AATATTAAATT

       2232 TTTTATTATT


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  21    4  0.22
  22   14  0.78

ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48


Consensus pattern (22 bp):   
TAAATTTAAAATATTAAATTCT
Done.