Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005376.1 Kokia drynarioides strain JFW-HI SEQ_119363, 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: 1915
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33


Found at i:77 original size:3 final size:3

Alignment explanation


    Indices: 69--111  Score: 50
    Period size: 3  Copynumber: 14.0  Consensus size: 3

         59 AGTTATTAAT

                                           * * *                    
         69 TAA TAA TAA TAA TAA TTAA TAA TAG CAT TAA TAA TAA TAA TAA
          1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA

        112 AGTGAAAAAC


Statistics
Matches: 34,  Mismatches: 5, Indels: 2
        0.83            0.12        0.05

Matches are distributed among these distances:
   3   31  0.91
   4    3  0.09

ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35


Consensus pattern (3 bp):   
TAA

Found at i:98 original size:12 final size:10

Alignment explanation


    Indices: 63--111  Score: 57
    Period size: 9  Copynumber: 4.8  Consensus size: 10

         53 TTTTAAAGTT

                       
         63 ATTAATTAATA
          1 ATTAA-TAATA

                      
         74 A-TAATAATA
          1 ATTAATAATA

                      
         83 ATTAATAATA
          1 ATTAATAATA

                        
         93 GCATTAATAATA
          1 --ATTAATAATA

                    
        105 A-TAATAA
          1 ATTAATAA

        112 AGTGAAAAAC


Statistics
Matches: 35,  Mismatches: 0, Indels: 8
        0.81            0.00        0.19

Matches are distributed among these distances:
   9   12  0.34
  10   12  0.34
  11    1  0.03
  12   10  0.29

ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37


Consensus pattern (10 bp):   
ATTAATAATA

Found at i:1416 original size:16 final size:18

Alignment explanation


    Indices: 1395--1433  Score: 64
    Period size: 16  Copynumber: 2.3  Consensus size: 18

       1385 ATTTAACTTA

                              
       1395 TTTATTTTA-TTT-TTGT
          1 TTTATTTTAGTTTGTTGT

                              
       1411 TTTATTTTAGTTTGTTGT
          1 TTTATTTTAGTTTGTTGT

                 
       1429 TTTAT
          1 TTTAT

       1434 CTCTAAACCC


Statistics
Matches: 21,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  16    9  0.43
  17    3  0.14
  18    9  0.43

ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77


Consensus pattern (18 bp):   
TTTATTTTAGTTTGTTGT
Done.