Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001098.1 Kokia drynarioides strain JFW-HI SEQ_112370, 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, 831

Length: 1386
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:142 original size:44 final size:44

Alignment explanation


    Indices: 92--223  Score: 246
    Period size: 44  Copynumber: 3.0  Consensus size: 44

         82 ATATCAAATC

                                              *         
         92 TTATCACTATTTCAGGACACGGGATAAGCGATATTGTAACACAA
          1 TTATCACTATTTCAGGACACGGGATAAGCGATATCGTAACACAA

                        *                               
        136 TTATCACTATTTAAGGACACGGGATAAGCGATATCGTAACACAA
          1 TTATCACTATTTCAGGACACGGGATAAGCGATATCGTAACACAA

                                                        
        180 TTATCACTATTTCAGGACACGGGATAAGCGATATCGTAACACAA
          1 TTATCACTATTTCAGGACACGGGATAAGCGATATCGTAACACAA

        224 GGACTAGAAT


Statistics
Matches: 85,  Mismatches: 3, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  44   85  1.00

ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26


Consensus pattern (44 bp):   
TTATCACTATTTCAGGACACGGGATAAGCGATATCGTAACACAA

Found at i:567 original size:25 final size:26

Alignment explanation


    Indices: 539--589  Score: 77
    Period size: 25  Copynumber: 2.0  Consensus size: 26

        529 TCTCCTGTAA

                *        *            
        539 TTTAGGTTTTAGTTATTTTC-TTTTC
          1 TTTAAGTTTTAGTCATTTTCATTTTC

                                      
        564 TTTAAGTTTTAGTCATTTTCATTTTC
          1 TTTAAGTTTTAGTCATTTTCATTTTC

        590 GTTTTACAGT


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  25   18  0.78
  26    5  0.22

ACGTcount: A:0.16, C:0.10, G:0.10, T:0.65


Consensus pattern (26 bp):   
TTTAAGTTTTAGTCATTTTCATTTTC

Found at i:836 original size:44 final size:44

Alignment explanation


    Indices: 785--873  Score: 178
    Period size: 44  Copynumber: 2.0  Consensus size: 44

        775 ATTGGATGTA

                                                        
        785 TGATTATTTAATTATTGTATAGGGATCTTCAATGGATCAACTAT
          1 TGATTATTTAATTATTGTATAGGGATCTTCAATGGATCAACTAT

                                                        
        829 TGATTATTTAATTATTGTATAGGGATCTTCAATGGATCAACTAT
          1 TGATTATTTAATTATTGTATAGGGATCTTCAATGGATCAACTAT

             
        873 T
          1 T

        874 TGGAAAAGGA


Statistics
Matches: 45,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  44   45  1.00

ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44


Consensus pattern (44 bp):   
TGATTATTTAATTATTGTATAGGGATCTTCAATGGATCAACTAT
Done.