Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007189.1 Kokia drynarioides strain JFW-HI SEQ_121802, 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: 5333
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35


Found at i:3643 original size:15 final size:17

Alignment explanation


    Indices: 3611--3658  Score: 52
    Period size: 14  Copynumber: 3.1  Consensus size: 17

       3601 AAATATATAA

                             
       3611 TATTATATATAAACTTT
          1 TATTATATATAAACTTT

                    *        
       3628 TATTATATGT-AA-TTT
          1 TATTATATATAAACTTT

                             
       3643 TATT-TATA-AAA-TTT
          1 TATTATATATAAACTTT

              
       3657 TA
          1 TA

       3659 ATTTTATTTT


Statistics
Matches: 28,  Mismatches: 2, Indels: 5
        0.80            0.06        0.14

Matches are distributed among these distances:
  14   10  0.36
  15    7  0.25
  16    2  0.07
  17    9  0.32

ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56


Consensus pattern (17 bp):   
TATTATATATAAACTTT

Found at i:3645 original size:29 final size:29

Alignment explanation


    Indices: 3603--3658  Score: 76
    Period size: 29  Copynumber: 1.9  Consensus size: 29

       3593 TTTTGATCAA

                                 *       
       3603 ATATATAATATTATATATAAACTTTTATT
          1 ATATATAATATTATATATAAAATTTTATT

                *    *    *            
       3632 ATATGTAATTTTATTTATAAAATTTTA
          1 ATATATAATATTATATATAAAATTTTA

       3659 ATTTTATTTT


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  29   23  1.00

ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54


Consensus pattern (29 bp):   
ATATATAATATTATATATAAAATTTTATT

Found at i:3887 original size:29 final size:27

Alignment explanation


    Indices: 3812--3887  Score: 80
    Period size: 31  Copynumber: 2.6  Consensus size: 27

       3802 ACCATAATAA

                                        
       3812 AAAATTATATGTATAATTACATCAAATT
          1 AAAATT-TATGTATAATTACATCAAATT

                     *            *   *    
       3840 AAAATTTATATATTAAATTATTTATCGAATT
          1 AAAATTTATGTA-T-AATTA--CATCAAATT

                             
       3871 AAAATTTATGTATAATT
          1 AAAATTTATGTATAATT

       3888 TTAATATTTA


Statistics
Matches: 40,  Mismatches: 4, Indels: 7
        0.78            0.08        0.14

Matches are distributed among these distances:
  27    5  0.12
  28    7  0.17
  29    9  0.22
  30    1  0.03
  31   18  0.45

ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45


Consensus pattern (27 bp):   
AAAATTTATGTATAATTACATCAAATT
Done.