Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004012.1 Kokia drynarioides strain JFW-HI SEQ_117131, 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: 18114
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31

Warning! 154 characters in sequence are not A, C, G, or T


Found at i:539 original size:31 final size:31

Alignment explanation


    Indices: 459--543  Score: 84
    Period size: 31  Copynumber: 2.7  Consensus size: 31

        449 GTCACTGTTC

                              *    *          
        459 TAAATATTAAAAAAATTATAATTATAAATTTTTA
          1 TAAATATTAAAAAAATT-CAA--CTAAATTTTTA

                  *     *           *      
        493 -AAA-ACTAAAACAATTCAACTAATTTTTTA
          1 TAAATATTAAAAAAATTCAACTAAATTTTTA

                                  
        522 TAAATATTAAAAAAATTCAACT
          1 TAAATATTAAAAAAATTCAACT

        544 CGATTCGTTT


Statistics
Matches: 42,  Mismatches: 7, Indels: 7
        0.75            0.12        0.12

Matches are distributed among these distances:
  29    9  0.21
  30    3  0.07
  31   17  0.40
  32   10  0.24
  33    3  0.07

ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38


Consensus pattern (31 bp):   
TAAATATTAAAAAAATTCAACTAAATTTTTA

Found at i:4003 original size:16 final size:16

Alignment explanation


    Indices: 3982--4028  Score: 51
    Period size: 16  Copynumber: 2.9  Consensus size: 16

       3972 TCAACGTTTT

                            
       3982 AATTAAAATAATTATA
          1 AATTAAAATAATTATA

                  *  *      
       3998 AATTAATATCATTATA
          1 AATTAAAATAATTATA

               *            
       4014 AA-AATAAATAATTAT
          1 AATTA-AAATAATTAT

       4029 GTCTAATTAA


Statistics
Matches: 25,  Mismatches: 5, Indels: 2
        0.78            0.16        0.06

Matches are distributed among these distances:
  15    1  0.04
  16   24  0.96

ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38


Consensus pattern (16 bp):   
AATTAAAATAATTATA

Found at i:6040 original size:26 final size:25

Alignment explanation


    Indices: 6011--6069  Score: 73
    Period size: 26  Copynumber: 2.3  Consensus size: 25

       6001 TATATATTTA

                              *       
       6011 TAATATTATTAATTAATTCAAATAGT
          1 TAATATTATTAATTAATTAAAATA-T

                      **             
       6037 TAATATTATTTTTTAATTAAAATAT
          1 TAATATTATTAATTAATTAAAATAT

                    
       6062 TACATATT
          1 TA-ATATT

       6070 TATAGATAAT


Statistics
Matches: 29,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  25    3  0.10
  26   26  0.90

ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51


Consensus pattern (25 bp):   
TAATATTATTAATTAATTAAAATAT
Done.