Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014869.1 Kokia drynarioides strain JFW-HI SEQ_129912, 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: 43943
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34

Warning! 16 characters in sequence are not A, C, G, or T


Found at i:7345 original size:60 final size:60

Alignment explanation


    Indices: 7252--7377  Score: 216
    Period size: 60  Copynumber: 2.1  Consensus size: 60

       7242 TTATTATTTA

                             *    *                                  *  
       7252 AATAAAAATAATTCTATGCAAATCACGGGATAAAAAAATAGTTTAGTATATAATTTTGTT
          1 AATAAAAATAATTCTATACAAAGCACGGGATAAAAAAATAGTTTAGTATATAATTTTCTT

                                 *                                      
       7312 AATAAAAATAATTCTATACAACGCACGGGATAAAAAAATAGTTTAGTATATAATTTTCTT
          1 AATAAAAATAATTCTATACAAAGCACGGGATAAAAAAATAGTTTAGTATATAATTTTCTT

                  
       7372 AATAAA
          1 AATAAA

       7378 TTGTAGGTTT


Statistics
Matches: 62,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  60   62  1.00

ACGTcount: A:0.48, C:0.08, G:0.10, T:0.33


Consensus pattern (60 bp):   
AATAAAAATAATTCTATACAAAGCACGGGATAAAAAAATAGTTTAGTATATAATTTTCTT

Found at i:13005 original size:16 final size:16

Alignment explanation


    Indices: 12989--13024  Score: 56
    Period size: 16  Copynumber: 2.2  Consensus size: 16

      12979 AGTTTAGATA

                            
      12989 AAAT-AAAATAAATAT
          1 AAATAAAAATAAATAT

                             
      13004 AAATAAAAATAAATATT
          1 AAATAAAAATAAATA-T

                
      13021 AAAT
          1 AAAT

      13025 TTATACATAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  15    4  0.21
  16   10  0.53
  17    5  0.26

ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28


Consensus pattern (16 bp):   
AAATAAAAATAAATAT

Found at i:20024 original size:23 final size:23

Alignment explanation


    Indices: 19989--20035  Score: 69
    Period size: 23  Copynumber: 2.0  Consensus size: 23

      19979 AGATTTAAAT

                             *     
      19989 TTTAACATTTTAAAAATTAAAAA
          1 TTTAACATTTTAAAAATAAAAAA

                                    
      20012 TTTAA-ATTCTTAAAAATAAAAAA
          1 TTTAACATT-TTAAAAATAAAAAA

             
      20035 T
          1 T

      20036 CAGGAATAAT


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  22    3  0.14
  23   19  0.86

ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38


Consensus pattern (23 bp):   
TTTAACATTTTAAAAATAAAAAA

Found at i:33267 original size:34 final size:34

Alignment explanation


    Indices: 33224--33288  Score: 130
    Period size: 34  Copynumber: 1.9  Consensus size: 34

      33214 CTAGGTCAAC

                                              
      33224 ATTAAGCTCACTCCATTGCATTTATGTCATAAAT
          1 ATTAAGCTCACTCCATTGCATTTATGTCATAAAT

                                           
      33258 ATTAAGCTCACTCCATTGCATTTATGTCATA
          1 ATTAAGCTCACTCCATTGCATTTATGTCATA

      33289 GGATCAACTT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  34   31  1.00

ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38


Consensus pattern (34 bp):   
ATTAAGCTCACTCCATTGCATTTATGTCATAAAT
Done.