Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007808.1 Kokia drynarioides strain JFW-HI SEQ_122444, 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: 7142
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34


Found at i:3533 original size:90 final size:87

Alignment explanation


    Indices: 3429--3624  Score: 212
    Period size: 90  Copynumber: 2.2  Consensus size: 87

       3419 AACTTTAAAA

                     *          *          *    * *          *             * 
       3429 AAAAAAACAGTTAAGCTCTTGCTTTTATTTTGTACTTATTTGAATATTTGAACTTTTAAAATGTA
          1 AAAAAAACAATTAAGCTCTTACTTTTATTTTATACTCAATTGAATATTTAAAC-TTTAAAATGCA

                   **        *      
       3494 TTAAAAAGGCCTTCAAATTTTTTC
         65 TTAAAAAAACC-TCAAACTTTTTC

                   *          *                         **            *      
       3518 AGAAAAAGCAATTAAGCCCCTTACTTTTATTTTATACTCAATTGGGTATTTAAACTTTCAAATGC
          1 A-AAAAAACAATTAAG-CTCTTACTTTTATTTTATACTCAATTGAATATTTAAACTTTAAAATGC

                                    
       3583 ATTAAAAAAACCTCAAACTTTTTC
         64 ATTAAAAAAACCTCAAACTTTTTC

                              
       3607 AAAAGAAACAATTAAGCT
          1 AAAA-AAACAATTAAGCT

       3625 TCTAATTTTT


Statistics
Matches: 87,  Mismatches: 17, Indels: 7
        0.78            0.15        0.06

Matches are distributed among these distances:
  88    4  0.05
  89   23  0.26
  90   30  0.34
  91   30  0.34

ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38


Consensus pattern (87 bp):   
AAAAAAACAATTAAGCTCTTACTTTTATTTTATACTCAATTGAATATTTAAACTTTAAAATGCAT
TAAAAAAACCTCAAACTTTTTC

Found at i:3546 original size:91 final size:89

Alignment explanation


    Indices: 3428--3623  Score: 207
    Period size: 91  Copynumber: 2.2  Consensus size: 89

       3418 AAACTTTAAA

                *     *       *   *          *    * *          *             
       3428 AAAAAAAACAGTTAAG-CTCTTGCTTTTATTTTGTACTTATTTGAATATTTGAACTTTTAAAATG
          1 AAAAGAAACAATTAAGCCCCTTACTTTTATTTTATACTCAATTGAATATTTAAAC-TTTAAAATG

            *        **        *      
       3492 TATTAAAAAGGCCTTCAAATTTTTTC
         65 CATTAAAAAAACC-TCAAACTTTTTC

                    *                                    **            *     
       3518 AGAAA-AAGCAATTAAGCCCCTTACTTTTATTTTATACTCAATTGGGTATTTAAACTTTCAAATG
          1 A-AAAGAAACAATTAAGCCCCTTACTTTTATTTTATACTCAATTGAATATTTAAACTTTAAAATG

                                     
       3582 CATTAAAAAAACCTCAAACTTTTTC
         65 CATTAAAAAAACCTCAAACTTTTTC

                             
       3607 AAAAGAAACAATTAAGC
          1 AAAAGAAACAATTAAGC

       3624 TTCTAATTTT


Statistics
Matches: 87,  Mismatches: 16, Indels: 7
        0.79            0.15        0.06

Matches are distributed among these distances:
  88    3  0.03
  89   23  0.26
  90   28  0.32
  91   33  0.38

ACGTcount: A:0.39, C:0.14, G:0.09, T:0.37


Consensus pattern (89 bp):   
AAAAGAAACAATTAAGCCCCTTACTTTTATTTTATACTCAATTGAATATTTAAACTTTAAAATGC
ATTAAAAAAACCTCAAACTTTTTC
Done.