Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009714.1 Kokia drynarioides strain JFW-HI SEQ_124433, 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: 17582
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:4075 original size:42 final size:42

Alignment explanation


    Indices: 4028--4116  Score: 169
    Period size: 42  Copynumber: 2.1  Consensus size: 42

       4018 TATTCAAGAA

                                                      
       4028 GTTTCGCAACATTGCTTATCTGGTATTACTGAATAATTTTTT
          1 GTTTCGCAACATTGCTTATCTGGTATTACTGAATAATTTTTT

                                                      
       4070 GTTTCGCAACATTGCTTATCTGGTATTACTGAATAATTTTTT
          1 GTTTCGCAACATTGCTTATCTGGTATTACTGAATAATTTTTT

            *    
       4112 TTTTC
          1 GTTTC

       4117 TTTGAAGGGT


Statistics
Matches: 46,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  42   46  1.00

ACGTcount: A:0.22, C:0.15, G:0.13, T:0.49


Consensus pattern (42 bp):   
GTTTCGCAACATTGCTTATCTGGTATTACTGAATAATTTTTT

Found at i:6558 original size:17 final size:17

Alignment explanation


    Indices: 6536--6583  Score: 55
    Period size: 15  Copynumber: 2.9  Consensus size: 17

       6526 AAATTTTAAT

                             
       6536 TTTTTATATTTAAAATA
          1 TTTTTATATTTAAAATA

                       ***   
       6553 TTTTTAT-TTTTTGA-A
          1 TTTTTATATTTAAAATA

                            
       6568 TTTTTATATTTAAAAT
          1 TTTTTATATTTAAAAT

       6584 GCATTGAATT


Statistics
Matches: 23,  Mismatches: 6, Indels: 4
        0.70            0.18        0.12

Matches are distributed among these distances:
  15    8  0.35
  16    8  0.35
  17    7  0.30

ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65


Consensus pattern (17 bp):   
TTTTTATATTTAAAATA

Found at i:9916 original size:19 final size:19

Alignment explanation


    Indices: 9892--9929  Score: 58
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       9882 TGGAGAAAAC

                     *         
       9892 ACGTCTGTGTAGTCTACAT
          1 ACGTCTGTGAAGTCTACAT

                         *     
       9911 ACGTCTGTGAAGTTTACAT
          1 ACGTCTGTGAAGTCTACAT

       9930 CGGGAATCTT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  19   17  1.00

ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37


Consensus pattern (19 bp):   
ACGTCTGTGAAGTCTACAT

Found at i:17545 original size:29 final size:29

Alignment explanation


    Indices: 17503--17563  Score: 113
    Period size: 29  Copynumber: 2.1  Consensus size: 29

      17493 TACGGGGTAG

                                         
      17503 GCACTTAGTACCGAAGCGTGTTATCGATT
          1 GCACTTAGTACCGAAGCGTGTTATCGATT

                          *              
      17532 GCACTTAGTACCGAGGCGTGTTATCGATT
          1 GCACTTAGTACCGAAGCGTGTTATCGATT

               
      17561 GCA
          1 GCA

      17564 TAACTCTGTT


Statistics
Matches: 31,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  29   31  1.00

ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30


Consensus pattern (29 bp):   
GCACTTAGTACCGAAGCGTGTTATCGATT
Done.