Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011974.1 Kokia drynarioides strain JFW-HI SEQ_126972, 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: 5856
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--26  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

                                                  
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

         27 TAATCCATTC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:3323 original size:28 final size:28

Alignment explanation


    Indices: 3274--3327  Score: 74
    Period size: 28  Copynumber: 1.9  Consensus size: 28

       3264 TTTTTGTTGG

                            *           
       3274 AATTAATTAAGTTTATGATTGAATTTGA
          1 AATTAATTAAGTTTATAATTGAATTTGA

                     *                 
       3302 AATTAATTATGTTTA-AATTTGAATTT
          1 AATTAATTAAGTTTATAA-TTGAATTT

       3328 ATTTAATAAT


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  27    1  0.04
  28   22  0.96

ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50


Consensus pattern (28 bp):   
AATTAATTAAGTTTATAATTGAATTTGA

Found at i:3342 original size:26 final size:26

Alignment explanation


    Indices: 3304--3360  Score: 78
    Period size: 26  Copynumber: 2.2  Consensus size: 26

       3294 GAATTTGAAA

                 *                    
       3304 TTAATTATGTTTAAATTTGAATTTAT
          1 TTAATAATGTTTAAATTTGAATTTAT

                    *    **           
       3330 TTAATAATTTTTATGTTTGAATTTAT
          1 TTAATAATGTTTAAATTTGAATTTAT

                 
       3356 TTAAT
          1 TTAAT

       3361 GAGTTTTAGC


Statistics
Matches: 27,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  26   27  1.00

ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60


Consensus pattern (26 bp):   
TTAATAATGTTTAAATTTGAATTTAT

Found at i:3367 original size:26 final size:26

Alignment explanation


    Indices: 3319--3368  Score: 82
    Period size: 26  Copynumber: 1.9  Consensus size: 26

       3309 TATGTTTAAA

                              *       
       3319 TTTGAATTTATTTAATAATTTTTATG
          1 TTTGAATTTATTTAATAAGTTTTATG

                            *       
       3345 TTTGAATTTATTTAATGAGTTTTA
          1 TTTGAATTTATTTAATAAGTTTTA

       3369 GCAAATGACA


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  26   22  1.00

ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60


Consensus pattern (26 bp):   
TTTGAATTTATTTAATAAGTTTTATG

Found at i:3445 original size:6 final size:6

Alignment explanation


    Indices: 3434--3474  Score: 57
    Period size: 6  Copynumber: 6.8  Consensus size: 6

       3424 ATATTTGCAT

                           *                                
       3434 ACATAA ACATAA ATA-AGA ACATAA ACATAA ACATAA ACATA
          1 ACATAA ACATAA ACATA-A ACATAA ACATAA ACATAA ACATA

       3475 TTTAATTCTA


Statistics
Matches: 31,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
   5    1  0.03
   6   29  0.94
   7    1  0.03

ACGTcount: A:0.66, C:0.15, G:0.02, T:0.17


Consensus pattern (6 bp):   
ACATAA

Done.