Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008367.1 Kokia drynarioides strain JFW-HI SEQ_123034, 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: 6781
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37


Found at i:1874 original size:6 final size:6

Alignment explanation


    Indices: 1863--1902  Score: 80
    Period size: 6  Copynumber: 6.7  Consensus size: 6

       1853 TGGGCACCAT

                                                          
       1863 GAGGCG GAGGCG GAGGCG GAGGCG GAGGCG GAGGCG GAGG
          1 GAGGCG GAGGCG GAGGCG GAGGCG GAGGCG GAGGCG GAGG

       1903 AGCGGGGAAG


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   34  1.00

ACGTcount: A:0.17, C:0.15, G:0.68, T:0.00


Consensus pattern (6 bp):   
GAGGCG

Found at i:2684 original size:49 final size:49

Alignment explanation


    Indices: 2631--2726  Score: 183
    Period size: 49  Copynumber: 2.0  Consensus size: 49

       2621 CTACATTGAA

                                 *                           
       2631 GCTTGAATTTTTTTGTTCAAGGTAGACACTAAATTTGGTAATTGTTCGG
          1 GCTTGAATTTTTTTGTTCAAGATAGACACTAAATTTGGTAATTGTTCGG

                                                           
       2680 GCTTGAATTTTTTTGTTCAAGATAGACACTAAATTTGGTAATTGTTC
          1 GCTTGAATTTTTTTGTTCAAGATAGACACTAAATTTGGTAATTGTTC

       2727 CTACATTGGG


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

Matches are distributed among these distances:
  49   46  1.00

ACGTcount: A:0.26, C:0.10, G:0.20, T:0.44


Consensus pattern (49 bp):   
GCTTGAATTTTTTTGTTCAAGATAGACACTAAATTTGGTAATTGTTCGG

Found at i:5042 original size:17 final size:17

Alignment explanation


    Indices: 5002--5044  Score: 52
    Period size: 17  Copynumber: 2.5  Consensus size: 17

       4992 ATAAAATTTA

                              
       5002 TAAATACAAATTTTAATT
          1 TAAATA-AAATTTTAATT

             *                
       5020 TTAATAAAATATTTAA-T
          1 TAAATAAAAT-TTTAATT

                    
       5037 TAAATAAA
          1 TAAATAAA

       5045 TTTATTTGAT


Statistics
Matches: 22,  Mismatches: 2, Indels: 3
        0.81            0.07        0.11

Matches are distributed among these distances:
  17   12  0.55
  18   10  0.45

ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42


Consensus pattern (17 bp):   
TAAATAAAATTTTAATT

Found at i:5111 original size:16 final size:16

Alignment explanation


    Indices: 5079--5131  Score: 56
    Period size: 16  Copynumber: 3.3  Consensus size: 16

       5069 TATTTACAAG

                         *   
       5079 TAAA-AAATTATTTTAT
          1 TAAATAAATT-TTATAT

                            
       5095 TAAATAAATTTTATAT
          1 TAAATAAATTTTATAT

                       *     
       5111 TAAATTAAATTATAT-T
          1 TAAA-TAAATTTTATAT

                 
       5127 TAAAT
          1 TAAAT

       5132 TATTATGTTT


Statistics
Matches: 33,  Mismatches: 2, Indels: 5
        0.82            0.05        0.12

Matches are distributed among these distances:
  15    1  0.03
  16   18  0.55
  17   14  0.42

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (16 bp):   
TAAATAAATTTTATAT

Found at i:5132 original size:16 final size:17

Alignment explanation


    Indices: 5092--5133  Score: 61
    Period size: 16  Copynumber: 2.6  Consensus size: 17

       5082 AAAATTATTT

                          *  
       5092 TATTAAA-TAAATTTTA
          1 TATTAAATTAAATTATA

                             
       5108 TATTAAATTAAATTATA
          1 TATTAAATTAAATTATA

                      
       5125 T-TTAAATTA
          1 TATTAAATTA

       5134 TTATGTTTTC


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  16   15  0.62
  17    9  0.38

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


Consensus pattern (17 bp):   
TATTAAATTAAATTATA
Done.