Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009040.1 Kokia drynarioides strain JFW-HI SEQ_123738, 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: 3243
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.34

Warning! 37 characters in sequence are not A, C, G, or T


Found at i:904 original size:15 final size:14

Alignment explanation


    Indices: 850--910  Score: 59
    Period size: 15  Copynumber: 4.1  Consensus size: 14

        840 AATCCTATTT

                     *     
        850 ATTTTAGTTATTAAA
          1 ATTTTA-TTTTTAAA

                           *
        865 ATTAATTATTTTTAAG
          1 ATT--TTATTTTTAAA

                *          
        881 ATTTAATTTTATAAA
          1 ATTTTATTTT-TAAA

                          
        896 ATTTTATTTTTAAA
          1 ATTTTATTTTTAAA

             
        910 A
          1 A

        911 AACTTTCACA


Statistics
Matches: 38,  Mismatches: 5, Indels: 7
        0.76            0.10        0.14

Matches are distributed among these distances:
  14   11  0.29
  15   15  0.39
  16    9  0.24
  17    3  0.08

ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56


Consensus pattern (14 bp):   
ATTTTATTTTTAAA

Found at i:3154 original size:4 final size:4

Alignment explanation


    Indices: 3139--3179  Score: 55
    Period size: 4  Copynumber: 10.0  Consensus size: 4

       3129 GTTATAAAAT

                  *              *                            
       3139 AGAA AAAA AGAA AGAA AAAA GAGAA AGAA AGAA AGAA AGAA
          1 AGAA AGAA AGAA AGAA AGAA -AGAA AGAA AGAA AGAA AGAA

       3180 GAAGGAAGAA


Statistics
Matches: 32,  Mismatches: 4, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
   4   29  0.91
   5    3  0.09

ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00


Consensus pattern (4 bp):   
AGAA

Found at i:3163 original size:21 final size:21

Alignment explanation


    Indices: 3134--3181  Score: 69
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       3124 TTTTTGTTAT

                *                
       3134 AAAATAGAAAAAAAGAAAGAA
          1 AAAAGAGAAAAAAAGAAAGAA

                      *          
       3155 AAAAGAGAAAGAAAGAAAGAA
          1 AAAAGAGAAAAAAAGAAAGAA

             *    
       3176 AGAAGA
          1 AAAAGA

       3182 AGGAAGAAGG


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02


Consensus pattern (21 bp):   
AAAAGAGAAAAAAAGAAAGAA

Found at i:3198 original size:9 final size:9

Alignment explanation


    Indices: 3176--3212  Score: 51
    Period size: 9  Copynumber: 4.3  Consensus size: 9

       3166 AAAGAAAGAA

                     
       3176 AGAAGAA-G
          1 AGAAGAAGG

                     
       3184 -GAAGAAGG
          1 AGAAGAAGG

                     
       3192 AGAAGAAGG
          1 AGAAGAAGG

            *        
       3201 GGAAGAAGG
          1 AGAAGAAGG

               
       3210 AGA
          1 AGA

       3213 GGAAAAAAAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
   7    6  0.24
   8    1  0.04
   9   18  0.72

ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00


Consensus pattern (9 bp):   
AGAAGAAGG
Done.