Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010311.1 Kokia drynarioides strain JFW-HI SEQ_125173, 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: 1742
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.36


Found at i:160 original size:3 final size:3

Alignment explanation


    Indices: 154--196  Score: 59
    Period size: 3  Copynumber: 14.0  Consensus size: 3

        144 TATTAATAAT

                        *                *                          
        154 TTA TTA TTA ATA TTA TTA TTAA CTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA

        197 AAAACAATTA


Statistics
Matches: 35,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
   3   33  0.94
   4    2  0.06

ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60


Consensus pattern (3 bp):   
TTA

Found at i:182 original size:22 final size:22

Alignment explanation


    Indices: 155--197  Score: 77
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        145 ATTAATAATT

                                  
        155 TATTATTAATATTATTATTAAC
          1 TATTATTAATATTATTATTAAC

                    *            
        177 TATTATTATTATTATTATTAA
          1 TATTATTAATATTATTATTAA

        198 AAACAATTAT


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  22   20  1.00

ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58


Consensus pattern (22 bp):   
TATTATTAATATTATTATTAAC

Found at i:206 original size:25 final size:25

Alignment explanation


    Indices: 154--207  Score: 72
    Period size: 25  Copynumber: 2.2  Consensus size: 25

        144 TATTAATAAT

                              **   * 
        154 TTATTATTAATATTATTATTAACTA
          1 TTATTATTAATATTATTAAAAACAA

                     *               
        179 TTATTATTATTATTATTAAAAACAA
          1 TTATTATTAATATTATTAAAAACAA

                
        204 TTAT
          1 TTAT

        208 CAAGATTATT


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  25   25  1.00

ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54


Consensus pattern (25 bp):   
TTATTATTAATATTATTAAAAACAA

Found at i:494 original size:6 final size:6

Alignment explanation


    Indices: 483--538  Score: 69
    Period size: 6  Copynumber: 9.3  Consensus size: 6

        473 TATAATAAGT

                           *      *                 *               
        483 TTTAAA TTTAAA TATAAA TCTAAA TTTAAA -TTAAT TTTAAA TTTTAAA
          1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA

                     
        531 TTTAAA TT
          1 TTTAAA TT

        539 CAAAATCAAT


Statistics
Matches: 43,  Mismatches: 5, Indels: 4
        0.83            0.10        0.08

Matches are distributed among these distances:
   5    4  0.09
   6   33  0.77
   7    6  0.14

ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50


Consensus pattern (6 bp):   
TTTAAA

Done.