Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008772.1 Kokia drynarioides strain JFW-HI SEQ_123455, 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: 5315
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35


Found at i:212 original size:19 final size:18

Alignment explanation


    Indices: 166--213  Score: 51
    Period size: 19  Copynumber: 2.6  Consensus size: 18

        156 AATTTATTTT

                              
        166 TAAAATTAAAATAAAATA
          1 TAAAATTAAAATAAAATA

               * *              
        184 TATTAGTTAAAATGAAAATA
          1 TA-AAATTAAAAT-AAAATA

                *     
        204 TAAATTTAAA
          1 TAAAATTAAA

        214 TATTATATAA


Statistics
Matches: 24,  Mismatches: 4, Indels: 3
        0.77            0.13        0.10

Matches are distributed among these distances:
  18    2  0.08
  19   14  0.58
  20    8  0.33

ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33


Consensus pattern (18 bp):   
TAAAATTAAAATAAAATA

Found at i:2579 original size:45 final size:45

Alignment explanation


    Indices: 2515--2607  Score: 186
    Period size: 45  Copynumber: 2.1  Consensus size: 45

       2505 TTTTATTCTT

                                                         
       2515 GAGGGATAAAGTTGGTTGTCCAGGGATCATATGATCAGAAACCCC
          1 GAGGGATAAAGTTGGTTGTCCAGGGATCATATGATCAGAAACCCC

                                                         
       2560 GAGGGATAAAGTTGGTTGTCCAGGGATCATATGATCAGAAACCCC
          1 GAGGGATAAAGTTGGTTGTCCAGGGATCATATGATCAGAAACCCC

               
       2605 GAG
          1 GAG

       2608 ATTTAGCATG


Statistics
Matches: 48,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  45   48  1.00

ACGTcount: A:0.31, C:0.17, G:0.30, T:0.22


Consensus pattern (45 bp):   
GAGGGATAAAGTTGGTTGTCCAGGGATCATATGATCAGAAACCCC

Found at i:2984 original size:16 final size:18

Alignment explanation


    Indices: 2945--2978  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       2935 TAAATGTATA

                              
       2945 ATATTT-TATATTATGTT
          1 ATATTTATATATTATGTT

              *              
       2962 ATTTTTATATATTATGT
          1 ATATTTATATATTATGT

       2979 AATTTAAAAC


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    5  0.33
  18   10  0.67

ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65


Consensus pattern (18 bp):   
ATATTTATATATTATGTT

Found at i:3119 original size:14 final size:14

Alignment explanation


    Indices: 3102--3136  Score: 52
    Period size: 14  Copynumber: 2.5  Consensus size: 14

       3092 AAAATAAAAT

                    *     
       3102 AAAATAAATATTTA
          1 AAAATAAAAATTTA

                *         
       3116 AAAAAAAAAATTTA
          1 AAAATAAAAATTTA

                   
       3130 AAAATAA
          1 AAAATAA

       3137 TATGGGCGGC


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  14   18  1.00

ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26


Consensus pattern (14 bp):   
AAAATAAAAATTTA
Done.