Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002669.1 Kokia drynarioides strain JFW-HI SEQ_114923, 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: 3158
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.33


Found at i:393 original size:14 final size:15

Alignment explanation


    Indices: 368--404  Score: 67
    Period size: 14  Copynumber: 2.5  Consensus size: 15

        358 TTCCGCTTAT

                           
        368 TTTGACTATTCAAAG
          1 TTTGACTATTCAAAG

                           
        383 TTTGA-TATTCAAAG
          1 TTTGACTATTCAAAG

                    
        397 TTTGACTA
          1 TTTGACTA

        405 AGACAAACCC


Statistics
Matches: 21,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  14   14  0.67
  15    7  0.33

ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43


Consensus pattern (15 bp):   
TTTGACTATTCAAAG

Found at i:2191 original size:6 final size:6

Alignment explanation


    Indices: 2180--2234  Score: 51
    Period size: 6  Copynumber: 9.3  Consensus size: 6

       2170 TTAAGCTTAT

                                *                    *      *      *
       2180 TTTAAA TTTAAAA TTT-AT TTTAAA TTTAAA TTT-AT TTTAAT TTTAAT
          1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA

                     
       2227 TTTAAA TT
          1 TTTAAA TT

       2235 GGATTTAAAA


Statistics
Matches: 42,  Mismatches: 4, Indels: 6
        0.81            0.08        0.12

Matches are distributed among these distances:
   5    8  0.19
   6   28  0.67
   7    6  0.14

ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60


Consensus pattern (6 bp):   
TTTAAA

Found at i:2199 original size:18 final size:18

Alignment explanation


    Indices: 2176--2225  Score: 84
    Period size: 17  Copynumber: 2.8  Consensus size: 18

       2166 ATTTTTAAGC

                              
       2176 TTATTTTAAATTTAAAAT
          1 TTATTTTAAATTTAAAAT

                              
       2194 TTATTTTAAATTT-AAAT
          1 TTATTTTAAATTTAAAAT

                     *     
       2211 TTATTTTAATTTTAA
          1 TTATTTTAAATTTAA

       2226 TTTTAAATTG


Statistics
Matches: 30,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  17   16  0.53
  18   14  0.47

ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60


Consensus pattern (18 bp):   
TTATTTTAAATTTAAAAT

Found at i:2241 original size:23 final size:22

Alignment explanation


    Indices: 2178--2242  Score: 66
    Period size: 23  Copynumber: 3.0  Consensus size: 22

       2168 TTTTAAGCTT

                                  
       2178 ATTTTAAATTTAAA---ATTT-
          1 ATTTTAAATTTAAATTGATTTA

                            *      
       2196 ATTTTAAATTTAAATTTATTTTA
          1 ATTTTAAATTTAAATTGA-TTTA

                   *               
       2219 ATTTTAATTTTAAATTGGATTTA
          1 ATTTTAAATTTAAATT-GATTTA

             
       2242 A
          1 A

       2243 AAGTCCAAAT


Statistics
Matches: 39,  Mismatches: 2, Indels: 7
        0.81            0.04        0.15

Matches are distributed among these distances:
  18   14  0.36
  21    1  0.03
  22    3  0.08
  23   20  0.51
  24    1  0.03

ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57


Consensus pattern (22 bp):   
ATTTTAAATTTAAATTGATTTA
Done.