Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000298.1 Kokia drynarioides strain JFW-HI SEQ_111052, 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: 38839
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35


Found at i:1069 original size:18 final size:19

Alignment explanation


    Indices: 1046--1087  Score: 59
    Period size: 19  Copynumber: 2.3  Consensus size: 19

       1036 CACCTATTTA

                               
       1046 AATTTG-TCATGATAAAAT
          1 AATTTGTTCATGATAAAAT

                    *   *      
       1064 AATTTGTTTATGTTAAAAT
          1 AATTTGTTCATGATAAAAT

                 
       1083 AATTT
          1 AATTT

       1088 CTTAACAAAA


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  18    6  0.29
  19   15  0.71

ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48


Consensus pattern (19 bp):   
AATTTGTTCATGATAAAAT

Found at i:2200 original size:22 final size:23

Alignment explanation


    Indices: 2172--2216  Score: 65
    Period size: 22  Copynumber: 2.0  Consensus size: 23

       2162 GTGAAACTTT

                                   
       2172 TAAATTAAAATAAA-AATAAAAA
          1 TAAATTAAAATAAATAATAAAAA

                     *     *       
       2194 TAAATTAAATTAAATTATAAAAA
          1 TAAATTAAAATAAATAATAAAAA

       2217 ATCAAATTTA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  22   13  0.65
  23    7  0.35

ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29


Consensus pattern (23 bp):   
TAAATTAAAATAAATAATAAAAA

Found at i:2230 original size:30 final size:27

Alignment explanation


    Indices: 2174--2239  Score: 78
    Period size: 30  Copynumber: 2.3  Consensus size: 27

       2164 GAAACTTTTA

                                       
       2174 AATTAAAATAAAAATAAAAATAAATTA
          1 AATTAAAATAAAAATAAAAATAAATTA

                              *   * *     
       2201 AATTAAATTATAAAAAATCAAATTTAATTA
          1 AATTAAA--AT-AAAAATAAAAATAAATTA

                     
       2231 AATTAAAAT
          1 AATTAAAAT

       2240 TTTTCAATTT


Statistics
Matches: 33,  Mismatches: 3, Indels: 5
        0.80            0.07        0.12

Matches are distributed among these distances:
  27    7  0.21
  28    2  0.06
  29    2  0.06
  30   22  0.67

ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32


Consensus pattern (27 bp):   
AATTAAAATAAAAATAAAAATAAATTA

Found at i:4115 original size:18 final size:18

Alignment explanation


    Indices: 4089--4124  Score: 54
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       4079 GGTTAAGGGT

                *     *       
       4089 ATAAGTAGAAGAAACAAA
          1 ATAAATAGAAAAAACAAA

                              
       4107 ATAAATAGAAAAAACAAA
          1 ATAAATAGAAAAAACAAA

       4125 GGAATCTAAG


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.72, C:0.06, G:0.11, T:0.11


Consensus pattern (18 bp):   
ATAAATAGAAAAAACAAA

Found at i:26423 original size:38 final size:38

Alignment explanation


    Indices: 26363--26435  Score: 94
    Period size: 37  Copynumber: 1.9  Consensus size: 38

      26353 TTTTTCATAA

                          ** *         *          
      26363 TTTTTATTTAAAAATTATATATTTTT-TAATTTTTATG
          1 TTTTTATTTAAAAAAAAAATATTTTTAAAATTTTTATG

                                                
      26400 TTTTTATTTAAAATAAAAAATATTTTTAAAATTTTT
          1 TTTTTATTTAAAA-AAAAAATATTTTTAAAATTTTT

      26436 CAACTACTTT


Statistics
Matches: 30,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
  37   13  0.43
  38   10  0.33
  39    7  0.23

ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60


Consensus pattern (38 bp):   
TTTTTATTTAAAAAAAAAATATTTTTAAAATTTTTATG
Done.