Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012433.1 Kokia drynarioides strain JFW-HI SEQ_127437, 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: 3210
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37


Found at i:762 original size:18 final size:18

Alignment explanation


    Indices: 739--774  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

        729 ATGACTTAAT

                              
        739 CTGTAATTTTTGGTAGTA
          1 CTGTAATTTTTGGTAGTA

                              
        757 CTGTAATTTTTGGTAGTA
          1 CTGTAATTTTTGGTAGTA

        775 ATAAGAGAGT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.22, C:0.06, G:0.22, T:0.50


Consensus pattern (18 bp):   
CTGTAATTTTTGGTAGTA

Found at i:2184 original size:36 final size:35

Alignment explanation


    Indices: 2123--2199  Score: 109
    Period size: 36  Copynumber: 2.2  Consensus size: 35

       2113 TTGTGTGATC

                *           *         *       *
       2123 CAAATTCTAAGAGATTGCTTGCAAGTTAAGTTAAG
          1 CAAAATCTAAGAGATTACTTGCAAGTCAAGTTAAA

                                                
       2158 CAAAATCTAAGAGAATTACTTGCAAGTCAAGTTAAA
          1 CAAAATCTAAGAG-ATTACTTGCAAGTCAAGTTAAA

                  
       2194 CAAAAT
          1 CAAAAT

       2200 ATATTATATT


Statistics
Matches: 37,  Mismatches: 4, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  35   12  0.32
  36   25  0.68

ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27


Consensus pattern (35 bp):   
CAAAATCTAAGAGATTACTTGCAAGTCAAGTTAAA

Found at i:2245 original size:24 final size:24

Alignment explanation


    Indices: 2218--2268  Score: 75
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       2208 TTTCTAGAAG

                     *              
       2218 ATTTAGTAGTATAATATATTTAGC
          1 ATTTAGTAGCATAATATATTTAGC

                 *               *  
       2242 ATTTATTAGCATAATATATTTTGC
          1 ATTTAGTAGCATAATATATTTAGC

               
       2266 ATT
          1 ATT

       2269 GATTAGAATT


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

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.35, C:0.06, G:0.10, T:0.49


Consensus pattern (24 bp):   
ATTTAGTAGCATAATATATTTAGC

Found at i:2273 original size:24 final size:24

Alignment explanation


    Indices: 2228--2274  Score: 76
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       2218 ATTTAGTAGT

                             *      
       2228 ATAATATATTTAGCATTTATTAGC
          1 ATAATATATTTAGCATTGATTAGC

                       *           
       2252 ATAATATATTTTGCATTGATTAG
          1 ATAATATATTTAGCATTGATTAG

       2275 AATTAGGCTT


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

Matches are distributed among these distances:
  24   21  1.00

ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47


Consensus pattern (24 bp):   
ATAATATATTTAGCATTGATTAGC
Done.