Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011177.1 Kokia drynarioides strain JFW-HI SEQ_126153, 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: 2109
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.22

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:1724 original size:200 final size:200

Alignment explanation


    Indices: 1324--1729  Score: 688
    Period size: 200  Copynumber: 2.0  Consensus size: 200

       1314 NNNNNNNNNN

                                                                             
       1324 AAGAAGACCCAAATGAGGCTCAAAACGAGCGAAATCTTCAAAACCCAGCTTCCTGATGAGACACT
          1 AAGAAGACCCAAATGAGGCTCAAAACGAGCGAAATCTTCAAAACCCAGCTTCCTGATGAGACACT

                                                                             
       1389 GAGAAGCAGGTGGAAGCAATAAATGGTTAGCTTCCAGATGAGATACGGAGAAGTGAACCAAATCC
         66 GAGAAGCAGGTGGAAGCAATAAATGGTTAGCTTCCAGATGAGATACGGAGAAGTGAACCAAATCC

                                                     * *                     
       1454 GTCTTCCTGATGAGATACAGAGAAGCGGAATGAAACAGCGATGTGATCATCTTCCTAATGAGACA
        131 GTCTTCCTGATGAGATACAGAGAAGCGGAATGAAACAGCGACGCGATCATCTTCCTAATGAGACA

                 
       1519 CTGAG
        196 CTGAG

                                                                             
       1524 AAGAAGACCCAAATGAGGCTCAAAACGAGCGAAATCTTCAAAACCCAGCTTCCTGATGAGACACT
          1 AAGAAGACCCAAATGAGGCTCAAAACGAGCGAAATCTTCAAAACCCAGCTTCCTGATGAGACACT

                                                          *                * 
       1589 GAGAAGCAGGTGGAAGCAA-AAATGGTTAGCTTCCAGATGAGATACTGAGAAGTGAACCAAATTC
         66 GAGAAGCAGGTGGAAGCAATAAATGGTTAGCTTCCAGATGAGATACGGAGAAGTGAACCAAATCC

              *                          *         *      *    *   * *      *
       1653 GTTTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGACGCGGTCATTTTCTTGATGAGAT
        131 GTCTTCCTGATGAGATACAGAGAAGCGGAATGAAAC-AGCGACGCGATCATCTTCCTAATGAGAC

                  
       1718 ACTGAG
        195 ACTGAG

                  
       1724 AAGAAG
          1 AAGAAG

       1730 GCCAAGTCAA


Statistics
Matches: 193,  Mismatches: 12, Indels: 2
        0.93            0.06        0.01

Matches are distributed among these distances:
 199   77  0.40
 200  116  0.60

ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19


Consensus pattern (200 bp):   
AAGAAGACCCAAATGAGGCTCAAAACGAGCGAAATCTTCAAAACCCAGCTTCCTGATGAGACACT
GAGAAGCAGGTGGAAGCAATAAATGGTTAGCTTCCAGATGAGATACGGAGAAGTGAACCAAATCC
GTCTTCCTGATGAGATACAGAGAAGCGGAATGAAACAGCGACGCGATCATCTTCCTAATGAGACA
CTGAG

Found at i:2064 original size:18 final size:18

Alignment explanation


    Indices: 2041--2106  Score: 91
    Period size: 17  Copynumber: 3.7  Consensus size: 18

       2031 CGAACTCCCT

                              
       2041 TTAAATTTATTTTAAAAA
          1 TTAAATTTATTTTAAAAA

                     *        
       2059 TTAAATTT-GTTTAAAAA
          1 TTAAATTTATTTTAAAAA

                              *
       2076 TTTAAATTTATTTT-AAAT
          1 -TTAAATTTATTTTAAAAA

                         
       2094 TTAAATTTATTTT
          1 TTAAATTTATTTT

       2107 GAA


Statistics
Matches: 43,  Mismatches: 3, Indels: 5
        0.84            0.06        0.10

Matches are distributed among these distances:
  17   21  0.49
  18   19  0.44
  19    3  0.07

ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56


Consensus pattern (18 bp):   
TTAAATTTATTTTAAAAA

Found at i:2106 original size:17 final size:17

Alignment explanation


    Indices: 2040--2106  Score: 89
    Period size: 18  Copynumber: 3.8  Consensus size: 17

       2030 CCGAACTCCC

                              
       2040 TTTAAATTTATTTTAAAA
          1 TTTAAATTTATTTT-AAA

            *        *    *   
       2058 ATTAAATTTGTTTAAAAA
          1 TTTAAATTTATTT-TAAA

                             
       2076 TTTAAATTTATTTTAAA
          1 TTTAAATTTATTTTAAA

                          
       2093 TTTAAATTTATTTT
          1 TTTAAATTTATTTT

       2107 GAA


Statistics
Matches: 42,  Mismatches: 6, Indels: 3
        0.82            0.12        0.06

Matches are distributed among these distances:
  17   17  0.40
  18   25  0.60

ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57


Consensus pattern (17 bp):   
TTTAAATTTATTTTAAA
Done.