Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013637.1 Kokia drynarioides strain JFW-HI SEQ_128665, 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: 6390
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33


Found at i:896 original size:23 final size:23

Alignment explanation


    Indices: 867--944  Score: 113
    Period size: 23  Copynumber: 3.4  Consensus size: 23

        857 AACACTAGCA

                     *             
        867 TGCTTACTGTTTAGCACTGTGTG
          1 TGCTTACTGATTAGCACTGTGTG

              *        *           
        890 TGTTTACTGATCAGCACTGTGTG
          1 TGCTTACTGATTAGCACTGTGTG

                                    
        913 TGCTTACTGGATT-GCACTGTGTG
          1 TGCTTACT-GATTAGCACTGTGTG

                     
        936 TGCTTACTG
          1 TGCTTACTG

        945 TTGCCCAGCA


Statistics
Matches: 49,  Mismatches: 5, Indels: 3
        0.86            0.09        0.05

Matches are distributed among these distances:
  22    1  0.02
  23   45  0.92
  24    3  0.06

ACGTcount: A:0.14, C:0.18, G:0.27, T:0.41


Consensus pattern (23 bp):   
TGCTTACTGATTAGCACTGTGTG

Found at i:1313 original size:27 final size:27

Alignment explanation


    Indices: 1282--1334  Score: 106
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       1272 GGTTAAATGA

                                       
       1282 TATATATATATATATGAAAGGTATGTG
          1 TATATATATATATATGAAAGGTATGTG

                                      
       1309 TATATATATATATATGAAAGGTATGT
          1 TATATATATATATATGAAAGGTATGT

       1335 ATTTTATATG


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   26  1.00

ACGTcount: A:0.42, C:0.00, G:0.17, T:0.42


Consensus pattern (27 bp):   
TATATATATATATATGAAAGGTATGTG

Found at i:2485 original size:24 final size:24

Alignment explanation


    Indices: 2424--2486  Score: 90
    Period size: 24  Copynumber: 2.6  Consensus size: 24

       2414 AAGACTAATA

                       *            
       2424 AGAGTTTAACTCAAACAAATAAAC
          1 AGAGTTTAACTGAAACAAATAAAC

                     *      *      *
       2448 AGAGTTTAATTGAAACTAATAAAT
          1 AGAGTTTAACTGAAACAAATAAAC

                           
       2472 AGAGTTTAACTGAAA
          1 AGAGTTTAACTGAAA

       2487 GATTATTTCT


Statistics
Matches: 34,  Mismatches: 5, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  24   34  1.00

ACGTcount: A:0.51, C:0.10, G:0.13, T:0.27


Consensus pattern (24 bp):   
AGAGTTTAACTGAAACAAATAAAC

Found at i:4422 original size:24 final size:24

Alignment explanation


    Indices: 4406--4456  Score: 84
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       4396 AGTTTGACTT

                                    
       4406 AAACAAATAAATAGAGTTTAATTG
          1 AAACAAATAAATAGAGTTTAATTG

                         *       *  
       4430 AAACAAATAAATAAAGTTTAACTG
          1 AAACAAATAAATAGAGTTTAATTG

               
       4454 AAA
          1 AAA

       4457 GATTATTTCT


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  24   25  1.00

ACGTcount: A:0.59, C:0.06, G:0.10, T:0.25


Consensus pattern (24 bp):   
AAACAAATAAATAGAGTTTAATTG
Done.