Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013990.1 Kokia drynarioides strain JFW-HI SEQ_129021, 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: 10088
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34


Found at i:75 original size:15 final size:15

Alignment explanation


    Indices: 11--98  Score: 54
    Period size: 15  Copynumber: 5.8  Consensus size: 15

          1 AATATTAATA

                      *   *
         11 ATTATTATTACTGTC
          1 ATTATTATTATTGTT

                *             
         26 ATTAATATTACTAATGTT
          1 ATTATTATTA-T--TGTT

                *  *       
         44 ATTAGTAATA-T-TT
          1 ATTATTATTATTGTT

                           
         57 ATTATTATTATTGTT
          1 ATTATTATTATTGTT

                **         
         72 ATTAACATTATTGTT
          1 ATTATTATTATTGTT

            *     *     
         87 GTTATTGTTATT
          1 ATTATTATTATT

         99 ATGACCAAAG


Statistics
Matches: 55,  Mismatches: 13, Indels: 10
        0.71            0.17        0.13

Matches are distributed among these distances:
  13   10  0.18
  14    2  0.04
  15   32  0.58
  18   11  0.20

ACGTcount: A:0.31, C:0.05, G:0.08, T:0.57


Consensus pattern (15 bp):   
ATTATTATTATTGTT

Found at i:838 original size:18 final size:17

Alignment explanation


    Indices: 803--895  Score: 87
    Period size: 17  Copynumber: 5.4  Consensus size: 17

        793 CTTTATTTAT

                      **    *
        803 TTTAAATTTATGATAAT
          1 TTTAAATTTAAAATAAA

                             *
        820 TTTAAATTTGAAAATAAT
          1 TTTAAATTT-AAAATAAA

                  *     *    
        838 TTTAAACTTAAATTAAA
          1 TTTAAATTTAAAATAAA

                      *   *   
        855 TTTAAATTTTTAAACAAA
          1 TTTAAA-TTTAAAATAAA

                 *           
        873 TTTAATTTTAAAATAAA
          1 TTTAAATTTAAAATAAA

                  
        890 TTTAAA
          1 TTTAAA

        896 GGGAGTTTGG


Statistics
Matches: 61,  Mismatches: 13, Indels: 4
        0.78            0.17        0.05

Matches are distributed among these distances:
  17   35  0.57
  18   26  0.43

ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46


Consensus pattern (17 bp):   
TTTAAATTTAAAATAAA

Found at i:859 original size:35 final size:35

Alignment explanation


    Indices: 815--895  Score: 90
    Period size: 35  Copynumber: 2.3  Consensus size: 35

        805 TAAATTTATG

                *              *  *            
        815 ATAATTTTAAATTTGAAAATAATTTTAAACTTAAA
          1 ATAAATTTAAATTTGAAAACAAATTTAAACTTAAA

            *             **            **     
        850 TTAAATTTAAATTTTTAAACAAATTTAATTTTAAA
          1 ATAAATTTAAATTTGAAAACAAATTTAAACTTAAA

                       
        885 ATAAATTTAAA
          1 ATAAATTTAAA

        896 GGGAGTTTGG


Statistics
Matches: 37,  Mismatches: 9, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  35   37  1.00

ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44


Consensus pattern (35 bp):   
ATAAATTTAAATTTGAAAACAAATTTAAACTTAAA

Found at i:8247 original size:24 final size:24

Alignment explanation


    Indices: 8220--8276  Score: 78
    Period size: 24  Copynumber: 2.4  Consensus size: 24

       8210 AAGCCTAATT

                 *                  
       8220 CTAATCAATGCAAAATATATTATG
          1 CTAATAAATGCAAAATATATTATG

                       *           *
       8244 CTAATAAATGCTAAATATATTATA
          1 CTAATAAATGCAAAATATATTATG

               *     
       8268 CTACTAAAT
          1 CTAATAAAT

       8277 CTTCTTGAAA


Statistics
Matches: 29,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  24   29  1.00

ACGTcount: A:0.47, C:0.12, G:0.05, T:0.35


Consensus pattern (24 bp):   
CTAATAAATGCAAAATATATTATG

Found at i:8350 original size:36 final size:35

Alignment explanation


    Indices: 8299--8371  Score: 110
    Period size: 36  Copynumber: 2.1  Consensus size: 35

       8289 TAATATATTC

                      *         *            *  
       8299 TGTTTAACTTGACTTGCAAGTAATTCTCTTAGATTT
          1 TGTTTAACTTAACTTGCAAGCAA-TCTCTTAGAATT

                                               
       8335 TGTTTAACTTAACTTGCAAGCAATCTCTTAGAATT
          1 TGTTTAACTTAACTTGCAAGCAATCTCTTAGAATT

              
       8370 TG
          1 TG

       8372 GATGACACAA


Statistics
Matches: 34,  Mismatches: 3, Indels: 1
        0.89            0.08        0.03

Matches are distributed among these distances:
  35   13  0.38
  36   21  0.62

ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44


Consensus pattern (35 bp):   
TGTTTAACTTAACTTGCAAGCAATCTCTTAGAATT
Done.