Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013992.1 Kokia drynarioides strain JFW-HI SEQ_129023, 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: 30107
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36


Found at i:8492 original size:19 final size:20

Alignment explanation


    Indices: 8468--8519  Score: 61
    Period size: 22  Copynumber: 2.5  Consensus size: 20

       8458 TGTTTATTTC

                                
       8468 ATGGAAAATAACTT-GGTCA
          1 ATGGAAAATAACTTAGGTCA

                  *  *            
       8487 ATGGAATATGACTTACAGGTCA
          1 ATGGAAAATAACTT--AGGTCA

                       
       8509 ATGGAAAATAA
          1 ATGGAAAATAA

       8520 GTTATTTTTC


Statistics
Matches: 26,  Mismatches: 4, Indels: 3
        0.79            0.12        0.09

Matches are distributed among these distances:
  19   12  0.46
  22   14  0.54

ACGTcount: A:0.44, C:0.10, G:0.21, T:0.25


Consensus pattern (20 bp):   
ATGGAAAATAACTTAGGTCA

Found at i:18242 original size:21 final size:21

Alignment explanation


    Indices: 18218--18275  Score: 71
    Period size: 21  Copynumber: 2.8  Consensus size: 21

      18208 TACTGCAGAC

                  *              
      18218 TTCTACTGATACAAGTGACAG
          1 TTCTACCGATACAAGTGACAG

                               **
      18239 TTCTACCGATACAAGTGACTT
          1 TTCTACCGATACAAGTGACAG

                   * *      
      18260 TTCTACCAAAACAAGT
          1 TTCTACCGATACAAGT

      18276 CTTACTTCTA


Statistics
Matches: 32,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   32  1.00

ACGTcount: A:0.34, C:0.22, G:0.14, T:0.29


Consensus pattern (21 bp):   
TTCTACCGATACAAGTGACAG

Found at i:29185 original size:19 final size:19

Alignment explanation


    Indices: 29161--29200  Score: 80
    Period size: 19  Copynumber: 2.1  Consensus size: 19

      29151 CCAAGTTACT

                               
      29161 ATCACCAGCAACTTGCACC
          1 ATCACCAGCAACTTGCACC

                               
      29180 ATCACCAGCAACTTGCACC
          1 ATCACCAGCAACTTGCACC

              
      29199 AT
          1 AT

      29201 TGCTACCGCC


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   21  1.00

ACGTcount: A:0.33, C:0.40, G:0.10, T:0.17


Consensus pattern (19 bp):   
ATCACCAGCAACTTGCACC

Found at i:29774 original size:18 final size:17

Alignment explanation


    Indices: 29733--29775  Score: 54
    Period size: 16  Copynumber: 2.6  Consensus size: 17

      29723 TGATAATAAT

                             
      29733 AATAATAAT-TTTATTA
          1 AATAATAATATTTATTA

               *             
      29749 AA-GATAATATTTATTA
          1 AATAATAATATTTATTA

                       
      29765 AATAATTAATA
          1 AATAA-TAATA

      29776 ACATTAGTAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 4
        0.79            0.07        0.14

Matches are distributed among these distances:
  15    5  0.23
  16   11  0.50
  17    1  0.05
  18    5  0.23

ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44


Consensus pattern (17 bp):   
AATAATAATATTTATTA
Done.