Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013480.1 Kokia drynarioides strain JFW-HI SEQ_128506, 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: 7408
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33


Found at i:84 original size:18 final size:18

Alignment explanation


    Indices: 61--97  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

         51 CTGTATGACT

                         *    
         61 TTCTCCATTCGCATTACC
          1 TTCTCCATTCGCACTACC

                     *        
         79 TTCTCCATTTGCACTACC
          1 TTCTCCATTCGCACTACC

             
         97 T
          1 T

         98 GCACCAATGA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.16, C:0.38, G:0.05, T:0.41


Consensus pattern (18 bp):   
TTCTCCATTCGCACTACC

Found at i:355 original size:31 final size:31

Alignment explanation


    Indices: 317--377  Score: 95
    Period size: 31  Copynumber: 2.0  Consensus size: 31

        307 AAAATGTCGT

                                           
        317 AATGACTTAAATAAAAACTTCCAAATAGTTC
          1 AATGACTTAAATAAAAACTTCCAAATAGTTC

                        *       * *       
        348 AATGACTTAAATGAAAACTTTCTAATAGTT
          1 AATGACTTAAATAAAAACTTCCAAATAGTT

        378 TAGACCATTT


Statistics
Matches: 27,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  31   27  1.00

ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33


Consensus pattern (31 bp):   
AATGACTTAAATAAAAACTTCCAAATAGTTC

Found at i:4419 original size:27 final size:27

Alignment explanation


    Indices: 4379--4447  Score: 75
    Period size: 27  Copynumber: 2.5  Consensus size: 27

       4369 TTTTTAAAAA

                          *         *    
       4379 TTTTAAAATATTTTTATAATCTTTGTACT
          1 TTTTAAAAT-TTTTAATAATCTTTATA-T

                   *         * *       
       4408 TTTTAAAGTTTTTAATACTTTTTATAT
          1 TTTTAAAATTTTTAATAATCTTTATAT

                         
       4435 TTTTAAAATTTTT
          1 TTTTAAAATTTTT

       4448 TATATTTAAA


Statistics
Matches: 34,  Mismatches: 6, Indels: 2
        0.81            0.14        0.05

Matches are distributed among these distances:
  27   13  0.38
  28   13  0.38
  29    8  0.24

ACGTcount: A:0.30, C:0.04, G:0.03, T:0.62


Consensus pattern (27 bp):   
TTTTAAAATTTTTAATAATCTTTATAT

Found at i:4437 original size:18 final size:18

Alignment explanation


    Indices: 4404--4454  Score: 66
    Period size: 18  Copynumber: 2.8  Consensus size: 18

       4394 ATAATCTTTG

                     *         
       4404 TACTTTTTAAAGTTTTTAA
          1 TACTTTTTATA-TTTTTAA

                              
       4423 TACTTTTTATATTTTTAA
          1 TACTTTTTATATTTTTAA

            * *           
       4441 AATTTTTTATATTT
          1 TACTTTTTATATTT

       4455 AAAAATTAAT


Statistics
Matches: 29,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  18   19  0.66
  19   10  0.34

ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65


Consensus pattern (18 bp):   
TACTTTTTATATTTTTAA

Found at i:4447 original size:28 final size:29

Alignment explanation


    Indices: 4379--4449  Score: 76
    Period size: 28  Copynumber: 2.5  Consensus size: 29

       4369 TTTTTAAAAA

                                     *    
       4379 TTTTAAAATATTTTT-ATAATCTTTGTACT
          1 TTTTAAAAT-TTTTTAATAATCTTTATACT

                    *         * *        
       4408 TTTT-AAAGTTTTTAATACTTTTTATA-T
          1 TTTTAAAATTTTTTAATAATCTTTATACT

                           
       4435 TTTTAAAATTTTTTA
          1 TTTTAAAATTTTTTA

       4450 TATTTAAAAA


Statistics
Matches: 35,  Mismatches: 5, Indels: 5
        0.78            0.11        0.11

Matches are distributed among these distances:
  27   10  0.29
  28   21  0.60
  29    4  0.11

ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62


Consensus pattern (29 bp):   
TTTTAAAATTTTTTAATAATCTTTATACT

Found at i:4455 original size:16 final size:17

Alignment explanation


    Indices: 4426--4458  Score: 50
    Period size: 16  Copynumber: 2.0  Consensus size: 17

       4416 TTTTTAATAC

                     *       
       4426 TTTTTATATTTTTAAAA
          1 TTTTTATATATTTAAAA

                             
       4443 TTTTT-TATATTTAAAA
          1 TTTTTATATATTTAAAA

       4459 ATTAATTAAT


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  16   10  0.67
  17    5  0.33

ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64


Consensus pattern (17 bp):   
TTTTTATATATTTAAAA

Found at i:6665 original size:21 final size:21

Alignment explanation


    Indices: 6641--6682  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       6631 CACATGCTAG

                         *       
       6641 GGAAATAGTTGTGTGAGGTAT
          1 GGAAATAGTTGTGCGAGGTAT

                                 
       6662 GGAAATAGTTGTGCGAGGTAT
          1 GGAAATAGTTGTGCGAGGTAT

       6683 ATCATCGTTT


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.29, C:0.02, G:0.38, T:0.31


Consensus pattern (21 bp):   
GGAAATAGTTGTGCGAGGTAT
Done.