Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007315.1 Kokia drynarioides strain JFW-HI SEQ_121931, 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: 22470
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34


Found at i:9572 original size:9 final size:9

Alignment explanation


    Indices: 9558--9596  Score: 51
    Period size: 9  Copynumber: 4.2  Consensus size: 9

       9548 ACTTTCGTCC

                     
       9558 ATAAATATT
          1 ATAAATATT

                     
       9567 ATAAATATT
          1 ATAAATATT

                  *  
       9576 ATAAATTTT
          1 ATAAATATT

                  *   
       9585 AATAAAAATT
          1 -ATAAATATT

              
       9595 AT
          1 AT

       9597 TTAAAAAATT


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
   9   19  0.73
  10    7  0.27

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (9 bp):   
ATAAATATT

Found at i:9595 original size:19 final size:18

Alignment explanation


    Indices: 9558--9596  Score: 51
    Period size: 19  Copynumber: 2.1  Consensus size: 18

       9548 ACTTTCGTCC

                          *   
       9558 ATAAATATTATAAATATT
          1 ATAAATATTATAAAAATT

                  *            
       9576 ATAAATTTTAATAAAAATT
          1 ATAAATATT-ATAAAAATT

              
       9595 AT
          1 AT

       9597 TTAAAAAATT


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  18    8  0.44
  19   10  0.56

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (18 bp):   
ATAAATATTATAAAAATT

Found at i:10542 original size:24 final size:24

Alignment explanation


    Indices: 10505--10551  Score: 76
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      10495 TAAACTAATA

                    *               
      10505 AGAGTTTAGCTGAAACAAATAAAT
          1 AGAGTTTAACTGAAACAAATAAAT

                     *             
      10529 AGAGTTTAATTGAAACAAATAAA
          1 AGAGTTTAACTGAAACAAATAAA

      10552 CAGTTTAATT


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  24   21  1.00

ACGTcount: A:0.53, C:0.06, G:0.15, T:0.26


Consensus pattern (24 bp):   
AGAGTTTAACTGAAACAAATAAAT

Found at i:10559 original size:22 final size:24

Alignment explanation


    Indices: 10515--10561  Score: 71
    Period size: 22  Copynumber: 2.0  Consensus size: 24

      10505 AGAGTTTAGC

                           *        
      10515 TGAAACAAATAAATAGAGTTTAAT
          1 TGAAACAAATAAATACAGTTTAAT

                                    
      10539 TGAAACAAAT-AA-ACAGTTTAAT
          1 TGAAACAAATAAATACAGTTTAAT

             
      10561 T
          1 T

      10562 AAAGATTATT


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  22   10  0.45
  23    2  0.09
  24   10  0.45

ACGTcount: A:0.53, C:0.06, G:0.11, T:0.30


Consensus pattern (24 bp):   
TGAAACAAATAAATACAGTTTAAT

Found at i:12451 original size:24 final size:24

Alignment explanation


    Indices: 12416--12478  Score: 90
    Period size: 24  Copynumber: 2.6  Consensus size: 24

      12406 TAAACTAATA

                   *                
      12416 AGAGTTTGATTGAAACAAATAAAC
          1 AGAGTTTAATTGAAACAAATAAAC

             *                    **
      12440 ATAGTTTAATTGAAACAAATAAGT
          1 AGAGTTTAATTGAAACAAATAAAC

                           
      12464 AGAGTTTAATTGAAA
          1 AGAGTTTAATTGAAA

      12479 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:0.49, C:0.05, G:0.16, T:0.30


Consensus pattern (24 bp):   
AGAGTTTAATTGAAACAAATAAAC

Found at i:21829 original size:23 final size:24

Alignment explanation


    Indices: 21780--21829  Score: 57
    Period size: 23  Copynumber: 2.1  Consensus size: 24

      21770 ATAATTACTT

                  *      *        * 
      21780 AAATTATTTAATTTTTTAAATTTA
          1 AAATTAATTAATTATTTAAATTGA

                               *    
      21804 AAATTAATT-ATTATTTAACTTGA
          1 AAATTAATTAATTATTTAAATTGA

               
      21827 AAA
          1 AAA

      21830 AACTAAAATA


Statistics
Matches: 22,  Mismatches: 4, Indels: 1
        0.81            0.15        0.04

Matches are distributed among these distances:
  23   14  0.64
  24    8  0.36

ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50


Consensus pattern (24 bp):   
AAATTAATTAATTATTTAAATTGA
Done.