Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009006.1 Kokia drynarioides strain JFW-HI SEQ_123704, 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: 17905
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33


Found at i:10463 original size:21 final size:21

Alignment explanation


    Indices: 10439--10492  Score: 92
    Period size: 21  Copynumber: 2.6  Consensus size: 21

      10429 CTTGTGTCAG

                                  
      10439 TTCTACCGATACAAGT-ATAAC
          1 TTCTACCGATACAAGTCAT-AC

                                 
      10460 TTCTACCGATACAAGTCATAC
          1 TTCTACCGATACAAGTCATAC

                        
      10481 TTCTACCGATAC
          1 TTCTACCGATAC

      10493 TAAAAACTCT


Statistics
Matches: 32,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
  21   30  0.94
  22    2  0.06

ACGTcount: A:0.33, C:0.28, G:0.09, T:0.30


Consensus pattern (21 bp):   
TTCTACCGATACAAGTCATAC

Found at i:10560 original size:21 final size:21

Alignment explanation


    Indices: 10533--10607  Score: 71
    Period size: 21  Copynumber: 3.4  Consensus size: 21

      10523 CTACATCTTC

                                 
      10533 TACCGATACAAGTATACAAAT
          1 TACCGATACAAGTATACAAAT

              *            * *      *
      10554 TATCGATACGTCAA-AACACATAAC
          1 TACCGATA---CAAGTATACA-AAT

                                 
      10578 TACCGATACAAGTATACAAAT
          1 TACCGATACAAGTATACAAAT

                     
      10599 TACCGATAC
          1 TACCGATAC

      10608 GTCAAAACAC


Statistics
Matches: 41,  Mismatches: 8, Indels: 10
        0.69            0.14        0.17

Matches are distributed among these distances:
  21   21  0.51
  22    4  0.10
  23    4  0.10
  24   12  0.29

ACGTcount: A:0.45, C:0.23, G:0.09, T:0.23


Consensus pattern (21 bp):   
TACCGATACAAGTATACAAAT

Found at i:10589 original size:45 final size:45

Alignment explanation


    Indices: 10532--10631  Score: 191
    Period size: 45  Copynumber: 2.2  Consensus size: 45

      10522 CCTACATCTT

                                    *                    
      10532 CTACCGATACAAGTATACAAATTATCGATACGTCAAAACACATAA
          1 CTACCGATACAAGTATACAAATTACCGATACGTCAAAACACATAA

                                                         
      10577 CTACCGATACAAGTATACAAATTACCGATACGTCAAAACACATAA
          1 CTACCGATACAAGTATACAAATTACCGATACGTCAAAACACATAA

                      
      10622 CTACCGATAC
          1 CTACCGATAC

      10632 TTGCAATTCA


Statistics
Matches: 54,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  45   54  1.00

ACGTcount: A:0.45, C:0.25, G:0.09, T:0.21


Consensus pattern (45 bp):   
CTACCGATACAAGTATACAAATTACCGATACGTCAAAACACATAA

Found at i:10631 original size:24 final size:24

Alignment explanation


    Indices: 10557--10631  Score: 86
    Period size: 24  Copynumber: 3.2  Consensus size: 24

      10547 TACAAATTAT

                                    
      10557 CGATACGTCAAAACACATAACTAC
          1 CGATACGTCAAAACACATAACTAC

                        * *      *   
      10581 CGATA---CAAGTATACA-AATTAC
          1 CGATACGTCAA-AACACATAACTAC

                                    
      10602 CGATACGTCAAAACACATAACTAC
          1 CGATACGTCAAAACACATAACTAC

                  
      10626 CGATAC
          1 CGATAC

      10632 TTGCAATTCA


Statistics
Matches: 40,  Mismatches: 6, Indels: 10
        0.71            0.11        0.18

Matches are distributed among these distances:
  21   13  0.32
  22    4  0.10
  23    4  0.10
  24   19  0.47

ACGTcount: A:0.45, C:0.27, G:0.09, T:0.19


Consensus pattern (24 bp):   
CGATACGTCAAAACACATAACTAC

Found at i:12956 original size:29 final size:29

Alignment explanation


    Indices: 12914--12971  Score: 98
    Period size: 29  Copynumber: 2.0  Consensus size: 29

      12904 TTAAATCTAT

                                *   *    
      12914 TTCGAAAGAAACTTAGACCTGATGGGTCA
          1 TTCGAAAGAAACTTAGACCTAATGAGTCA

                                         
      12943 TTCGAAAGAAACTTAGACCTAATGAGTCA
          1 TTCGAAAGAAACTTAGACCTAATGAGTCA

      12972 ATACAAAAGT


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  29   27  1.00

ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24


Consensus pattern (29 bp):   
TTCGAAAGAAACTTAGACCTAATGAGTCA

Found at i:15416 original size:17 final size:16

Alignment explanation


    Indices: 15391--15431  Score: 55
    Period size: 16  Copynumber: 2.6  Consensus size: 16

      15381 ATTAATTAAT

                     **     
      15391 TTTTTAAAATTTAAAA
          1 TTTTTAAAAAATAAAA

                            
      15407 TTTTTAAAAAATAAAA
          1 TTTTTAAAAAATAAAA

              *      
      15423 TTATTAAAA
          1 TTTTTAAAA

      15432 GAGTAATTTT


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  16   22  1.00

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


Consensus pattern (16 bp):   
TTTTTAAAAAATAAAA
Done.