Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006210.1 Kokia drynarioides strain JFW-HI SEQ_120781, 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: 67540
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32

Warning! 8 characters in sequence are not A, C, G, or T


Found at i:5768 original size:21 final size:21

Alignment explanation


    Indices: 5742--5792  Score: 66
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       5732 TTTTTAGTAC

                        * *    * 
       5742 CGGTAGAAGCATGATTTGTTT
          1 CGGTAGAAGCATCACTTGTAT

                      *          
       5763 CGGTAGAAGCTTCACTTGTAT
          1 CGGTAGAAGCATCACTTGTAT

                     
       5784 CGGTAGAAG
          1 CGGTAGAAG

       5793 TCTGCACTAT


Statistics
Matches: 26,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  21   26  1.00

ACGTcount: A:0.25, C:0.14, G:0.29, T:0.31


Consensus pattern (21 bp):   
CGGTAGAAGCATCACTTGTAT

Found at i:20646 original size:17 final size:17

Alignment explanation


    Indices: 20606--20672  Score: 62
    Period size: 17  Copynumber: 3.9  Consensus size: 17

      20596 TATATATATG

                     *       
      20606 AAAATGCAATGACAATA
          1 AAAATGCAACGACAATA

            * *     *        
      20623 TAGATGCAGCGACAATA
          1 AAAATGCAACGACAATA

                     *    *  
      20640 AAAATGCAATGACATTA
          1 AAAATGCAACGACAATA

             *       *      
      20657 ACAATGCAATGACAAT
          1 AAAATGCAACGACAAT

      20673 TATACTACAA


Statistics
Matches: 39,  Mismatches: 11, Indels: 0
        0.78            0.22        0.00

Matches are distributed among these distances:
  17   39  1.00

ACGTcount: A:0.51, C:0.15, G:0.15, T:0.19


Consensus pattern (17 bp):   
AAAATGCAACGACAATA

Found at i:20671 original size:34 final size:34

Alignment explanation


    Indices: 20606--20672  Score: 82
    Period size: 34  Copynumber: 2.0  Consensus size: 34

      20596 TATATATATG

                               *     *        
      20606 AAAATGCAATGACAATATAGATGCAGCGACAATA
          1 AAAATGCAATGACAATATAAATGCAACGACAATA

                          *            *      
      20640 AAAATGCAATGACATTA-ACAATGCAATGACAAT
          1 AAAATGCAATGACAATATA-AATGCAACGACAAT

      20673 TATACTACAA


Statistics
Matches: 28,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  33    1  0.04
  34   27  0.96

ACGTcount: A:0.51, C:0.15, G:0.15, T:0.19


Consensus pattern (34 bp):   
AAAATGCAATGACAATATAAATGCAACGACAATA

Found at i:28466 original size:30 final size:31

Alignment explanation


    Indices: 28430--28496  Score: 82
    Period size: 31  Copynumber: 2.2  Consensus size: 31

      28420 ACACGGGCAA

                    *               *     *
      28430 ACACACGGGCGTGTGG-CCAAGTCCGTATAT
          1 ACACACGGACGTGTGGTCCAAGTCAGTATAG

                      *            *       
      28460 ACACACGGACTTGTGGTCCAAGTTAGTATAG
          1 ACACACGGACGTGTGGTCCAAGTCAGTATAG

                  
      28491 ACACAC
          1 ACACAC

      28497 CGCCTGACAT


Statistics
Matches: 31,  Mismatches: 5, Indels: 1
        0.84            0.14        0.03

Matches are distributed among these distances:
  30   14  0.45
  31   17  0.55

ACGTcount: A:0.28, C:0.25, G:0.25, T:0.21


Consensus pattern (31 bp):   
ACACACGGACGTGTGGTCCAAGTCAGTATAG

Found at i:44341 original size:17 final size:17

Alignment explanation


    Indices: 44302--44349  Score: 60
    Period size: 17  Copynumber: 2.8  Consensus size: 17

      44292 TGACATATGG

                            *
      44302 AAATGCAATGACAATAT
          1 AAATGCAATGACAATAA

             *     *   *     
      44319 AGATGCAGTGATAATAA
          1 AAATGCAATGACAATAA

                          
      44336 AAATGCAATGACAA
          1 AAATGCAATGACAA

      44350 AGGAAATGTG


Statistics
Matches: 24,  Mismatches: 7, Indels: 0
        0.77            0.23        0.00

Matches are distributed among these distances:
  17   24  1.00

ACGTcount: A:0.52, C:0.10, G:0.17, T:0.21


Consensus pattern (17 bp):   
AAATGCAATGACAATAA

Found at i:44426 original size:12 final size:13

Alignment explanation


    Indices: 44394--44426  Score: 50
    Period size: 12  Copynumber: 2.6  Consensus size: 13

      44384 GATATGCATG

                         
      44394 AAAACTAAAACTA
          1 AAAACTAAAACTA

             *           
      44407 AGAACTAAAA-TA
          1 AAAACTAAAACTA

                    
      44419 AAAACTAA
          1 AAAACTAA

      44427 CTCAATTTGC


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

Matches are distributed among these distances:
  12    9  0.50
  13    9  0.50

ACGTcount: A:0.70, C:0.12, G:0.03, T:0.15


Consensus pattern (13 bp):   
AAAACTAAAACTA

Found at i:56761 original size:35 final size:35

Alignment explanation


    Indices: 56715--56785  Score: 133
    Period size: 35  Copynumber: 2.0  Consensus size: 35

      56705 AAGGCACCGG

                                         *     
      56715 GAAATGGTCCTTCTTTATGGTCGCATTTAGTCGAT
          1 GAAATGGTCCTTCTTTATGGTCGCATTTAATCGAT

                                               
      56750 GAAATGGTCCTTCTTTATGGTCGCATTTAATCGAT
          1 GAAATGGTCCTTCTTTATGGTCGCATTTAATCGAT

             
      56785 G
          1 G

      56786 GTAATCCATG


Statistics
Matches: 35,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  35   35  1.00

ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39


Consensus pattern (35 bp):   
GAAATGGTCCTTCTTTATGGTCGCATTTAATCGAT
Done.