Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001231.1 Kokia drynarioides strain JFW-HI SEQ_112592, 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: 21406
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33


Found at i:2591 original size:25 final size:26

Alignment explanation


    Indices: 2563--2617  Score: 67
    Period size: 26  Copynumber: 2.2  Consensus size: 26

       2553 CGAACTAGAT

                         *            
       2563 AGTTTACC-AAAAGATAAAGAAAAAG
          1 AGTTTACCTAAAAAATAAAGAAAAAG

                 *              **    
       2588 AGTTTCCCTAAAAAATAAAGCGAAAG
          1 AGTTTACCTAAAAAATAAAGAAAAAG

                
       2614 AGTT
          1 AGTT

       2618 AAAAGACTTC


Statistics
Matches: 25,  Mismatches: 4, Indels: 1
        0.83            0.13        0.03

Matches are distributed among these distances:
  25    7  0.28
  26   18  0.72

ACGTcount: A:0.53, C:0.11, G:0.16, T:0.20


Consensus pattern (26 bp):   
AGTTTACCTAAAAAATAAAGAAAAAG

Found at i:3185 original size:25 final size:24

Alignment explanation


    Indices: 3154--3202  Score: 80
    Period size: 25  Copynumber: 2.0  Consensus size: 24

       3144 AATTTAAAAT

                                     
       3154 TTATATTAATATTAAATAAATATAA
          1 TTATATTAATATTAAA-AAATATAA

                             *      
       3179 TTATATTAATATTAAAATATATAA
          1 TTATATTAATATTAAAAAATATAA

       3203 AAATCCTCCA


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  24    7  0.30
  25   16  0.70

ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45


Consensus pattern (24 bp):   
TTATATTAATATTAAAAAATATAA

Found at i:11685 original size:16 final size:16

Alignment explanation


    Indices: 11661--11691  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

      11651 TATATTTTAA

                *           
      11661 TTTTTAATTTGTTTTG
          1 TTTTGAATTTGTTTTG

                           
      11677 TTTTGAATTTGTTTT
          1 TTTTGAATTTGTTTT

      11692 AATTCTAATT


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.13, C:0.00, G:0.13, T:0.74


Consensus pattern (16 bp):   
TTTTGAATTTGTTTTG

Found at i:11701 original size:16 final size:16

Alignment explanation


    Indices: 11655--11701  Score: 51
    Period size: 16  Copynumber: 2.9  Consensus size: 16

      11645 TATGAATATA

                             
      11655 TTTTAATTTTTAATTTG
          1 TTTTAA-TTTTAATTTG

                 *           
      11672 TTTT-GTTTTGAATTTG
          1 TTTTAATTTT-AATTTG

                    *     
      11688 TTTTAATTCTAATT
          1 TTTTAATTTTAATT

      11702 GATGGAATAT


Statistics
Matches: 25,  Mismatches: 3, Indels: 5
        0.76            0.09        0.15

Matches are distributed among these distances:
  15    4  0.16
  16   14  0.56
  17    7  0.28

ACGTcount: A:0.21, C:0.02, G:0.09, T:0.68


Consensus pattern (16 bp):   
TTTTAATTTTAATTTG

Found at i:20778 original size:22 final size:24

Alignment explanation


    Indices: 20750--20803  Score: 76
    Period size: 24  Copynumber: 2.3  Consensus size: 24

      20740 TCAAATTAAA

                                    
      20750 CATCGTATCT-AA-AAAAACCATC
          1 CATCGTATCTAAATAAAAACCATC

                               *    
      20772 CATCGTATCTAAATAAAAATCATC
          1 CATCGTATCTAAATAAAAACCATC

               *    
      20796 CATTGTAT
          1 CATCGTAT

      20804 GTTAACAAAA


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  22   10  0.36
  23    2  0.07
  24   16  0.57

ACGTcount: A:0.43, C:0.22, G:0.06, T:0.30


Consensus pattern (24 bp):   
CATCGTATCTAAATAAAAACCATC

Found at i:20813 original size:24 final size:24

Alignment explanation


    Indices: 20750--20813  Score: 69
    Period size: 24  Copynumber: 2.8  Consensus size: 24

      20740 TCAAATTAAA

                                    
      20750 CATCGTATCT-AA-AAAAACCATC
          1 CATCGTATCTAAACAAAAACCATC

                         *     *    
      20772 CATCGTATCTAAATAAAAATCATC
          1 CATCGTATCTAAACAAAAACCATC

               *    * *       
      20796 CATTGTATGTTAACAAAA
          1 CATCGTATCTAAACAAAA

      20814 CTATCTCCAT


Statistics
Matches: 35,  Mismatches: 5, Indels: 2
        0.83            0.12        0.05

Matches are distributed among these distances:
  22   10  0.29
  23    2  0.06
  24   23  0.66

ACGTcount: A:0.45, C:0.20, G:0.06, T:0.28


Consensus pattern (24 bp):   
CATCGTATCTAAACAAAAACCATC
Done.