Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004528.1 Kokia drynarioides strain JFW-HI SEQ_117977, 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: 28036
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32


Found at i:11384 original size:13 final size:13

Alignment explanation


    Indices: 11363--11395  Score: 57
    Period size: 13  Copynumber: 2.5  Consensus size: 13

      11353 AATATAAAAC

                *        
      11363 AAAAGTAATATTA
          1 AAAACTAATATTA

                         
      11376 AAAACTAATATTA
          1 AAAACTAATATTA

                   
      11389 AAAACTA
          1 AAAACTA

      11396 TTAACAATAT


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  13   19  1.00

ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27


Consensus pattern (13 bp):   
AAAACTAATATTA

Found at i:11959 original size:16 final size:18

Alignment explanation


    Indices: 11938--11984  Score: 64
    Period size: 16  Copynumber: 2.7  Consensus size: 18

      11928 ACTTAACATG

                              
      11938 AAATAATTTAAAT-T-CA
          1 AAATAATTTAAATCTACA

                               
      11954 AAATAATTTAAATCTAACA
          1 AAATAATTTAAATCT-ACA

                         
      11973 AAAT-ATTTAAAT
          1 AAATAATTTAAAT

      11985 GTAAATTGAA


Statistics
Matches: 28,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
  16   13  0.46
  17    1  0.04
  18    8  0.29
  19    6  0.21

ACGTcount: A:0.57, C:0.06, G:0.00, T:0.36


Consensus pattern (18 bp):   
AAATAATTTAAATCTACA

Found at i:19583 original size:15 final size:15

Alignment explanation


    Indices: 19560--19601  Score: 52
    Period size: 15  Copynumber: 2.9  Consensus size: 15

      19550 GTAACACGTG

                *          
      19560 TATAAATAAATAATT
          1 TATATATAAATAATT

                            
      19575 TATATATAAATTAATT
          1 TATATATAAA-TAATT

                         
      19591 TA-ATA-AAATAA
          1 TATATATAAATAA

      19602 AATATCTAAA


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

Matches are distributed among these distances:
  13    3  0.12
  14    3  0.12
  15   12  0.48
  16    7  0.28

ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40


Consensus pattern (15 bp):   
TATATATAAATAATT

Found at i:19628 original size:17 final size:17

Alignment explanation


    Indices: 19582--19628  Score: 51
    Period size: 17  Copynumber: 2.7  Consensus size: 17

      19572 ATTTATATAT

                             * 
      19582 AAATTAATTTAATAAAATA
          1 AAATT-ATTTAA-AAAAAA

                   *         
      19601 AAA-TATCTAAAAAAAA
          1 AAATTATTTAAAAAAAA

                        
      19617 AAATTATTTAAA
          1 AAATTATTTAAA

      19629 TTATTTTAAA


Statistics
Matches: 24,  Mismatches: 3, Indels: 4
        0.77            0.10        0.13

Matches are distributed among these distances:
  16    8  0.33
  17   12  0.50
  18    1  0.04
  19    3  0.12

ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32


Consensus pattern (17 bp):   
AAATTATTTAAAAAAAA

Found at i:22067 original size:20 final size:20

Alignment explanation


    Indices: 22042--22080  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      22032 AGAGTTTAGA

                                
      22042 GTTCAAAGTTCGAGATTCAT
          1 GTTCAAAGTTCGAGATTCAT

                  *       *    
      22062 GTTCAAGGTTCGAGGTTCA
          1 GTTCAAAGTTCGAGATTCA

      22081 AAATAAAAAA


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

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33


Consensus pattern (20 bp):   
GTTCAAAGTTCGAGATTCAT

Found at i:26904 original size:20 final size:20

Alignment explanation


    Indices: 26870--26913  Score: 56
    Period size: 20  Copynumber: 2.2  Consensus size: 20

      26860 CCTTCTTTCA

                                 
      26870 TTTTTTTTAATTTCTGA-TTG
          1 TTTTTTTTAATTTCT-ATTTG

                                 
      26890 TTTTGTTTTAA-TTCTATTTG
          1 TTTT-TTTTAATTTCTATTTG

                
      26910 TTTT
          1 TTTT

      26914 CATCGGAGAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
  19    1  0.05
  20   15  0.68
  21    6  0.27

ACGTcount: A:0.14, C:0.05, G:0.09, T:0.73


Consensus pattern (20 bp):   
TTTTTTTTAATTTCTATTTG
Done.