Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002424.1 Kokia drynarioides strain JFW-HI SEQ_114525, 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: 2180
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32


Found at i:196 original size:84 final size:83

Alignment explanation


    Indices: 1--214  Score: 268
    Period size: 84  Copynumber: 2.5  Consensus size: 83

                                                           *            *    
          1 AATCAACACATTATTTGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATTTAAAA
          1 AATCAACACATTATTTGATAAAAATTGTAAT-T--TAATAATAATTTGTATTTAAATATTGAAAA

                                 
         66 TTAATAAATAATATATTGTAA
         63 TTAATAAATAATATATTGTAA

                    *                                                      * 
         87 AATCAACATATTATTTGATAAAAATTGTAATTTAATAATAATTTGTACTTTAAATA-TGAAATTT
          1 AATCAACACATTATTTGATAAAAATTGTAATTTAATAATAATTTGTA-TTTAAATATTGAAA-AT

             *      *  *      * 
        151 TGATAAATGATGTATTGTCA
         64 TAATAAATAATATATTGTAA

               *      *         *          *            
        171 AATTAACACAATATTTGATATAAATTGTAATATAATAATAATTT
          1 AATCAACACATTATTTGATAAAAATTGTAATTTAATAATAATTT

        215 TTTTATTTAA


Statistics
Matches: 113,  Mismatches: 13, Indels: 6
        0.86            0.10        0.05

Matches are distributed among these distances:
  83   18  0.16
  84   64  0.57
  85    1  0.01
  86   30  0.27

ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42


Consensus pattern (83 bp):   
AATCAACACATTATTTGATAAAAATTGTAATTTAATAATAATTTGTATTTAAATATTGAAAATTA
ATAAATAATATATTGTAA

Found at i:254 original size:12 final size:11

Alignment explanation


    Indices: 220--259  Score: 57
    Period size: 11  Copynumber: 3.7  Consensus size: 11

        210 AATTTTTTTA

                       
        220 TTTAAA-TAAT
          1 TTTAAATTAAT

                       
        230 TTTAAATTAAT
          1 TTTAAATTAAT

                        
        241 TTTAAATGTAA-
          1 TTTAAAT-TAAT

                    
        252 TTTAAATT
          1 TTTAAATT

        260 TCAACTTCAA


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

Matches are distributed among these distances:
  10    7  0.25
  11   18  0.64
  12    3  0.11

ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53


Consensus pattern (11 bp):   
TTTAAATTAAT

Found at i:358 original size:12 final size:12

Alignment explanation


    Indices: 341--391  Score: 57
    Period size: 12  Copynumber: 3.9  Consensus size: 12

        331 AAACATGTTC

                        
        341 ATTAATTTTTAA
          1 ATTAATTTTTAA

                            
        353 ATTAATTTCAACTTAA
          1 ATTAATTT----TTAA

                     *  
        369 ATTAATTTTCAA
          1 ATTAATTTTTAA

                       
        381 ATTAATTTTTA
          1 ATTAATTTTTA

        392 CACAAATATT


Statistics
Matches: 33,  Mismatches: 2, Indels: 8
        0.77            0.05        0.19

Matches are distributed among these distances:
  12   21  0.64
  16   12  0.36

ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53


Consensus pattern (12 bp):   
ATTAATTTTTAA

Found at i:387 original size:16 final size:16

Alignment explanation


    Indices: 349--385  Score: 56
    Period size: 17  Copynumber: 2.2  Consensus size: 16

        339 TCATTAATTT

                           *
        349 TTAAATTAATTTCAAC
          1 TTAAATTAATTTCAAA

                             
        365 TTAAATTAATTTTCAAA
          1 TTAAATTAA-TTTCAAA

                
        382 TTAA
          1 TTAA

        386 TTTTTACACA


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  16    9  0.47
  17   10  0.53

ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46


Consensus pattern (16 bp):   
TTAAATTAATTTCAAA

Found at i:398 original size:28 final size:28

Alignment explanation


    Indices: 341--398  Score: 71
    Period size: 28  Copynumber: 2.1  Consensus size: 28

        331 AAACATGTTC

                     *              **  
        341 ATTAATTTTTAAATTAATTTCAACTTAA
          1 ATTAATTTTCAAATTAATTTCAACACAA

                                **      
        369 ATTAATTTTCAAATTAATTTTTACACAA
          1 ATTAATTTTCAAATTAATTTCAACACAA

              
        397 AT
          1 AT

        399 ATTCTTCGTG


Statistics
Matches: 25,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  28   25  1.00

ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48


Consensus pattern (28 bp):   
ATTAATTTTCAAATTAATTTCAACACAA
Done.