Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009397.1 Kokia drynarioides strain JFW-HI SEQ_124104, 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: 4847
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34


Found at i:1845 original size:189 final size:188

Alignment explanation


    Indices: 1521--2008  Score: 825
    Period size: 189  Copynumber: 2.6  Consensus size: 188

       1511 TACAACATGA

                          *        *            *     *     *                
       1521 TTTTTCTTTTTTGGCCACCAGTTAACTAACATAAAAATGAAAGTACTAAAAAATCCAAGATAGTT
          1 TTTTTCTTTTTTGGTCACCAGTTGACTAACATAAAAGTGAAAATACT-CAAAATCCAAGATAGTT

                  *                                                          
       1586 GGGTAATTAAAAAATAGATAAATTAGTCATTATATGTTAGATCAATCTCTCAACTATTAGTAAAT
         65 GGGTAACTAAAAAATAGATAAATTAGTCATTATATGTTAGATCAATCTCTCAACTATTAGTAAAT

                                                                        
       1651 TTATTTTTTGGTCACTAAATTATAAAAAGTTACAAAATAATTAT-TCAACTATTCAATTC
        130 TTATTTTTTGGTCACTAAATTATAAAAAGTTACAAAATAATTATCT-AACTATTCAATTC

                                                                             
       1710 TTTTTCTTTTTTGGTCACCAGTTGACTAACATAAAAGTGAAAATACTCAGAAATCCAAGATAGTT
          1 TTTTTCTTTTTTGGTCACCAGTTGACTAACATAAAAGTGAAAATACTCA-AAATCCAAGATAGTT

                                                                           * 
       1775 GGGTAACTAAAAAATAGATAAATTAGTCATTATATGTTAGATCAATCTCTCAACTATTAGTAAGT
         65 GGGTAACTAAAAAATAGATAAATTAGTCATTATATGTTAGATCAATCTCTCAACTATTAGTAAAT

                                                  *                    
       1840 TTATTTTTTGGTCACTAAATTATAAAAAGTTACAAAATGATTATCTAACTATTCAATTC
        130 TTATTTTTTGGTCACTAAATTATAAAAAGTTACAAAATAATTATCTAACTATTCAATTC

                                                                          *  
       1899 TTTTTCTTTTTTGGTCACCAGTTGACTAACATAAAAGTGAAAATACTCAAGAATCCAAGATAATT
          1 TTTTTCTTTTTTGGTCACCAGTTGACTAACATAAAAGTGAAAATACTCAA-AATCCAAGATAGTT

                              *        *   *             
       1964 GGGTAACTAAAAAATAGACAAATTAGTTATTGTATGTTAGATCAA
         65 GGGTAACTAAAAAATAGATAAATTAGTCATTATATGTTAGATCAA

       2009 AGAGTAAATT


Statistics
Matches: 284,  Mismatches: 12, Indels: 6
        0.94            0.04        0.02

Matches are distributed among these distances:
 188    2  0.01
 189  281  0.99
 190    1  0.00

ACGTcount: A:0.40, C:0.12, G:0.11, T:0.36


Consensus pattern (188 bp):   
TTTTTCTTTTTTGGTCACCAGTTGACTAACATAAAAGTGAAAATACTCAAAATCCAAGATAGTTG
GGTAACTAAAAAATAGATAAATTAGTCATTATATGTTAGATCAATCTCTCAACTATTAGTAAATT
TATTTTTTGGTCACTAAATTATAAAAAGTTACAAAATAATTATCTAACTATTCAATTC

Found at i:4170 original size:29 final size:28

Alignment explanation


    Indices: 4094--4382  Score: 265
    Period size: 29  Copynumber: 9.9  Consensus size: 28

       4084 TGATTCTTGA

                *             *     *     
       4094 GGGTGAAATGGTAATTTTGGGAAAATTCGG
          1 GGGTAAAATGG-AATTTTTGG-AAGTTCGG

              *                         *
       4124 GGTTAAAAATGGAATTTTTGGAAGTTCGA
          1 GGGT-AAAATGGAATTTTTGGAAGTTCGG

              *                      ** 
       4153 GGCTAAAATGGAATTTTTGGAAGTTTTG
          1 GGGTAAAATGGAATTTTTGGAAGTTCGG

                         *     *           
       4181 GGGTCAAAAATGGGATTTTAGGAAGTTCGAG
          1 GGGT--AAAATGGAATTTTTGGAAGTTCG-G

                               *       * 
       4212 GGGTAAAAATGG-ATTTTTTGAAGTTCAG
          1 GGGT-AAAATGGAATTTTTGGAAGTTCGG

                          *        *  ** 
       4240 GGGTAAAAATGGAAATTTTGGAAATTTTG
          1 GGGT-AAAATGGAATTTTTGGAAGTTCGG

                         *                
       4269 GGGTCAAAAATGGGATTTTTGGAAGTTCGG
          1 GGGT--AAAATGGAATTTTTGGAAGTTCGG

                                     ** 
       4299 GGGTAAAATGGAATTTTTGGAAGTTTTG
          1 GGGTAAAATGGAATTTTTGGAAGTTCGG

                        *       *        
       4327 GGGTCAAAATGGGATTTTTGAAAGTTCGG
          1 GGGT-AAAATGGAATTTTTGGAAGTTCGG

                                       
       4356 GGGTAAAATTGGAATTTTTGGACAGTT
          1 GGGTAAAA-TGGAATTTTTGGA-AGTT

       4383 TAGGGACCTT


Statistics
Matches: 214,  Mismatches: 36, Indels: 18
        0.80            0.13        0.07

Matches are distributed among these distances:
  28   66  0.31
  29   71  0.33
  30   66  0.31
  31   11  0.05

ACGTcount: A:0.31, C:0.04, G:0.32, T:0.34


Consensus pattern (28 bp):   
GGGTAAAATGGAATTTTTGGAAGTTCGG

Found at i:4219 original size:88 final size:88

Alignment explanation


    Indices: 4119--4323  Score: 310
    Period size: 88  Copynumber: 2.4  Consensus size: 88

       4109 TTTGGGAAAA

                   *                                         *        *      
       4119 TTCGGGGTTAAAAATGGAATTTTTGGAAGTTC-GAGGCT-AAAATGGAATTTTTGGAAGTTTTGG
          1 TTCGGGGGTAAAAATGGAATTTTTGGAAGTTCAG-GGCTAAAAATGGAAATTTTGGAAATTTTGG

                                    
       4182 GGTCAAAAATGGGATTTTAGGAAG
         65 GGTCAAAAATGGGATTTTAGGAAG

                                     *           *                           
       4206 TTCGAGGGGTAAAAATGG-ATTTTTTGAAGTTCAGGGGTAAAAATGGAAATTTTGGAAATTTTGG
          1 TTCG-GGGGTAAAAATGGAATTTTTGGAAGTTCAGGGCTAAAAATGGAAATTTTGGAAATTTTGG

                              *     
       4270 GGTCAAAAATGGGATTTTTGGAAG
         65 GGTCAAAAATGGGATTTTAGGAAG

                                           
       4294 TTCGGGGGT-AAAATGGAATTTTTGGAAGTT
          1 TTCGGGGGTAAAAATGGAATTTTTGGAAGTT

       4324 TTGGGGTCAA


Statistics
Matches: 107,  Mismatches: 7, Indels: 8
        0.88            0.06        0.07

Matches are distributed among these distances:
  86    7  0.07
  87   37  0.35
  88   63  0.59

ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34


Consensus pattern (88 bp):   
TTCGGGGGTAAAAATGGAATTTTTGGAAGTTCAGGGCTAAAAATGGAAATTTTGGAAATTTTGGG
GTCAAAAATGGGATTTTAGGAAG
Done.