Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012886.1 Kokia drynarioides strain JFW-HI SEQ_127900, 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: 10621
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31


Found at i:2529 original size:52 final size:52

Alignment explanation


    Indices: 2451--2554  Score: 208
    Period size: 52  Copynumber: 2.0  Consensus size: 52

       2441 TTTATTAAAT

                                                                
       2451 ATTTACTTAGTTTTAACAATCAATTTGAGTAAAAAGGTGATAAATTATATAG
          1 ATTTACTTAGTTTTAACAATCAATTTGAGTAAAAAGGTGATAAATTATATAG

                                                                
       2503 ATTTACTTAGTTTTAACAATCAATTTGAGTAAAAAGGTGATAAATTATATAG
          1 ATTTACTTAGTTTTAACAATCAATTTGAGTAAAAAGGTGATAAATTATATAG

       2555 GAAAAACCTA


Statistics
Matches: 52,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  52   52  1.00

ACGTcount: A:0.42, C:0.06, G:0.13, T:0.38


Consensus pattern (52 bp):   
ATTTACTTAGTTTTAACAATCAATTTGAGTAAAAAGGTGATAAATTATATAG

Found at i:4447 original size:56 final size:56

Alignment explanation


    Indices: 4380--4692  Score: 394
    Period size: 56  Copynumber: 5.5  Consensus size: 56

       4370 AAGAGGTCCA

                            *            *    *                    *
       4380 ATGATTTTGTGTCATCATGAGTATTAAATAAATCTTATTACGGATTAAAAGGTTCA
          1 ATGATTTTGTGTCATCGTGAGTATTAAATGAATCCTATTACGGATTAAAAGGTTCG

                  *                 *                                
       4436 ATGATTATGTGTCATCGTGAGTATCAAATGAATCCTATTACGGATTAAAA-GTTCTG
          1 ATGATTTTGTGTCATCGTGAGTATTAAATGAATCCTATTACGGATTAAAAGGTTC-G

                                                     *              
       4492 ATGATTTTGTGTCATCGTGAGTATTAAATGAATCCTATTACTGATTAAAAGGTTCG
          1 ATGATTTTGTGTCATCGTGAGTATTAAATGAATCCTATTACGGATTAAAAGGTTCG

                                                    *            *  
       4548 ATGATTTTGTGTCATCGTGAGTATTAAATGAATCCTATTATGGATTAAAAGGTCCG
          1 ATGATTTTGTGTCATCGTGAGTATTAAATGAATCCTATTACGGATTAAAAGGTTCG

              *                    *              *   *    *          *  
       4604 ATTATTTTGTGTCATCTTGTGTATTAATTGAAATGAATTCTACTACGAATTAAAAGGTCCG
          1 ATGATTTTGTGTCATC--GTG-AGT-ATT-AAATGAATCCTATTACGGATTAAAAGGTTCG

               **         *       *     
       4665 ATGGCTTTGTGTCACCGTGAGTGTTAAA
          1 ATGATTTTGTGTCATCGTGAGTATTAAA

       4693 ATATATGAAT


Statistics
Matches: 226,  Mismatches: 24, Indels: 14
        0.86            0.09        0.05

Matches are distributed among these distances:
  55    4  0.02
  56  164  0.73
  57    6  0.03
  58    5  0.02
  59    5  0.02
  60    3  0.01
  61   39  0.17

ACGTcount: A:0.31, C:0.11, G:0.19, T:0.38


Consensus pattern (56 bp):   
ATGATTTTGTGTCATCGTGAGTATTAAATGAATCCTATTACGGATTAAAAGGTTCG

Done.