Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003520.1 Kokia drynarioides strain JFW-HI SEQ_116362, 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: 8155
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31


Found at i:7442 original size:16 final size:16

Alignment explanation


    Indices: 7421--7475  Score: 56
    Period size: 16  Copynumber: 3.2  Consensus size: 16

       7411 GTGAGCTGTA

                            
       7421 AGCTCAACAAGGTGCG
          1 AGCTCAACAAGGTGCG

                      *    *    
       7437 AGCTCAGCAAAAAGAATGCG
          1 AGCT---CAACAAG-GTGCG

                            
       7457 AGCTCAACAAGGTGCG
          1 AGCTCAACAAGGTGCG

               
       7473 AGC
          1 AGC

       7476 CATCAAAAGT


Statistics
Matches: 31,  Mismatches: 4, Indels: 8
        0.72            0.09        0.19

Matches are distributed among these distances:
  16   11  0.35
  17    6  0.19
  19    6  0.19
  20    8  0.26

ACGTcount: A:0.36, C:0.24, G:0.29, T:0.11


Consensus pattern (16 bp):   
AGCTCAACAAGGTGCG

Found at i:7522 original size:30 final size:30

Alignment explanation


    Indices: 7481--7593  Score: 172
    Period size: 30  Copynumber: 3.8  Consensus size: 30

       7471 CGAGCCATCA

                           *     *       *
       7481 AAAGTGCGAGCCTGTTAAAGATAGTAAGCT
          1 AAAGTGCGAGCCTGTCAAAGACAGTAAGCC

                  *                       
       7511 AAAGTGTGAGCCTGTCAAAGACAGTAAGCC
          1 AAAGTGCGAGCCTGTCAAAGACAGTAAGCC

                  *                       
       7541 AAAGTGTGAGCCTGTCAAAGACAGTAAGCC
          1 AAAGTGCGAGCCTGTCAAAGACAGTAAGCC

                           *       
       7571 AAAGTGCGAGCCTGTTAAAGACA
          1 AAAGTGCGAGCCTGTCAAAGACA

       7594 ACAAGCAAAT


Statistics
Matches: 77,  Mismatches: 6, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  30   77  1.00

ACGTcount: A:0.37, C:0.18, G:0.27, T:0.19


Consensus pattern (30 bp):   
AAAGTGCGAGCCTGTCAAAGACAGTAAGCC

Found at i:7575 original size:60 final size:59

Alignment explanation


    Indices: 7481--7619  Score: 170
    Period size: 60  Copynumber: 2.3  Consensus size: 59

       7471 CGAGCCATCA

                  *        *     *       *      *                **     
       7481 AAAGTGCGAGCCTGTTAAAGATAGTAAGCTAAAGTGTGAGCCTGTCAAAGACAGTAAGCC
          1 AAAGTGTGAGCCTGTCAAAGACAGTAAGCCAAAGTGCGAGCCTGTCAAAGACAACAAG-C

                                                         *             
       7541 AAAGTGTGAGCCTGTCAAAGACAGTAAGCCAAAGTGCGAGCCTGTTAAAGACAACAAGC
          1 AAAGTGTGAGCCTGTCAAAGACAGTAAGCCAAAGTGCGAGCCTGTCAAAGACAACAAGC

               * *    *         
       7600 AAATTATGAGTCTGTCAAAG
          1 AAAGTGTGAGCCTGTCAAAG

       7620 TGTGAGCCTG


Statistics
Matches: 68,  Mismatches: 11, Indels: 1
        0.85            0.14        0.01

Matches are distributed among these distances:
  59   18  0.26
  60   50  0.74

ACGTcount: A:0.38, C:0.17, G:0.25, T:0.19


Consensus pattern (59 bp):   
AAAGTGTGAGCCTGTCAAAGACAGTAAGCCAAAGTGCGAGCCTGTCAAAGACAACAAGC
Done.