Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001838.1 Kokia drynarioides strain JFW-HI SEQ_113586, 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: 7497
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35


Found at i:13 original size:2 final size:2

Alignment explanation


    Indices: 7--55  Score: 62
    Period size: 2  Copynumber: 23.5  Consensus size: 2

          1 CTCCGC

                                                       *  *                 
          7 TA TA TA TA TA TA TA TA TA TA TA TA TGA TA AA AA TCA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA T-A TA TA TA TA

                   
         51 TA TA T
          1 TA TA T

         56 TTGATCTAGT


Statistics
Matches: 43,  Mismatches: 2, Indels: 4
        0.88            0.04        0.08

Matches are distributed among these distances:
   2   39  0.91
   3    4  0.09

ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45


Consensus pattern (2 bp):   
TA

Found at i:1478 original size:30 final size:30

Alignment explanation


    Indices: 1442--1518  Score: 127
    Period size: 30  Copynumber: 2.6  Consensus size: 30

       1432 TACCTCCCCG

                                 *        
       1442 CAGTATTATCCACCTTCACAATCGGAGCCA
          1 CAGTATTATCCACCTTCACAACCGGAGCCA

                     *                   *
       1472 CAGTATTATTCACCTTCACAACCGGAGCCG
          1 CAGTATTATCCACCTTCACAACCGGAGCCA

                             
       1502 CAGTATTATCCACCTTC
          1 CAGTATTATCCACCTTC

       1519 GCAAAACCGT


Statistics
Matches: 43,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  30   43  1.00

ACGTcount: A:0.27, C:0.34, G:0.13, T:0.26


Consensus pattern (30 bp):   
CAGTATTATCCACCTTCACAACCGGAGCCA

Found at i:4541 original size:33 final size:33

Alignment explanation


    Indices: 4504--4575  Score: 135
    Period size: 33  Copynumber: 2.2  Consensus size: 33

       4494 GGTATGTGCA

                                             
       4504 TTGTTGCCAATATAAGAGGATGTGAATTCGAGT
          1 TTGTTGCCAATATAAGAGGATGTGAATTCGAGT

                                             
       4537 TTGTTGCCAATATAAGAGGATGTGAATTCGAGT
          1 TTGTTGCCAATATAAGAGGATGTGAATTCGAGT

            *     
       4570 GTGTTG
          1 TTGTTG

       4576 AAGCATCTTA


Statistics
Matches: 38,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  33   38  1.00

ACGTcount: A:0.28, C:0.08, G:0.29, T:0.35


Consensus pattern (33 bp):   
TTGTTGCCAATATAAGAGGATGTGAATTCGAGT
Done.