Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000221.1 Kokia drynarioides strain JFW-HI SEQ_110931, 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, 911

Length: 1519
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29


Found at i:1345 original size:29 final size:29

Alignment explanation


    Indices: 1313--1470  Score: 226
    Period size: 29  Copynumber: 5.4  Consensus size: 29

       1303 CGGATTCCCA

                                         
       1313 GGGGTAAAAATGGGATTTTTGGAAGTTCG
          1 GGGGTAAAAATGGGATTTTTGGAAGTTCG

                       * *                
       1342 GGGGTAAAAATAGAATTTTTGGAAGTTTCG
          1 GGGGTAAAAATGGGATTTTTGGAAG-TTCG

               *                         
       1372 GGGTTAAAAATGGGATTTTTGGAAGTTCG
          1 GGGGTAAAAATGGGATTTTTGGAAGTTCG

            *           *               * 
       1401 AGGGTAAAAATGAGATTTTTGGAAGTTTTG
          1 GGGGTAAAAATGGGATTTTTGGAAG-TTCG

               *                       * 
       1431 GGGTTAAAAATGGGATTTTTGGAAGTTTG
          1 GGGGTAAAAATGGGATTTTTGGAAGTTCG

                       
       1460 GGGGTAAAAAT
          1 GGGGTAAAAAT

       1471 ATAATTTTTG


Statistics
Matches: 114,  Mismatches: 13, Indels: 4
        0.87            0.10        0.03

Matches are distributed among these distances:
  29   63  0.55
  30   51  0.45

ACGTcount: A:0.31, C:0.02, G:0.34, T:0.34


Consensus pattern (29 bp):   
GGGGTAAAAATGGGATTTTTGGAAGTTCG

Found at i:1374 original size:30 final size:30

Alignment explanation


    Indices: 1313--1488  Score: 216
    Period size: 29  Copynumber: 5.9  Consensus size: 30

       1303 CGGATTCCCA

                         *                
       1313 GGGGTAAAAATGGGATTTTTGGAAG-TTCG
          1 GGGGTAAAAATGGAATTTTTGGAAGTTTCG

                       *                  
       1342 GGGGTAAAAATAGAATTTTTGGAAGTTTCG
          1 GGGGTAAAAATGGAATTTTTGGAAGTTTCG

               *         *                
       1372 GGGTTAAAAATGGGATTTTTGGAAG-TTCG
          1 GGGGTAAAAATGGAATTTTTGGAAGTTTCG

            *                            * 
       1401 AGGGTAAAAAT-GAGATTTTTGGAAGTTTTG
          1 GGGGTAAAAATGGA-ATTTTTGGAAGTTTCG

               *         *                
       1431 GGGTTAAAAATGGGATTTTTGGAAGTTT-G
          1 GGGGTAAAAATGGAATTTTTGGAAGTTTCG

                       **                
       1460 GGGGTAAAAATATAATTTTTGGATAGTTT
          1 GGGGTAAAAATGGAATTTTTGGA-AGTTT

       1489 AGGGACCTCC


Statistics
Matches: 126,  Mismatches: 16, Indels: 9
        0.83            0.11        0.06

Matches are distributed among these distances:
  28    1  0.01
  29   67  0.53
  30   57  0.45
  31    1  0.01

ACGTcount: A:0.31, C:0.02, G:0.32, T:0.36


Consensus pattern (30 bp):   
GGGGTAAAAATGGAATTTTTGGAAGTTTCG

Found at i:1381 original size:59 final size:59

Alignment explanation


    Indices: 1313--1488  Score: 284
    Period size: 59  Copynumber: 3.0  Consensus size: 59

       1303 CGGATTCCCA

                                                                       
       1313 GGGG-TAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATAGAATTTTTGGAAGTTTC
          1 GGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATAGAATTTTTGGAAGTTTC

                                          *                            *
       1371 GGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAAT-GAGATTTTTGGAAGTTTT
          1 GGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATAGA-ATTTTTGGAAGTTTC

                                        *             *                
       1430 GGGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAATATAATTTTTGGATAGTTT
          1 GGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATAGAATTTTTGGA-AGTTT

       1489 AGGGACCTCC


Statistics
Matches: 109,  Mismatches: 5, Indels: 6
        0.91            0.04        0.05

Matches are distributed among these distances:
  58    6  0.06
  59   97  0.89
  60    6  0.06

ACGTcount: A:0.31, C:0.02, G:0.32, T:0.36


Consensus pattern (59 bp):   
GGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATAGAATTTTTGGAAGTTTC

Done.