Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010766.1 Kokia drynarioides strain JFW-HI SEQ_125727, 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: 19055
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Found at i:12369 original size:36 final size:37

Alignment explanation


    Indices: 12329--12399  Score: 101
    Period size: 38  Copynumber: 1.9  Consensus size: 37

      12319 ATACATTTCT

                                                  
      12329 CTGAAGG-GTAAAAA-ACCATACCTTTGACATTACTAA
          1 CTGAAGGAG-AAAAATACCATACCTTTGACATTACTAA

                            *                  
      12365 CTGAAGGAAGAAAAATCCCATACCTTTGACATTAC
          1 CTGAAGG-AGAAAAATACCATACCTTTGACATTAC

      12400 ACCCTCTTAG


Statistics
Matches: 31,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
  36    7  0.23
  37    5  0.16
  38   19  0.61

ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24


Consensus pattern (37 bp):   
CTGAAGGAGAAAAATACCATACCTTTGACATTACTAA

Found at i:18887 original size:4 final size:4

Alignment explanation


    Indices: 18878--18970  Score: 66
    Period size: 4  Copynumber: 23.0  Consensus size: 4

      18868 AAATAAACGG

                                           *        *     *               
      18878 GAAA GAAA GAAA GAAAA GAAA GAAA AAAA GGAAG GAGAG GAAA GAAA G-AA
          1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA -GAAA GA-AA GAAA GAAA GAAA

               *     *                   *              *          
      18928 GAAG GAGAG GAAA GAAA G-AA GAAT GAAA G-AA GAAT GAAA GAAA
          1 GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA

      18971 AGTAATGCGT


Statistics
Matches: 72,  Mismatches: 10, Indels: 14
        0.75            0.10        0.15

Matches are distributed among these distances:
   3    9  0.12
   4   49  0.68
   5   14  0.19

ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02


Consensus pattern (4 bp):   
GAAA

Found at i:18933 original size:20 final size:20

Alignment explanation


    Indices: 18908--18950  Score: 86
    Period size: 20  Copynumber: 2.1  Consensus size: 20

      18898 AGAAAAAAAG

                                
      18908 GAAGGAGAGGAAAGAAAGAA
          1 GAAGGAGAGGAAAGAAAGAA

                                
      18928 GAAGGAGAGGAAAGAAAGAA
          1 GAAGGAGAGGAAAGAAAGAA

               
      18948 GAA
          1 GAA

      18951 TGAAAGAAGA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   23  1.00

ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00


Consensus pattern (20 bp):   
GAAGGAGAGGAAAGAAAGAA

Found at i:18957 original size:11 final size:11

Alignment explanation


    Indices: 18941--18969  Score: 58
    Period size: 11  Copynumber: 2.6  Consensus size: 11

      18931 GGAGAGGAAA

                       
      18941 GAAAGAAGAAT
          1 GAAAGAAGAAT

                       
      18952 GAAAGAAGAAT
          1 GAAAGAAGAAT

                   
      18963 GAAAGAA
          1 GAAAGAA

      18970 AAGTAATGCG


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   18  1.00

ACGTcount: A:0.66, C:0.00, G:0.28, T:0.07


Consensus pattern (11 bp):   
GAAAGAAGAAT
Done.