Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001919.1 Kokia drynarioides strain JFW-HI SEQ_113718, 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: 27839
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Found at i:1381 original size:41 final size:40

Alignment explanation


    Indices: 1311--1438  Score: 132
    Period size: 40  Copynumber: 3.1  Consensus size: 40

       1301 GGGAAAATAT

                            *    *   *               *
       1311 CGCTAAAGGTCA-AAGGATTAACGGTGCTTATGGAAAAGCGT
          1 CGCTAAAGGTCAGAA-CATTAGCGGCGCTTAT-GAAAAGCGC

                             *               *      
       1352 CGCTAAAGGTCAGAACACTAGCGGCGCTTATGAGAAGCGC
          1 CGCTAAAGGTCAGAACATTAGCGGCGCTTATGAAAAGCGC

              *           *       **                 
       1392 CGTTAAAGGTCAGAGCATTAGCAACGCTTATGAGAAAGCGC
          1 CGCTAAAGGTCAGAACATTAGCGGCGCTTATGA-AAAGCGC

                  
       1433 CGCTAA
          1 CGCTAA

       1439 TTTATTTACA


Statistics
Matches: 72,  Mismatches: 13, Indels: 4
        0.81            0.15        0.04

Matches are distributed among these distances:
  40   35  0.49
  41   35  0.49
  42    2  0.03

ACGTcount: A:0.33, C:0.20, G:0.28, T:0.19


Consensus pattern (40 bp):   
CGCTAAAGGTCAGAACATTAGCGGCGCTTATGAAAAGCGC

Found at i:16468 original size:5 final size:5

Alignment explanation


    Indices: 16458--16487  Score: 60
    Period size: 5  Copynumber: 6.0  Consensus size: 5

      16448 GAAAATGAGA

                                               
      16458 AAGAG AAGAG AAGAG AAGAG AAGAG AAGAG
          1 AAGAG AAGAG AAGAG AAGAG AAGAG AAGAG

      16488 CGAAAGCTTA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   25  1.00

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


Consensus pattern (5 bp):   
AAGAG

Found at i:18497 original size:2 final size:2

Alignment explanation


    Indices: 18490--18517  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      18480 TTTCTTTTGA

                                                     
      18490 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      18518 TGGTAATAGG


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:22870 original size:22 final size:22

Alignment explanation


    Indices: 22844--22888  Score: 63
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      22834 AAACATTATA

                     *            
      22844 TTTGTAACTGTCCTCATAATGT
          1 TTTGTAACTCTCCTCATAATGT

                        *    *    
      22866 TTTGTAACTCTCTTCATTATGT
          1 TTTGTAACTCTCCTCATAATGT

             
      22888 T
          1 T

      22889 AGTTTTAAAT


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  22   20  1.00

ACGTcount: A:0.20, C:0.18, G:0.11, T:0.51


Consensus pattern (22 bp):   
TTTGTAACTCTCCTCATAATGT

Found at i:23284 original size:11 final size:11

Alignment explanation


    Indices: 23268--23292  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

      23258 TAAATTTGTT

                       
      23268 ATTAAATTTAA
          1 ATTAAATTTAA

                       
      23279 ATTAAATTTAA
          1 ATTAAATTTAA

               
      23290 ATT
          1 ATT

      23293 TTTTATATAC


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (11 bp):   
ATTAAATTTAA
Done.