Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013108.1 Kokia drynarioides strain JFW-HI SEQ_128127, 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: 3052
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.37

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:1863 original size:30 final size:30

Alignment explanation


    Indices: 1815--1875  Score: 77
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       1805 CGAATTTGGA

                      *  *     **         
       1815 GATTTTAGGTTGTTGAATTTGGGGATTTTG
          1 GATTTTAGGTGGTCGAATTAAGGGATTTTG

                  *                       
       1845 GATTTTGGGTGGTCGAATTAAGGGATTTTG
          1 GATTTTAGGTGGTCGAATTAAGGGATTTTG

             
       1875 G
          1 G

       1876 TTAAGAGTTT


Statistics
Matches: 26,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  30   26  1.00

ACGTcount: A:0.18, C:0.02, G:0.36, T:0.44


Consensus pattern (30 bp):   
GATTTTAGGTGGTCGAATTAAGGGATTTTG

Found at i:1912 original size:27 final size:29

Alignment explanation


    Indices: 1866--1931  Score: 82
    Period size: 27  Copynumber: 2.3  Consensus size: 29

       1856 GTCGAATTAA

                                         
       1866 GGGATTTTGGTTAAGAG-TTTTGA-TTTG
          1 GGGATTTTGGTTAAGAGTTTTTGATTTTG

                    *   *  *             
       1893 GGGATTTTTGTTTAGGGTTTTTGATTTTG
          1 GGGATTTTGGTTAAGAGTTTTTGATTTTG

             *        
       1922 GAGATTTTGG
          1 GGGATTTTGG

       1932 GATAGTGTTG


Statistics
Matches: 32,  Mismatches: 5, Indels: 2
        0.82            0.13        0.05

Matches are distributed among these distances:
  27   14  0.44
  28    6  0.19
  29   12  0.38

ACGTcount: A:0.15, C:0.00, G:0.33, T:0.52


Consensus pattern (29 bp):   
GGGATTTTGGTTAAGAGTTTTTGATTTTG

Found at i:1914 original size:14 final size:15

Alignment explanation


    Indices: 1883--1929  Score: 53
    Period size: 14  Copynumber: 3.2  Consensus size: 15

       1873 TGGTTAAGAG

                     *     
       1883 TTTTGATTTGGGGAT
          1 TTTTGATTTAGGGAT

                           
       1898 TTTTG-TTTAGGG-T
          1 TTTTGATTTAGGGAT

                     *      
       1911 TTTTGATTTTGGAGAT
          1 TTTTGATTTAGG-GAT

               
       1927 TTT
          1 TTT

       1930 GGGATAGTGT


Statistics
Matches: 27,  Mismatches: 2, Indels: 5
        0.79            0.06        0.15

Matches are distributed among these distances:
  13    6  0.22
  14   11  0.41
  15    6  0.22
  16    4  0.15

ACGTcount: A:0.13, C:0.00, G:0.28, T:0.60


Consensus pattern (15 bp):   
TTTTGATTTAGGGAT

Found at i:2487 original size:12 final size:12

Alignment explanation


    Indices: 2472--2496  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       2462 TTTTTACTGC

                        
       2472 TATTTTGGTTGT
          1 TATTTTGGTTGT

                        
       2484 TATTTTGGTTGT
          1 TATTTTGGTTGT

             
       2496 T
          1 T

       2497 TGGATGTTAT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68


Consensus pattern (12 bp):   
TATTTTGGTTGT

Found at i:2670 original size:13 final size:13

Alignment explanation


    Indices: 2646--2678  Score: 50
    Period size: 13  Copynumber: 2.5  Consensus size: 13

       2636 ATTTTTAATT

                          
       2646 TGTTTATTTTTTAA
          1 TGTTT-TTTTTTAA

                         
       2660 TGTTTTTTTTTAA
          1 TGTTTTTTTTTAA

                   
       2673 -GTTTTT
          1 TGTTTTT

       2679 AAGCGTATTT


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  12    6  0.32
  13    8  0.42
  14    5  0.26

ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76


Consensus pattern (13 bp):   
TGTTTTTTTTTAA
Done.