Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006154.1 Kokia drynarioides strain JFW-HI SEQ_120699, 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: 26437
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:2738 original size:17 final size:17

Alignment explanation


    Indices: 2714--2748  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       2704 TGAAAAAAAG

                             
       2714 AAAAAAAGAAA-AAATT
          1 AAAAAAAGAAACAAATT

                              
       2730 AAAACAAAGAAACAAATT
          1 AAAA-AAAGAAACAAATT

             
       2748 A
          1 A

       2749 TCATGGCAAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  16    4  0.24
  17    7  0.41
  18    6  0.35

ACGTcount: A:0.77, C:0.06, G:0.06, T:0.11


Consensus pattern (17 bp):   
AAAAAAAGAAACAAATT

Found at i:16956 original size:21 final size:21

Alignment explanation


    Indices: 16932--16982  Score: 93
    Period size: 21  Copynumber: 2.4  Consensus size: 21

      16922 AATTATTTAA

                                 
      16932 TTTGGATTTATAAATTTTATG
          1 TTTGGATTTATAAATTTTATG

                     *           
      16953 TTTGGATTTCTAAATTTTATG
          1 TTTGGATTTATAAATTTTATG

                     
      16974 TTTGGATTT
          1 TTTGGATTT

      16983 TTAAGTTTGT


Statistics
Matches: 29,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  21   29  1.00

ACGTcount: A:0.24, C:0.02, G:0.16, T:0.59


Consensus pattern (21 bp):   
TTTGGATTTATAAATTTTATG

Found at i:26295 original size:48 final size:46

Alignment explanation


    Indices: 26218--26320  Score: 118
    Period size: 48  Copynumber: 2.2  Consensus size: 46

      26208 AGGAACACTA

                                    *          *          
      26218 GCGTGCTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTTAGCACGTC
          1 GCGTGCTCTCTGTTTAGCACTGTGCGTGCTCTCTGATTAGCACGTC

            *           *                      *          *  
      26264 TCGTGCTCTCTATTATTAGCACT-TCGCGTGCTCTTTGATTAGCACTTC
          1 GCGTGCTCTCT-GT-TTAGCACTGT-GCGTGCTCTCTGATTAGCACGTC

                     
      26312 GCGTGCTCT
          1 GCGTGCTCT

      26321 TTGATTAGTA


Statistics
Matches: 47,  Mismatches: 7, Indels: 4
        0.81            0.12        0.07

Matches are distributed among these distances:
  46   10  0.21
  47    2  0.04
  48   35  0.74

ACGTcount: A:0.11, C:0.27, G:0.22, T:0.40


Consensus pattern (46 bp):   
GCGTGCTCTCTGTTTAGCACTGTGCGTGCTCTCTGATTAGCACGTC

Found at i:26310 original size:23 final size:23

Alignment explanation


    Indices: 26218--26333  Score: 117
    Period size: 23  Copynumber: 5.0  Consensus size: 23

      26208 AGGAACACTA

                     *  *           
      26218 GCGTGCTCTCTGTTTAGCACTGT-
          1 GCGTGCTCTTTGATTAGCACT-TC

             *       *  *       *  
      26241 GTGTGCTCTCTGTTTAGCACGTC
          1 GCGTGCTCTTTGATTAGCACTTC

            *            *           
      26264 TCGTGCTCTCTATTATTAGCACTTC
          1 GCGTGCTCT-T-TGATTAGCACTTC

                                   
      26289 GCGTGCTCTTTGATTAGCACTTC
          1 GCGTGCTCTTTGATTAGCACTTC

                             *    
      26312 GCGTGCTCTTTGATTAGTACTT
          1 GCGTGCTCTTTGATTAGCACTT

      26334 TGGTACTCTT


Statistics
Matches: 79,  Mismatches: 11, Indels: 6
        0.82            0.11        0.06

Matches are distributed among these distances:
  22    1  0.01
  23   59  0.75
  24    1  0.01
  25   18  0.23

ACGTcount: A:0.12, C:0.25, G:0.22, T:0.41


Consensus pattern (23 bp):   
GCGTGCTCTTTGATTAGCACTTC

Found at i:26345 original size:22 final size:23

Alignment explanation


    Indices: 26278--26345  Score: 93
    Period size: 23  Copynumber: 3.0  Consensus size: 23

      26268 GCTCTCTATT

                           *       
      26278 ATTAGCACTTCGCGTGCTCTTTG
          1 ATTAGCACTTCGCGTACTCTTTG

                           *       
      26301 ATTAGCACTTCGCGTGCTCTTTG
          1 ATTAGCACTTCGCGTACTCTTTG

                 *    *            
      26324 ATTAGTACTTTG-GTACTCTTTG
          1 ATTAGCACTTCGCGTACTCTTTG

      26346 TTTGTTTTGT


Statistics
Matches: 42,  Mismatches: 3, Indels: 1
        0.91            0.07        0.02

Matches are distributed among these distances:
  22    9  0.21
  23   33  0.79

ACGTcount: A:0.15, C:0.22, G:0.21, T:0.43


Consensus pattern (23 bp):   
ATTAGCACTTCGCGTACTCTTTG
Done.