Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000339.1 Kokia drynarioides strain JFW-HI SEQ_111111, 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: 6207
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34


Found at i:772 original size:56 final size:55

Alignment explanation


    Indices: 712--902  Score: 229
    Period size: 56  Copynumber: 3.4  Consensus size: 55

        702 TCTACTTACA

                                *                       *   *       
        712 TCTCGGTTAGAGCGTAATGCCATGTATAGCTTGGGTAGAGCTTTTGAACGCTTATG
          1 TCTCGGTTAGAGCGTAATGCTATGTATAGCTT-GGTAGAGCTTTGGAATGCTTATG

                    *    *                  **                    * 
        768 TCTCGGTTGGAGCATAATGCTATGTATAGCTCAAGTAGAGCTTTGGAATGCTTACG
          1 TCTCGGTTAGAGCGTAATGCTATGTATAGCT-TGGTAGAGCTTTGGAATGCTTATG

                     *                                    **        
        824 TCTCGGTTACAGCGTAATGCTATGTATAGCTCTGGTAGAGCTTTGGGTTGCTTATG
          1 TCTCGGTTAGAGCGTAATGCTATGTATAGCT-TGGTAGAGCTTTGGAATGCTTATG

             *    *          *     
        880 TTTCGGCTAGAGCGTAAAGCTAT
          1 TCTCGGTTAGAGCGTAATGCTAT

        903 TTTGCTTCAG


Statistics
Matches: 114,  Mismatches: 20, Indels: 2
        0.84            0.15        0.01

Matches are distributed among these distances:
  56  114  1.00

ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34


Consensus pattern (55 bp):   
TCTCGGTTAGAGCGTAATGCTATGTATAGCTTGGTAGAGCTTTGGAATGCTTATG

Found at i:3180 original size:16 final size:16

Alignment explanation


    Indices: 3155--3190  Score: 54
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       3145 GAATAAAGTG

                          * 
       3155 TTTTTGAGACTTATCA
          1 TTTTTGAGACTTATAA

                 *          
       3171 TTTTTTAGACTTATAA
          1 TTTTTGAGACTTATAA

                
       3187 TTTT
          1 TTTT

       3191 GGGATTATTT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  16   18  1.00

ACGTcount: A:0.25, C:0.08, G:0.08, T:0.58


Consensus pattern (16 bp):   
TTTTTGAGACTTATAA
Done.