Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001691.1 Kokia drynarioides strain JFW-HI SEQ_113370, 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: 4139
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35


Found at i:828 original size:18 final size:20

Alignment explanation


    Indices: 807--848  Score: 54
    Period size: 20  Copynumber: 2.2  Consensus size: 20

        797 AATGATACTG

                                
        807 AATAAATT-TCAA-ATATAA
          1 AATAAATTATCAATATATAA

                                 
        825 AAT-AATTATCAATTATATAA
          1 AATAAATTATCAA-TATATAA

                
        845 AATA
          1 AATA

        849 TTCATTAATA


Statistics
Matches: 20,  Mismatches: 0, Indels: 5
        0.80            0.00        0.20

Matches are distributed among these distances:
  17    4  0.20
  18    7  0.35
  20    9  0.45

ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36


Consensus pattern (20 bp):   
AATAAATTATCAATATATAA

Found at i:2986 original size:43 final size:43

Alignment explanation


    Indices: 2863--3175  Score: 293
    Period size: 43  Copynumber: 7.1  Consensus size: 43

       2853 ATCTGTTAAT

                            *          *        ** *   
       2863 TTTAGCGGCGTTTGTGAGAAAAGCGCCTCTAAAGACTGTTTTC
          1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC

                  *  *   *          *      *        *  
       2906 TTTAGCAGCATTTATGGGAAAAGCACCGCTATAGACCATGGTC
          1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC

             *                *                    **  
       2949 TCTAGCGGCGTTTGTGGGCAAAGCGCCGCTAAAGACCATAATC
          1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC

                 *       *    *                        
       2992 TTTAGTGGCGTTTATGGGGAAAGCGCCGCTAAAGACCATGTTC
          1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC

                    *         *      *  *              
       3035 TTTAGCGGGGTTTGTGGGGAAAGCGTCGTTAAAGACCATGTTC
          1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC

                                    *      **             *  
       3078 TTTAGCGGTAGCGGCGTTTGTGGGGAAAGCGGAGCTAAAGACCATGATC
          1 -TT-----TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC

                *    *            *  *                 
       3127 TTTAACGGCATTTGTGGGAAAAACGTCGCTAAAGACCATGTTC
          1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC

             *    
       3170 TATAGC
          1 TTTAGC

       3176 AACGTTTTTC


Statistics
Matches: 219,  Mismatches: 45, Indels: 12
        0.79            0.16        0.04

Matches are distributed among these distances:
  43  179  0.82
  44    2  0.01
  48    2  0.01
  49   36  0.16

ACGTcount: A:0.26, C:0.19, G:0.29, T:0.27


Consensus pattern (43 bp):   
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC

Done.