Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014552.1 Kokia drynarioides strain JFW-HI SEQ_129591, 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: 4059
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36


Found at i:2909 original size:48 final size:48

Alignment explanation


    Indices: 2850--2944  Score: 138
    Period size: 48  Copynumber: 2.0  Consensus size: 48

       2840 TTTCATTTCT

                *                                *           
       2850 TTTCGTTTCTTTTATTTTATTTTATT-TTTTCCTTTTGGTTTCGTTTTG
          1 TTTCATTTCTTTTATTTTATTTTATTCTTTTCCTTTTCGTTTC-TTTTG

                                   *       *               
       2898 TTTCATTTCTTTTATTTTATTTTTTTCTTTTTCTTTTCGTTTCTTTT
          1 TTTCATTTCTTTTATTTTATTTTATTCTTTTCCTTTTCGTTTCTTTT

       2945 CTTTGCTTTT


Statistics
Matches: 42,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
  48   28  0.67
  49   14  0.33

ACGTcount: A:0.06, C:0.12, G:0.06, T:0.76


Consensus pattern (48 bp):   
TTTCATTTCTTTTATTTTATTTTATTCTTTTCCTTTTCGTTTCTTTTG

Found at i:2911 original size:43 final size:43

Alignment explanation


    Indices: 2845--2928  Score: 125
    Period size: 43  Copynumber: 2.0  Consensus size: 43

       2835 TTTCATTTCA

                          *                            
       2845 TTTCTTTTCGTTTCTTTTATTTTATTTTATTTTTTCCTTTTGG
          1 TTTCTTTTCGTTTCATTTATTTTATTTTATTTTTTCCTTTTGG

                               *                *     
       2888 TTTCGTTTT-GTTTCATTTCTTTTATTTTATTTTTTTCTTTT
          1 TTTC-TTTTCGTTTCATTTATTTTATTTTATTTTTTCCTTTT

       2929 TCTTTTCGTT


Statistics
Matches: 37,  Mismatches: 3, Indels: 2
        0.88            0.07        0.05

Matches are distributed among these distances:
  43   33  0.89
  44    4  0.11

ACGTcount: A:0.07, C:0.11, G:0.06, T:0.76


Consensus pattern (43 bp):   
TTTCTTTTCGTTTCATTTATTTTATTTTATTTTTTCCTTTTGG

Found at i:2928 original size:5 final size:5

Alignment explanation


    Indices: 2898--2957  Score: 52
    Period size: 5  Copynumber: 12.2  Consensus size: 5

       2888 TTTCGTTTTG

                *          *      *                        *            
       2898 TTTCA TTTCT TTTAT TTT-A TTT-T TTTCTT TTTCT TTTCG TTTCT TTTCT
          1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTC-T TTTCT TTTCT TTTCT TTTCT

              *          
       2947 TTGCT TTTCT T
          1 TTTCT TTTCT T

       2958 CCAAACAGCA


Statistics
Matches: 45,  Mismatches: 8, Indels: 4
        0.79            0.14        0.07

Matches are distributed among these distances:
   4    6  0.13
   5   34  0.76
   6    5  0.11

ACGTcount: A:0.05, C:0.15, G:0.03, T:0.77


Consensus pattern (5 bp):   
TTTCT
Done.