Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006802.1 Kokia drynarioides strain JFW-HI SEQ_121401, 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: 5265
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32


Found at i:384 original size:3 final size:3

Alignment explanation


    Indices: 376--428  Score: 97
    Period size: 3  Copynumber: 17.7  Consensus size: 3

        366 TACATATATA

                                                                         * 
        376 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

                  
        424 TAT TA
          1 TAT TA

        429 ACTTTTCTTT


Statistics
Matches: 48,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   3   48  1.00

ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66


Consensus pattern (3 bp):   
TAT

Found at i:876 original size:3 final size:3

Alignment explanation


    Indices: 868--924  Score: 59
    Period size: 3  Copynumber: 20.0  Consensus size: 3

        858 GAGGCAACGC

                                                 *                      
        868 CTT CTT CTT CTT CTT CCTT C-T CTT CTT TTT CTT CTT CTT -TT C-T
          1 CTT CTT CTT CTT CTT -CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT

                        *      
        911 CTT C-T CTT TTT CTT
          1 CTT CTT CTT CTT CTT

        925 TTGCTTCAAT


Statistics
Matches: 45,  Mismatches: 4, Indels: 10
        0.76            0.07        0.17

Matches are distributed among these distances:
   2    8  0.18
   3   34  0.76
   4    3  0.07

ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68


Consensus pattern (3 bp):   
CTT

Found at i:904 original size:24 final size:22

Alignment explanation


    Indices: 872--924  Score: 72
    Period size: 22  Copynumber: 2.4  Consensus size: 22

        862 CAACGCCTTC

                                  * 
        872 TTCTTCTTCTTCCTTCTCTTCTTT
          1 TTCTTCTTCTT--TTCTCTTCTCT

                                  
        896 TTCTTCTTCTTTTCTCTTCTCT
          1 TTCTTCTTCTTTTCTCTTCTCT

                    
        918 TT-TTCTT
          1 TTCTTCTT

        925 TTGCTTCAAT


Statistics
Matches: 28,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  21    5  0.18
  22   12  0.43
  24   11  0.39

ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70


Consensus pattern (22 bp):   
TTCTTCTTCTTTTCTCTTCTCT
Done.