Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003353.1 Kokia drynarioides strain JFW-HI SEQ_116071, 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: 11277
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32


Found at i:73 original size:4 final size:4

Alignment explanation


    Indices: 53--133  Score: 65
    Period size: 4  Copynumber: 19.5  Consensus size: 4

         43 AACACATTAC

                       *    *                  *              *   *      *
         53 CTTT CTTT CCTT -ATT CTTT CTTT CCTCTC CTTT CTTT CCTCT CCTT CTTC
          1 CTTT CTTT CTTT CTTT CTTT CTTT -CT-TT CTTT CTTT -CTTT CTTT CTTT

                                                  
        103 CTTT CTTT CTTT CTTT CCTTT CTTT CTTT CT
          1 CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CT

        134 CGTTTATTTG


Statistics
Matches: 61,  Mismatches: 11, Indels: 10
        0.74            0.13        0.12

Matches are distributed among these distances:
   3    2  0.03
   4   47  0.77
   5   11  0.18
   6    1  0.02

ACGTcount: A:0.01, C:0.35, G:0.00, T:0.64


Consensus pattern (4 bp):   
CTTT

Found at i:120 original size:17 final size:17

Alignment explanation


    Indices: 53--133  Score: 81
    Period size: 17  Copynumber: 4.4  Consensus size: 17

         43 AACACATTAC

                               
         53 CTTTCTTTCCTTATTCTTT
          1 CTTTCTTTCC-T-TTCTTT

                   *          
         72 CTTTCCTCTCCTTTCTTT
          1 CTTT-CTTTCCTTTCTTT

                 *               
         90 CCTCTCCTTCTTCCTTTCTTT
          1 -CT-TTC-T-TTCCTTTCTTT

                             
        111 CTTTCTTTCCTTTCTTT
          1 CTTTCTTTCCTTTCTTT

                  
        128 CTTTCT
          1 CTTTCT

        134 CGTTTATTTG


Statistics
Matches: 53,  Mismatches: 4, Indels: 12
        0.77            0.06        0.17

Matches are distributed among these distances:
  17   17  0.32
  18    7  0.13
  19   10  0.19
  20    9  0.17
  21   10  0.19

ACGTcount: A:0.01, C:0.35, G:0.00, T:0.64


Consensus pattern (17 bp):   
CTTTCTTTCCTTTCTTT
Done.