Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004884.1 Kokia drynarioides strain JFW-HI SEQ_118565, 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: 1969
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33


Found at i:1913 original size:4 final size:4

Alignment explanation


    Indices: 1891--1956  Score: 62
    Period size: 4  Copynumber: 16.2  Consensus size: 4

       1881 AACATATTAC

                 *     *                     *   *      *               
       1891 CTTT ATTT CCTT C-TT CTTT CTTT CCTCT CCTT CTTC CTTT CTTT CTTT
          1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT

                                  
       1939 CTTT CCTTT CTTT CTTT C
          1 CTTT -CTTT CTTT CTTT C

       1957 CCGTTTATTT


Statistics
Matches: 50,  Mismatches: 9, Indels: 6
        0.77            0.14        0.09

Matches are distributed among these distances:
   3    3  0.06
   4   40  0.80
   5    7  0.14

ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65


Consensus pattern (4 bp):   
CTTT

Found at i:1925 original size:17 final size:15

Alignment explanation


    Indices: 1891--1957  Score: 63
    Period size: 13  Copynumber: 4.7  Consensus size: 15

       1881 AACATATTAC

                *          
       1891 CTTTATTTCCTTCTT
          1 CTTTCTTTCCTTCTT

                           
       1906 CTTTCTTTCC-TC-T
          1 CTTTCTTTCCTTCTT

             *               
       1919 CCTTC-TTCCTTTCTTT
          1 CTTTCTTTCC-TTC-TT

                           
       1935 CTTTCTTTCC-T-TT
          1 CTTTCTTTCCTTCTT

                      
       1948 CTTTCTTTCC
          1 CTTTCTTTCC

       1958 CGTTTATTTG


Statistics
Matches: 44,  Mismatches: 3, Indels: 12
        0.75            0.05        0.20

Matches are distributed among these distances:
  12    4  0.09
  13   17  0.39
  14    4  0.09
  15   10  0.23
  16    5  0.11
  17    4  0.09

ACGTcount: A:0.01, C:0.34, G:0.00, T:0.64


Consensus pattern (15 bp):   
CTTTCTTTCCTTCTT

Found at i:1936 original size:29 final size:27

Alignment explanation


    Indices: 1897--1954  Score: 80
    Period size: 29  Copynumber: 2.1  Consensus size: 27

       1887 TTACCTTTAT

                                       
       1897 TTCCTTCTTCTTTCTTTCCTCTCCTTC
          1 TTCCTTCTTCTTTCTTTCCTCTCCTTC

                                  *  *   
       1924 TTCCTTTCTTTCTTTCTTTCCTTTCTTTC
          1 TTCC-TTC-TTCTTTCTTTCCTCTCCTTC

              
       1953 TT
          1 TT

       1955 TCCCGTTTAT


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
  27    4  0.15
  28    3  0.11
  29   20  0.74

ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66


Consensus pattern (27 bp):   
TTCCTTCTTCTTTCTTTCCTCTCCTTC
Done.