Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012552.1 Kokia drynarioides strain JFW-HI SEQ_127561, 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, 659

Length: 1099
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33


Found at i:965 original size:25 final size:25

Alignment explanation


    Indices: 937--1013  Score: 72
    Period size: 25  Copynumber: 3.2  Consensus size: 25

        927 AAGAACACTA

                                     
        937 GTGCGCTCTTTGATTAGCACTGTGT
          1 GTGCGCTCTTTGATTAGCACTGTGT

                     *  *          * 
        962 GT--GCTCTCTGTTTAGCAC-GTCT
          1 GTGCGCTCTTTGATTAGCACTGTGT

                 *                     
        984 CGTGCTCTCTGTT-ATTAGCACTGTGT
          1 -GTGCGCTCT-TTGATTAGCACTGTGT

                
       1010 GTGC
          1 GTGC

       1014 TGTCTGTTGC


Statistics
Matches: 40,  Mismatches: 7, Indels: 10
        0.70            0.12        0.18

Matches are distributed among these distances:
  22    3  0.08
  23   16  0.40
  25   17  0.43
  26    4  0.10

ACGTcount: A:0.10, C:0.23, G:0.26, T:0.40


Consensus pattern (25 bp):   
GTGCGCTCTTTGATTAGCACTGTGT

Found at i:967 original size:23 final size:23

Alignment explanation


    Indices: 941--1014  Score: 78
    Period size: 23  Copynumber: 3.1  Consensus size: 23

        931 ACACTAGTGC

                                   
        941 GCTCTTTGATTAGCACTGTGTGT
          1 GCTCTTTGATTAGCACTGTGTGT

                 *  *          *    
        964 GCTCTCTGTTTAGCAC-GTCTCGT
          1 GCTCTTTGATTAGCACTGTGT-GT

                     *               
        987 GCTCTCTGTTATTAGCACTGTGTGT
          1 GCTCT-T-TGATTAGCACTGTGTGT

               
       1012 GCT
          1 GCT

       1015 GTCTGTTGCC


Statistics
Matches: 40,  Mismatches: 7, Indels: 6
        0.75            0.13        0.11

Matches are distributed among these distances:
  22    3  0.08
  23   21  0.52
  25   13  0.32
  26    3  0.08

ACGTcount: A:0.11, C:0.23, G:0.24, T:0.42


Consensus pattern (23 bp):   
GCTCTTTGATTAGCACTGTGTGT

Found at i:1014 original size:25 final size:25

Alignment explanation


    Indices: 949--1021  Score: 98
    Period size: 25  Copynumber: 3.0  Consensus size: 25

        939 GCGCTCTTTG

                                     
        949 ATTAGCACTGTGTGTGCTCTCTG-T
          1 ATTAGCACTGTGTGTGCTCTCTGTT

                       *              
        973 -TTAGCAC-GTCTCGTGCTCTCTGTT
          1 ATTAGCACTGTGT-GTGCTCTCTGTT

                              *      
        997 ATTAGCACTGTGTGTGCTGTCTGTT
          1 ATTAGCACTGTGTGTGCTCTCTGTT

       1022 GCCCAGCACT


Statistics
Matches: 42,  Mismatches: 3, Indels: 7
        0.81            0.06        0.13

Matches are distributed among these distances:
  22    3  0.07
  23   17  0.40
  24    1  0.02
  25   18  0.43
  26    3  0.07

ACGTcount: A:0.11, C:0.22, G:0.25, T:0.42


Consensus pattern (25 bp):   
ATTAGCACTGTGTGTGCTCTCTGTT
Done.