Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010177.1 Kokia drynarioides strain JFW-HI SEQ_124982, 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, 961

Length: 1602
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33


Found at i:1000 original size:23 final size:23

Alignment explanation


    Indices: 970--1065  Score: 140
    Period size: 23  Copynumber: 4.2  Consensus size: 23

        960 ACCCTAGCGC

                      *            
        970 GCTCTCTGATCAGCACTGTGTGT
          1 GCTCTCTGATTAGCACTGTGTGT

                    *               
        993 GCTCTCTGTTTAGCACT-TCGTGT
          1 GCTCTCTGATTAGCACTGT-GTGT

                                   
       1016 GCTCTCTGATTAGCACTGTGTGT
          1 GCTCTCTGATTAGCACTGTGTGT

                             *    *
       1039 GCTCTCTGATTAGCACTTTGTGG
          1 GCTCTCTGATTAGCACTGTGTGT

                
       1062 GCTC
          1 GCTC

       1066 AGTACTTTGT


Statistics
Matches: 66,  Mismatches: 5, Indels: 4
        0.88            0.07        0.05

Matches are distributed among these distances:
  22    1  0.02
  23   64  0.97
  24    1  0.02

ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39


Consensus pattern (23 bp):   
GCTCTCTGATTAGCACTGTGTGT

Found at i:1037 original size:46 final size:46

Alignment explanation


    Indices: 970--1065  Score: 156
    Period size: 46  Copynumber: 2.1  Consensus size: 46

        960 ACCCTAGCGC

                                           *             *
        970 GCTCTCTGATCAGCACTGTGTGTGCTCTCTGTTTAGCACTTCGTGT
          1 GCTCTCTGATCAGCACTGTGTGTGCTCTCTGATTAGCACTTCGTGG

                      *                              *    
       1016 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGG
          1 GCTCTCTGATCAGCACTGTGTGTGCTCTCTGATTAGCACTTCGTGG

                
       1062 GCTC
          1 GCTC

       1066 AGTACTTTGT


Statistics
Matches: 46,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  46   46  1.00

ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39


Consensus pattern (46 bp):   
GCTCTCTGATCAGCACTGTGTGTGCTCTCTGATTAGCACTTCGTGG

Found at i:1129 original size:25 final size:25

Alignment explanation


    Indices: 1089--1160  Score: 117
    Period size: 25  Copynumber: 2.8  Consensus size: 25

       1079 CTCTCTGTTT

                    *                 
       1089 AGCACTTTGTGTGCTCTTTGTTGCCC
          1 AGCAC-TTATGTGCTCTTTGTTGCCC

                                     
       1115 AGCACTTATGTGCTCTTTGTTGCCC
          1 AGCACTTATGTGCTCTTTGTTGCCC

                            *    
       1140 AGCACTTATGTGCTCTCTGTT
          1 AGCACTTATGTGCTCTTTGTT

       1161 TAGTAATTTG


Statistics
Matches: 44,  Mismatches: 2, Indels: 1
        0.94            0.04        0.02

Matches are distributed among these distances:
  25   39  0.89
  26    5  0.11

ACGTcount: A:0.11, C:0.26, G:0.21, T:0.42


Consensus pattern (25 bp):   
AGCACTTATGTGCTCTTTGTTGCCC
Done.