Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010774.1 Kokia drynarioides strain JFW-HI SEQ_125737, 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: 6822
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34


Found at i:2997 original size:25 final size:24

Alignment explanation


    Indices: 2960--3017  Score: 75
    Period size: 25  Copynumber: 2.4  Consensus size: 24

       2950 GCACTAGCGC

                                     
       2960 GCTCTCTG-TTTAGCAC-GTCTCGT
          1 GCTCTCTGTTTTAGCACTGTCT-GT

                                 *   
       2983 GCTCTCTGTTATTAGCACTGTGTGT
          1 GCTCTCTGTT-TTAGCACTGTCTGT

                      
       3008 GCTCTCTGTT
          1 GCTCTCTGTT

       3018 GCCCAGCACT


Statistics
Matches: 31,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
  23    8  0.26
  24    1  0.03
  25   19  0.61
  26    3  0.10

ACGTcount: A:0.09, C:0.26, G:0.22, T:0.43


Consensus pattern (24 bp):   
GCTCTCTGTTTTAGCACTGTCTGT

Found at i:4093 original size:23 final size:23

Alignment explanation


    Indices: 4064--4215  Score: 162
    Period size: 23  Copynumber: 6.5  Consensus size: 23

       4054 GAACACTAGC

                                 * 
       4064 GTGCTCTCTGTTTAGCAC-GTCT
          1 GTGCTCTCTGTTTAGCACTGTGT

                                      
       4086 CGTGCTCTCTGTTATTAGCACTGTGT
          1 -GTGCTCTCTG-T-TTAGCACTGTGT

                 *    *        * * 
       4112 GTGCTTTCTGATTAGCACTTTAT
          1 GTGCTCTCTGTTTAGCACTGTGT

               *      *    *   *   
       4135 GTGTTCTCTGATTAGTACTTTGT
          1 GTGCTCTCTGTTTAGCACTGTGT

              *                    
       4158 GTACTCTCTGTTTAGCACTGTGT
          1 GTGCTCTCTGTTTAGCACTGTGT

              *                    
       4181 GTACTCTCTGTTTAGCACTGTGT
          1 GTGCTCTCTGTTTAGCACTGTGT

              *         
       4204 GTACTCTCTGTT
          1 GTGCTCTCTGTT

       4216 GCCCAGCACT


Statistics
Matches: 112,  Mismatches: 14, Indels: 6
        0.85            0.11        0.05

Matches are distributed among these distances:
  23   92  0.82
  24    1  0.01
  25   16  0.14
  26    3  0.03

ACGTcount: A:0.12, C:0.21, G:0.21, T:0.45


Consensus pattern (23 bp):   
GTGCTCTCTGTTTAGCACTGTGT

Found at i:4173 original size:46 final size:46

Alignment explanation


    Indices: 4067--4262  Score: 166
    Period size: 46  Copynumber: 4.2  Consensus size: 46

       4057 CACTAGCGTG

                             *  *                           *
       4067 CTCTCTGTTTAGCACGTCT-CGTGCTCTCTGTTATTAGCACTGTGTGTG
          1 CTCTCTGTTTAGCAC-TTTATGTGCTCTCTG--ATTAGCACTGTGTGTA

              *    *               *           *   *      
       4115 CTTTCTGATTAGCACTTTATGTGTTCTCTGATTAGTACTTTGTGTA
          1 CTCTCTGTTTAGCACTTTATGTGCTCTCTGATTAGCACTGTGTGTA

                            * *   *       *               
       4161 CTCTCTGTTTAGCACTGTGTGTACTCTCTGTTTAGCACTGTGTGTA
          1 CTCTCTGTTTAGCACTTTATGTGCTCTCTGATTAGCACTGTGTGTA

                        *            *            *   *      
       4207 CTCTCTGTTGCCCAGCAC-TTATGTTCTCTCTG-TTAGTACTTTG-GTA
          1 CTCTCTGTT---TAGCACTTTATGTGCTCTCTGATTAGCACTGTGTGTA

                      
       4253 CTCTCTGTTT
          1 CTCTCTGTTT

       4263 GTTTCGTATA


Statistics
Matches: 120,  Mismatches: 24, Indels: 13
        0.76            0.15        0.08

Matches are distributed among these distances:
  46   71  0.59
  47   11  0.09
  48   33  0.28
  49    5  0.04

ACGTcount: A:0.13, C:0.22, G:0.19, T:0.45


Consensus pattern (46 bp):   
CTCTCTGTTTAGCACTTTATGTGCTCTCTGATTAGCACTGTGTGTA
Done.