Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003939.1 Kokia drynarioides strain JFW-HI SEQ_117021, 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: 6144
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32


Found at i:1197 original size:41 final size:41

Alignment explanation


    Indices: 1123--1254  Score: 149
    Period size: 41  Copynumber: 3.2  Consensus size: 41

       1113 GTTTTTTCAT

                           *  *    *  *  *           
       1123 AAACGCCGC-AAAAGGAAAAGCAATAACGACGTTTATGAGA
          1 AAACGCCGCAAAAAGTAAGAGCACTAGCGGCGTTTATGAGA

                    *                                
       1163 AAACGCCGGAAAAAGTAAGAGCACTAGCGGCGTTTATGAGA
          1 AAACGCCGCAAAAAGTAAGAGCACTAGCGGCGTTTATGAGA

               *  *      *         *   *              
       1204 AAATGCAGCAAAAGGTAAGAGCATTAGTGGCGTTTATGAGAA
          1 AAACGCCGCAAAAAGTAAGAGCACTAGCGGCGTTTATGAG-A

                     
       1246 AAACGCCGC
          1 AAACGCCGC

       1255 TAAAGGTTAA


Statistics
Matches: 76,  Mismatches: 14, Indels: 2
        0.83            0.15        0.02

Matches are distributed among these distances:
  40    8  0.11
  41   60  0.79
  42    8  0.11

ACGTcount: A:0.42, C:0.17, G:0.27, T:0.15


Consensus pattern (41 bp):   
AAACGCCGCAAAAAGTAAGAGCACTAGCGGCGTTTATGAGA

Found at i:3773 original size:28 final size:27

Alignment explanation


    Indices: 3736--3799  Score: 69
    Period size: 26  Copynumber: 2.4  Consensus size: 27

       3726 TATAATATAG

                            *           
       3736 ACAG-AACACAACGAATATGTAGCACAA
          1 ACAGAAACACAAC-AACATGTAGCACAA

             *            *            
       3763 ATAGAAACAC-ACAGCATGTAGCACAA
          1 ACAGAAACACAACAACATGTAGCACAA

                 *     
       3789 ACAGAGACACA
          1 ACAGAAACACA

       3800 CCTCAAATGG


Statistics
Matches: 30,  Mismatches: 5, Indels: 4
        0.77            0.13        0.10

Matches are distributed among these distances:
  26   20  0.67
  27    5  0.17
  28    5  0.17

ACGTcount: A:0.52, C:0.23, G:0.16, T:0.09


Consensus pattern (27 bp):   
ACAGAAACACAACAACATGTAGCACAA
Done.