Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002890.1 Kokia drynarioides strain JFW-HI SEQ_115303, 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: 5783
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:4287 original size:17 final size:17

Alignment explanation


    Indices: 4265--4303  Score: 53
    Period size: 17  Copynumber: 2.3  Consensus size: 17

       4255 AGGTGGAGAA

                     *        
       4265 CTTGTTCGTTGA-AAGTT
          1 CTTGTTCGTAGAGAA-TT

                             
       4282 CTTGTTCGTAGAGAATT
          1 CTTGTTCGTAGAGAATT

                 
       4299 CTTGT
          1 CTTGT

       4304 CGAGATGGAG


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  17   18  0.90
  18    2  0.10

ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46


Consensus pattern (17 bp):   
CTTGTTCGTAGAGAATT

Found at i:4987 original size:23 final size:23

Alignment explanation


    Indices: 4961--5078  Score: 139
    Period size: 23  Copynumber: 5.1  Consensus size: 23

       4951 AGTGCTGGGC

                                   
       4961 AACAGAGAGCACACACAGTGCTA
          1 AACAGAGAGCACACACAGTGCTA

                     * *   *   *   
       4984 AACAGAGAGTAGACAAAGTACTA
          1 AACAGAGAGCACACACAGTGCTA

             *    *                
       5007 ATCAGAAAGCACACACAGTGCTA
          1 AACAGAGAGCACACACAGTGCTA

             *                     
       5030 ATCAGAGAGCACACACAGTGCTA
          1 AACAGAGAGCACACACAGTGCTA

             *             *        
       5053 ATCAGAGAGCACA-AGACGTGCTA
          1 AACAGAGAGCACACACA-GTGCTA

               
       5076 AAC
          1 AAC

       5079 TGTTTTAATT


Statistics
Matches: 81,  Mismatches: 13, Indels: 2
        0.84            0.14        0.02

Matches are distributed among these distances:
  22    2  0.02
  23   79  0.98

ACGTcount: A:0.44, C:0.23, G:0.21, T:0.12


Consensus pattern (23 bp):   
AACAGAGAGCACACACAGTGCTA

Found at i:5022 original size:46 final size:46

Alignment explanation


    Indices: 4963--5078  Score: 153
    Period size: 46  Copynumber: 2.5  Consensus size: 46

       4953 TGCTGGGCAA

                                          * *             
       4963 CAGAGAGCACACACAGTGCTAAACAGAGAGTAGACAAAGTACTAAT
          1 CAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT

                *                 *             *   *     
       5009 CAGAAAGCACACACAGTGCTAATCAGAGAGCACACACAGTGCTAAT
          1 CAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT

                         *           
       5055 CAGAGAGCACA-AGACGTGCTAAAC
          1 CAGAGAGCACACACA-GTGCTAAAC

       5079 TGTTTTAATT


Statistics
Matches: 60,  Mismatches: 9, Indels: 2
        0.85            0.13        0.03

Matches are distributed among these distances:
  45    2  0.03
  46   58  0.97

ACGTcount: A:0.43, C:0.23, G:0.22, T:0.12


Consensus pattern (46 bp):   
CAGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAAT
Done.