Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002410.1 Kokia drynarioides strain JFW-HI SEQ_114500, 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: 18389
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:13218 original size:60 final size:60

Alignment explanation


    Indices: 13124--13260  Score: 165
    Period size: 60  Copynumber: 2.3  Consensus size: 60

      13114 CATTAAAATC

                                   **  *                                  
      13124 GGGTCAAATTTGAATTTTTGGAAGCTTTAGGGGTCAAA-TCAAAATCTTTGGAACAATTGA-
          1 GGGTCAAATTTGAATTTTTGGAAAATTCAGGGGTCAAATTC-AAATCTTTGGAA-AATTGAG

                      *                                   *           *  
      13184 GGGTCAAATTGGAATTTTTGGAAAATTCCA-GGGTCAAATTCAAATTTTTGGAAAATTTAG
          1 GGGTCAAATTTGAATTTTTGGAAAATT-CAGGGGTCAAATTCAAATCTTTGGAAAATTGAG

                              
      13244 GGGT-AAATTTGAATTTT
          1 GGGTCAAATTTGAATTTT

      13261 GAAAAAGTTT


Statistics
Matches: 67,  Mismatches: 7, Indels: 7
        0.83            0.09        0.09

Matches are distributed among these distances:
  59   17  0.25
  60   47  0.70
  61    3  0.04

ACGTcount: A:0.34, C:0.08, G:0.23, T:0.36


Consensus pattern (60 bp):   
GGGTCAAATTTGAATTTTTGGAAAATTCAGGGGTCAAATTCAAATCTTTGGAAAATTGAG

Found at i:13251 original size:29 final size:30

Alignment explanation


    Indices: 13124--13391  Score: 144
    Period size: 30  Copynumber: 9.0  Consensus size: 30

      13114 CATTAAAATC

                      **           **     
      13124 GGGTCAAATTTGAATTTTTGGAAGCTTTAG
          1 GGGTCAAATTCAAATTTTTGGAAAATTTAG

                            *            *  
      13154 GGGTCAAA-TCAAAATCTTTGGAACAATTGA-
          1 GGGTCAAATTC-AAATTTTTGGAA-AATTTAG

                      **                *  
      13184 GGGTCAAATTGGAATTTTTGGAAAATTCCA-
          1 GGGTCAAATTCAAATTTTTGGAAAATT-TAG

                                          
      13214 GGGTCAAATTCAAATTTTTGGAAAATTTAG
          1 GGGTCAAATTCAAATTTTTGGAAAATTTAG

                      **        *          
      13244 GGGT-AAATTTGAA-TTTTGAAAAAGTTT-G
          1 GGGTCAAATTCAAATTTTTGGAAAA-TTTAG

              * *     **            *     
      13272 GGTTTAAATTTGAATTTTTGGAAAGTTT-G
          1 GGGTCAAATTCAAATTTTTGGAAAATTTAG

              * *     **        *         *
      13301 GGATTAAATTTGAATTTTT-AAAAAGTTTAA
          1 GGGTCAAATTCAAATTTTTGGAAAA-TTTAG

                *                          *
      13331 GGGTTAAATTCAAAATTTTT--AAAATTTTAA
          1 GGGTCAAATTC-AAATTTTTGGAAAA-TTTAG

                     *             *       
      13361 GGGTCAAA-ACATAATTTTTGGACAATTTAG
          1 GGGTCAAATTCA-AATTTTTGGAAAATTTAG

             
      13391 G
          1 G

      13392 AGTTAAAAAA


Statistics
Matches: 193,  Mismatches: 31, Indels: 28
        0.77            0.12        0.11

Matches are distributed among these distances:
  28   17  0.09
  29   58  0.30
  30  104  0.54
  31   14  0.07

ACGTcount: A:0.36, C:0.06, G:0.21, T:0.38


Consensus pattern (30 bp):   
GGGTCAAATTCAAATTTTTGGAAAATTTAG

Found at i:13340 original size:30 final size:29

Alignment explanation


    Indices: 13226--13354  Score: 129
    Period size: 29  Copynumber: 4.4  Consensus size: 29

      13216 GTCAAATTCA

                    *            *        
      13226 AATTTTTGGAAAA-TTTAGGGGTAAATTTG
          1 AATTTTT-AAAAAGTTTAGGGTTAAATTTG

                  *                       
      13255 AATTTTGAAAAAGTTT-GGGTTTAAATTTG
          1 AATTTTTAAAAAGTTTAGGG-TTAAATTTG

                   **                     
      13284 AATTTTTGGAAAGTTT-GGGATTAAATTTG
          1 AATTTTTAAAAAGTTTAGGG-TTAAATTTG

                                         **
      13313 AATTTTTAAAAAGTTTAAGGGTTAAATTCAA
          1 AATTTTTAAAAAGTTT-AGGGTTAAATT-TG

                       
      13344 AATTTTTAAAA
          1 AATTTTTAAAA

      13355 TTTTAAGGGT


Statistics
Matches: 84,  Mismatches: 11, Indels: 8
        0.82            0.11        0.08

Matches are distributed among these distances:
  28    7  0.08
  29   56  0.67
  30    7  0.08
  31   14  0.17

ACGTcount: A:0.38, C:0.01, G:0.19, T:0.43


Consensus pattern (29 bp):   
AATTTTTAAAAAGTTTAGGGTTAAATTTG

Found at i:13956 original size:97 final size:96

Alignment explanation


    Indices: 13730--13973  Score: 301
    Period size: 97  Copynumber: 2.5  Consensus size: 96

      13720 ATCTAGTGCT

                                    *              *  *  *        *          
      13730 TCACTCCACTCCATTGTAACCTCAAGGACGTTGAGCTCTTCTAC-CTATTTTGATCCACTTCTCT
          1 TCACTCCACTCCATTGTAACCTCAGGGACGTTGAGCTCTACTTCATTATTTTGACCCACTTCTCT

                   *                       
      13794 ATACCTCGCCAAGAAGATGGGATACGAAGTC
         66 ATACCTCACCAAGAAGATGGGATACGAAGTC

                         * **     *            *   *                         
      13825 TCACTCCACTCCACTAAAACCTTAGGGACGTTGAGTTCTCCTTCATTATTTTGACCCACTTCTCT
          1 TCACTCCACTCCATTGTAACCTCAGGGACGTTGAGCTCTACTTCATTATTTTGACCCACTTCTCT

                     * *          * **      
      13890 ATACCTCACTAGGAAGATGAGGTTTTGAAGTC
         66 ATACCTCACCAAGAAGATG-GGATACGAAGTC

                                         *                 *    
      13922 TCACTCCACTCCATTGTAACCTCAGGGACATTGAGCTCTACTTCATTTTTTT
          1 TCACTCCACTCCATTGTAACCTCAGGGACGTTGAGCTCTACTTCATTATTTT

      13974 TCCAACCCAC


Statistics
Matches: 123,  Mismatches: 24, Indels: 2
        0.83            0.16        0.01

Matches are distributed among these distances:
  95   36  0.29
  96   34  0.28
  97   53  0.43

ACGTcount: A:0.24, C:0.28, G:0.15, T:0.33


Consensus pattern (96 bp):   
TCACTCCACTCCATTGTAACCTCAGGGACGTTGAGCTCTACTTCATTATTTTGACCCACTTCTCT
ATACCTCACCAAGAAGATGGGATACGAAGTC
Done.