Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012931.1 Kokia drynarioides strain JFW-HI SEQ_127949, 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: 5083
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32


Found at i:2095 original size:216 final size:214

Alignment explanation


    Indices: 1306--2112  Score: 878
    Period size: 216  Copynumber: 3.8  Consensus size: 214

       1296 AAAACTGTTC

                   *                         * *  *  *    **     *  *        
       1306 GAAGGAAAGGATCGTCTTGAATACTTTAAGGAATCAAAATTTTAAAGGAACTCGTATAAGTTTGA
          1 GAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAAAACTCATAAAAGTTTGA

                  *           *           *             * *                  
       1371 CAAGTTTGGAAGTTCGTCCAAGAACCAAGATAGAAACAATTCTCGCGTAAATAAGTTTTTAATTC
         66 CAAGTTCGGAAGTTCGTCAAAGAACCAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTC

                **      *             *                *   *        *        
       1436 AAAACCCTAAAGTAGTTTACAAAATGGCAAACTATTTAGACCATATGGTGTGATTTTTCGAGG-A
        131 -AAAGGCTAAA-AAGTTTACAAAATGACAAACTATTTAGACCAAATGATGTGATTTCTCG-GGCA

                   * *            
       1500 TGGAATGATCAAAAAATTGCTT
        193 TGGAATGTTGAAAAAATTGCTT

                        *                                  *                 
       1522 GAAGGAATGGATTGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCATAAAAGTTTGA
          1 GAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAAAACTCATAAAAGTTTGA

                    *     *   *  *      * *        *                        *
       1587 CAAGTTCGAAAGTTTGTCCAACAACCAACAAAGAAACAACTCTCACATAAATAAGTTTTTAATTG
         66 CAAGTTCGGAAGTTCGTCAAAGAACCAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTC

                *  *                     *    *   *         *        **      
       1652 AAAGAC-CAAAAGTTTACAAAATGACAAATTATTCAGATCAAATGATGCGATTTCTCAAGCATGG
        131 AAAGGCTAAAAAGTTTACAAAATGACAAACTATTTAGACCAAATGATGTGATTTCTCGGGCATGG

                  *            *
       1716 AATGTCCG-AAAAATTGCTC
        196 AATGT-TGAAAAAATTGCTT

                              *          *  **                               
       1735 GAAGGAATGGATCGTCTTCAATACTTTAAAGATTCGAAGTTAT----AAA-TCATAAAAGTTTGA
          1 GAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAAAACTCATAAAAGTTTGA

                           *                                                 
       1795 CAAGTTCGGAAGTTCATCCAAA-AACCAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATT
         66 CAAGTTCGGAAGTTCGT-CAAAGAACCAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATT

                  *        *             *          *    *                   
       1859 CAAA-GATCAAAAGTTGTTTACAAAATGATAAACTATTTAAACCAGATGATGTGATTTCTCGGGC
        130 CAAAGGCT-AAAA--AGTTTACAAAATGACAAACTATTTAGACCAAATGATGTGATTTCTCGGGC

             *                 *   
       1923 AGGGAATGTTGAAAAAATTCCTT
        192 ATGGAATGTTGAAAAAATTGCTT

                    *                *                                     **
       1946 GAAGGAATTGATCGTCTTGAATACTGTAAGGAACCGAAGTTATAAAAAAACTCATAAAAGTTTTT
          1 GAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAAAACTCATAAAAGTTTGA

                  *          *     *                     **                  
       2011 CAAGTTTGGAAGTTCGTTAAAGATCCAAGAGAGAAACAATTCTCATGTAAATAAGTTTTTAATTC
         66 CAAGTTCGGAAGTTCGTCAAAGAACCAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTC

                                                 
       2076 AAAGGCTAAAACATGTTTACAAAATGACAAACTATTT
        131 AAAGGCTAAAA-A-GTTTACAAAATGACAAACTATTT

       2113 TGATTATGCG


Statistics
Matches: 489,  Mismatches: 86, Indels: 32
        0.81            0.14        0.05

Matches are distributed among these distances:
 208   70  0.14
 209    8  0.02
 210    1  0.00
 211   94  0.19
 212    1  0.00
 213   94  0.19
 214    2  0.00
 215   10  0.02
 216  207  0.42
 217    2  0.00

ACGTcount: A:0.41, C:0.14, G:0.17, T:0.29


Consensus pattern (214 bp):   
GAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAAAACTCATAAAAGTTTGA
CAAGTTCGGAAGTTCGTCAAAGAACCAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTC
AAAGGCTAAAAAGTTTACAAAATGACAAACTATTTAGACCAAATGATGTGATTTCTCGGGCATGG
AATGTTGAAAAAATTGCTT

Found at i:2240 original size:15 final size:15

Alignment explanation


    Indices: 2190--2241  Score: 50
    Period size: 15  Copynumber: 3.5  Consensus size: 15

       2180 GCGGGCATTG

                     *     
       2190 GTGTTGCAAGCACTC
          1 GTGTTGCAAACACTC

            *     **      *
       2205 ATGTTGTGAACACTA
          1 GTGTTGCAAACACTC

             *             
       2220 GAGTTGCAAACACTC
          1 GTGTTGCAAACACTC

                   
       2235 GTGTTGC
          1 GTGTTGC

       2242 GAGCATGGAT


Statistics
Matches: 26,  Mismatches: 11, Indels: 0
        0.70            0.30        0.00

Matches are distributed among these distances:
  15   26  1.00

ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29


Consensus pattern (15 bp):   
GTGTTGCAAACACTC
Done.