Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006370.1 Kokia drynarioides strain JFW-HI SEQ_120946, 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: 4972
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:1154 original size:29 final size:28

Alignment explanation


    Indices: 1096--1486  Score: 246
    Period size: 29  Copynumber: 13.2  Consensus size: 28

       1086 GGTTAAAATG

                                 *        
       1096 ATTTTGGAAAAGTTTAGAGGTAAAAATGTA
          1 ATTTTGG-AAAGTTTAG-GGTCAAAATGTA

                       *    *            
       1126 ATTATTGGAAAATTTATGGTCAAAATGTA
          1 ATT-TTGGAAAGTTTAGGGTCAAAATGTA

                       *                 *
       1155 ATTTTAGGAAAATTT-GGGTTCAAAATGTG
          1 ATTTT-GGAAAGTTTAGGG-TCAAAATGTA

                                   *     
       1184 ATTTTGGAAAGGTTTAGGGTCAAGATGTA
          1 ATTTTGGAAA-GTTTAGGGTCAAAATGTA

                               *   *       *
       1213 ATTTTTGGAAAGTTTATTAAGGTTAAAATGTG
          1 A-TTTTGGAAAG--T-TTAGGGTCAAAATGTA

                  *              *        
       1245 ATTTTAAGAAAGTTTAGGGGTTAAAATGTA
          1 ATTTT-GGAAAGTTTA-GGGTCAAAATGTA

                           *             
       1275 ATTTTGGAAAGGTTTGGGGTCAAAATGTA
          1 ATTTTGGAAA-GTTTAGGGTCAAAATGTA

            *    *         *              
       1304 TTTTTAGAGAAGTTTGGTGGTCAAAATGTA
          1 ATTTTGGA-AAGTTTAG-GGTCAAAATGTA

                   *   ** * * * *      * 
       1334 ATTTTGTAAAAAATAATGTTTAAAATGCA
          1 ATTTTG-GAAAGTTTAGGGTCAAAATGTA

                 *         *      *   *   
       1363 ATTTTAGAGAAGTTTGGTGGTCGAAACGTA
          1 ATTTTGGA-AAGTTTAG-GGTCAAAATGTA

                                      **  
       1393 ATTTTGGAAAAGTTTAGGGGT-AAAAAATA
          1 ATTTTGG-AAAGTTTA-GGGTCAAAATGTA

                                        * 
       1422 ATTTTGGAGAAGTTTAGGGGTCAAAATGAA
          1 ATTTTGGA-AAGTTTA-GGGTCAAAATGTA

                   *       *  *          *
       1452 ATTTTAGAAAAGTTCAAGTGTCAAAATGTT
          1 ATTTT-GGAAAGTT-TAGGGTCAAAATGTA

                 
       1482 ATTTT
          1 ATTTT

       1487 TTTAAAAAGG


Statistics
Matches: 282,  Mismatches: 56, Indels: 46
        0.73            0.15        0.12

Matches are distributed among these distances:
  28   11  0.04
  29  122  0.43
  30  116  0.41
  31   15  0.05
  32   18  0.06

ACGTcount: A:0.37, C:0.03, G:0.24, T:0.37


Consensus pattern (28 bp):   
ATTTTGGAAAGTTTAGGGTCAAAATGTA

Found at i:1318 original size:59 final size:60

Alignment explanation


    Indices: 1077--1465  Score: 247
    Period size: 59  Copynumber: 6.6  Consensus size: 60

       1067 GAAGTTTCAA

                          *                         *   *       *   *  * 
       1077 AGAA-TTT-GGGGTTAAAATG--ATTTTGGAAAAGTTTAGAGGTAAAAATGTAATTATTGG
          1 AGAAGTTTAGGGGTCAAAATGTAATTTTGGAAAAGTTT-GGGGTCAAAATGTGATTTTTAG

                *     *                               *                * 
       1134 A-AAATTTA-TGGTCAAAATGTAATTTTAGGAAAA-TTTGGGTTCAAAATGTGA-TTTTGG
          1 AGAAGTTTAGGGGTCAAAATGTAATTTT-GGAAAAGTTTGGGGTCAAAATGTGATTTTTAG

                              *                        **   *             *  
       1191 A-AAGGTTTA-GGGTCAAGATGTAATTTTTGG-AAAGTTTATTAAGGTTAAAATGTGATTTTAAG
          1 AGAA-GTTTAGGGGTCAAAATGTAA-TTTTGGAAAAG--T-TTGGGGTCAAAATGTGATTTTTAG

                          *                  *                          
       1253 A-AAGTTTAGGGGTTAAAATGTAATTTTGGAAAGGTTTGGGGTCAAAATGT-ATTTTTAG
          1 AGAAGTTTAGGGGTCAAAATGTAATTTTGGAAAAGTTTGGGGTCAAAATGTGATTTTTAG

                                          *    ** *** * *       * *      
       1311 AGAAGTTT-GGTGGTCAAAATGTAATTTTGTAAAAAATAATGTTTAAAATG-CAATTTTAG
          1 AGAAGTTTAGG-GGTCAAAATGTAATTTTGGAAAAGTTTGGGGTCAAAATGTGATTTTTAG

                            *   *                             **   *    * 
       1370 AGAAGTTT-GGTGGTCGAAACGTAATTTTGGAAAAGTTTAGGGGT-AAAAAAT-AATTTTGG
          1 AGAAGTTTAGG-GGTCAAAATGTAATTTTGGAAAAGTTT-GGGGTCAAAATGTGATTTTTAG

                                 *      *        
       1429 AGAAGTTTAGGGGTCAAAATGAAATTTTAGAAAAGTT
          1 AGAAGTTTAGGGGTCAAAATGTAATTTTGGAAAAGTT

       1466 CAAGTGTCAA


Statistics
Matches: 262,  Mismatches: 50, Indels: 38
        0.75            0.14        0.11

Matches are distributed among these distances:
  56    2  0.01
  57   24  0.09
  58   39  0.15
  59  139  0.53
  60   12  0.05
  61   24  0.09
  62   22  0.08

ACGTcount: A:0.37, C:0.02, G:0.24, T:0.36


Consensus pattern (60 bp):   
AGAAGTTTAGGGGTCAAAATGTAATTTTGGAAAAGTTTGGGGTCAAAATGTGATTTTTAG
Done.