Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010240.1 Kokia drynarioides strain JFW-HI SEQ_125072, 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: 3468
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25


Found at i:2895 original size:201 final size:201

Alignment explanation


    Indices: 2543--2919  Score: 565
    Period size: 201  Copynumber: 1.9  Consensus size: 201

       2533 AAAGCAAGCA

                    *  *    *    *        *                        *         
       2543 AAATCTTCGAACCCCAGCTTCTTGATGAGATACCGAGAAGCAGGTCGAAGCAATAGACGGTTAGC
          1 AAATCTTCAAAACCCAACTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAACGGTTAGC

                 *                                             * *           
       2608 TTCCTGATAAGATACGGAGAAGTGAACCAAATTAGTCTTCCTGATGAGATATAGAGAAGCGGATT
         66 TTCCTAATAAGATACGGAGAAGTGAACCAAATTAGTCTTCCTGATGAGATACAAAGAAGCGGATT

                    *  * *                     *                             
       2673 GAAACAAGTGATGTAGTCATTTTCCTGATGAGACATTGAGAAGAAGACCCAAACGAGGCTTGAAA
        131 GAAACAAGCGACGCAGTCATTTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTTGAAA

                  
       2738 CGAGCG
        196 CGAGCG

                                             *           *           *       
       2744 AAATCTTCAAAACCCAACTTCCTGATGAGACACTGAGAAGCAGGTGGAAGCAATAAATGGTTAGC
          1 AAATCTTCAAAACCCAACTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAACGGTTAGC

                    *      *                 *                               
       2809 TTCCTAATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCGGATT
         66 TTCCTAATAAGATACGGAGAAGTGAACCAAATTAGTCTTCCTGATGAGATACAAAGAAGCGGATT

                          *                  *            
       2874 GAAACAAGCGACGCGGTCATTTTCCTGATGAGATACTGAGAAGAAG
        131 GAAACAAGCGACGCAGTCATTTTCCTGATGAGACACTGAGAAGAAG

       2920 GTCAAGTTAA


Statistics
Matches: 155,  Mismatches: 21, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
 201  155  1.00

ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22


Consensus pattern (201 bp):   
AAATCTTCAAAACCCAACTTCCTGATGAGACACCGAGAAGCAGGTCGAAGCAATAAACGGTTAGC
TTCCTAATAAGATACGGAGAAGTGAACCAAATTAGTCTTCCTGATGAGATACAAAGAAGCGGATT
GAAACAAGCGACGCAGTCATTTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTTGAAA
CGAGCG

Found at i:3283 original size:16 final size:18

Alignment explanation


    Indices: 3230--3323  Score: 95
    Period size: 18  Copynumber: 5.4  Consensus size: 18

       3220 CCAAACTCCC

                          *   
       3230 TTTAAATTTATTTTAAAA
          1 TTTAAATTTATTTTCAAA

            *        *   **   
       3248 ATTAAATTTGTTTAAAAA
          1 TTTAAATTTATTTTCAAA

                              
       3266 TTTAAA-TTATTTTC-AA
          1 TTTAAATTTATTTTCAAA

                              
       3282 TTTAAATTTATTTTCAAA
          1 TTTAAATTTATTTTCAAA

                  *   * *     
       3300 TTTAAAATTACTAT-AAA
          1 TTTAAATTTATTTTCAAA

                   
       3317 TTTAAAT
          1 TTTAAAT

       3324 AAAGCTAAAA


Statistics
Matches: 63,  Mismatches: 11, Indels: 5
        0.80            0.14        0.06

Matches are distributed among these distances:
  16    8  0.13
  17   22  0.35
  18   33  0.52

ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51


Consensus pattern (18 bp):   
TTTAAATTTATTTTCAAA

Found at i:3308 original size:35 final size:35

Alignment explanation


    Indices: 3230--3323  Score: 100
    Period size: 35  Copynumber: 2.7  Consensus size: 35

       3220 CCAAACTCCC

                  *           *        *        
       3230 TTTAAATTTATTTTAAAAATTAAATTTGTTTAAAAA
          1 TTTAAAATTATTTT-AAATTTAAATTTATTTAAAAA

                          *               **   
       3266 TTT-AAATTATTTTCAATTTAAATTTATTTTCAAA
          1 TTTAAAATTATTTTAAATTTAAATTTATTTAAAAA

                      * *           
       3300 TTTAAAATTACTATAAATTTAAAT
          1 TTTAAAATTATTTTAAATTTAAAT

       3324 AAAGCTAAAA


Statistics
Matches: 48,  Mismatches: 9, Indels: 3
        0.80            0.15        0.05

Matches are distributed among these distances:
  34   19  0.40
  35   26  0.54
  36    3  0.06

ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51


Consensus pattern (35 bp):   
TTTAAAATTATTTTAAATTTAAATTTATTTAAAAA
Done.