Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004772.1 Kokia drynarioides strain JFW-HI SEQ_118382, 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: 7433
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34


Found at i:54 original size:29 final size:28

Alignment explanation


    Indices: 1--248  Score: 130
    Period size: 30  Copynumber: 8.5  Consensus size: 28

                  *            **         
          1 AAAATGTAATTTTTGGAAAAATCGAGGTCA
          1 AAAATGGAATTTTTGG-AAGTTCGAGGT-A

                          *              
         31 AAAATGGAATTTTTCGAAGTTCGAGGGT-
          1 AAAATGGAATTTTTGGAAGTTCGA-GGTA

                               **          
         59 AAAATGGTAATTTTTGGAAAATC-ATGGTCA
          1 AAAATGG-AATTTTTGGAAGTTCGA-GGT-A

                 *       *        * *    
         89 AAAATTGAATTTTGGGAAGTTTAGGGGT-
          1 AAAATGGAATTTTTGGAAG-TTCGAGGTA

                   *           **         
        117 AAAATGGTATTTTTGGAAAAATCGAGGTAA
          1 AAAATGGAATTTTTGG-AAGTTCGAGGT-A

                                          
        147 AAAATGGAATTTTTTGGAAGTTCGGAGGT-
          1 AAAATGGAA-TTTTTGGAAGTTC-GAGGTA

                              *  *    *     
        176 -AAATGGTAATTTTTAGAAAAATT-GGGGTCA
          1 AAAATGG-AATTTTT-G-GAAGTTCGAGGT-A

                         * *     *       
        206 AAAATGGAATTTTAGAAAGTTTGAGGGTA
          1 AAAATGGAATTTTTGGAAGTTCGA-GGTA

                  *       
        235 AAAATGTAATTTTT
          1 AAAATGGAATTTTT

        249 TTGAAAATTT


Statistics
Matches: 167,  Mismatches: 32, Indels: 39
        0.70            0.13        0.16

Matches are distributed among these distances:
  28   49  0.29
  29   48  0.29
  30   52  0.31
  31   18  0.11

ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33


Consensus pattern (28 bp):   
AAAATGGAATTTTTGGAAGTTCGAGGTA

Found at i:91 original size:58 final size:59

Alignment explanation


    Indices: 1--248  Score: 296
    Period size: 58  Copynumber: 4.3  Consensus size: 59

                                                         *             
          1 AAAAT-GTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTCGAAGTTCGAGGGT
          1 AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGT

                                                 *       *        *      
         59 AAAATGGTAATTTTTGG-AAAATC-ATGGTCAAAAATTGAATTTTGGGAAGTT-TAGGGGT
          1 AAAATGGTAATTTTTGGAAAAATCGA-GGTCAAAAATGGAATTTTTGGAAGTTCGA-GGGT

                                         *                               
        117 AAAATGGT-ATTTTTGGAAAAATCGAGGTAAAAAATGGAATTTTTTGGAAGTTCG-GAGGT
          1 AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAA-TTTTTGGAAGTTCGAG-GGT

                           *       * *                  * *     *      
        176 -AAATGGTAATTTTTAGAAAAATTGGGGTCAAAAATGGAATTTTAGAAAGTTTGAGGGT
          1 AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGT

                            
        234 AAAAAT-GTAATTTTT
          1 -AAAATGGTAATTTTT

        249 TTGAAAATTT


Statistics
Matches: 163,  Mismatches: 15, Indels: 23
        0.81            0.07        0.11

Matches are distributed among these distances:
  57   10  0.06
  58   86  0.53
  59   63  0.39
  60    4  0.02

ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33


Consensus pattern (59 bp):   
AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGT

Found at i:269 original size:31 final size:30

Alignment explanation


    Indices: 176--278  Score: 102
    Period size: 31  Copynumber: 3.4  Consensus size: 30

        166 GTTCGGAGGT

                                *  *    *  
        176 AAATGGTAATTTTTAGAAAAATTGGGGTCAA
          1 AAAT-GTAATTTTTAGAAAATTTAGGGTTAA

                 *            *            
        207 AAATGGAA-TTTTAGAAAGTTTGAGGG-TAA
          1 AAATGTAATTTTTAGAAAATTT-AGGGTTAA

                          *                
        236 AAATGTAATTTTTTTGAAAATTTAGGGTTAA
          1 AAATGTAA-TTTTTAGAAAATTTAGGGTTAA

                *       
        267 AAATATAATTTT
          1 AAATGTAATTTT

        279 GGAGAATTTT


Statistics
Matches: 59,  Mismatches: 9, Indels: 9
        0.77            0.12        0.12

Matches are distributed among these distances:
  29   20  0.34
  30   14  0.24
  31   25  0.42

ACGTcount: A:0.42, C:0.01, G:0.19, T:0.38


Consensus pattern (30 bp):   
AAATGTAATTTTTAGAAAATTTAGGGTTAA

Found at i:1942 original size:17 final size:17

Alignment explanation


    Indices: 1902--1945  Score: 61
    Period size: 17  Copynumber: 2.6  Consensus size: 17

       1892 TTAAATTTCC

                             
       1902 AATTTAAATTTAAAATA
          1 AATTTAAATTTAAAATA

              *    *         
       1919 AACTTAACTTTAAAATA
          1 AATTTAAATTTAAAATA

             *        
       1936 ATTTTAAATT
          1 AATTTAAATT

       1946 CTGTTGGGCC


Statistics
Matches: 22,  Mismatches: 5, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  17   22  1.00

ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43


Consensus pattern (17 bp):   
AATTTAAATTTAAAATA
Done.