Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006928.1 Kokia drynarioides strain JFW-HI SEQ_121531, 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, 964

Length: 1608
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.31


Found at i:242 original size:59 final size:59

Alignment explanation


    Indices: 178--635  Score: 516
    Period size: 59  Copynumber: 7.8  Consensus size: 59

        168 ATTCGAGGTT

                      *     *                                *         
        178 AAAAATGGGAATTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGATTTAGGGTC
          1 AAAAATGGGATTTTTGAAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTC

            *      *        *        *                  **         *     
        237 GAAAATGAGATTTTTGGAA-TGTCGGGGGTAAAAATGGAATTATAAGG-AGTTTTGGGGTC
          1 AAAAATGGGATTTTTGAAAGT-TCGAGGGTAAAAATGGAATT-TTTGGAAGTTTTAGGGTC

                   *                *                             *     
        296 AAAAATGAGATTTTTGAAAGTTCGGGGGTAAAAAT-GAATTTTTTGGAAGTTTTTGGGTC
          1 AAAAATGGGATTTTTGAAAGTTCGAGGGTAAAAATGGAA-TTTTTGGAAGTTTTAGGGTC

                                                     *    *      *     
        355 AAAAATGGGATTTTTGAAAGTTCGAGGGTAAAAATGGAATTCTTGGGAGTTTTGGGGTC
          1 AAAAATGGGATTTTTGAAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTC

                           *        *          *          *            
        414 -AAAATGGGATTTTTAAAAGTTCGGGGGTAAAAATAGAATTTTTGGGAG-TTTAGGGT-
          1 AAAAATGGGATTTTTGAAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTC

            *               *      * *                *    *            
        470 TAAAATGGGATTTTTGGAAGTTTGGGGGGTAAAAATGGAATTCTTGGGAGTTTTAGGGTC
          1 AAAAATGGGATTTTTGAAAG-TTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTC

                            *      *                      *      *    *
        530 AAAAATGGGATTTTTGGAAGTTCAAGGGTAAAAATGGAATTTTTGGGAGTTTTGGGGTT
          1 AAAAATGGGATTTTTGAAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTC

                   *                           **           
        589 AAAAATGAGATTTTTGAAAGTTCCG-GGGTAAAAACAGAATTTTTGGA
          1 AAAAATGGGATTTTTGAAAGTT-CGAGGGTAAAAATGGAATTTTTGGA

        636 CAATTTAGGG


Statistics
Matches: 347,  Mismatches: 41, Indels: 22
        0.85            0.10        0.05

Matches are distributed among these distances:
  57   24  0.07
  58   77  0.22
  59  219  0.63
  60   27  0.08

ACGTcount: A:0.33, C:0.03, G:0.31, T:0.33


Consensus pattern (59 bp):   
AAAAATGGGATTTTTGAAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTC

Found at i:324 original size:30 final size:28

Alignment explanation


    Indices: 177--622  Score: 294
    Period size: 29  Copynumber: 15.2  Consensus size: 28

        167 AATTCGAGGT

                       *                  
        177 TAAAAATGGGAATTTTGGAAGTTC-GAGGG
          1 TAAAAAT-GGATTTTTGGAAGTTCTG-GGG

                                      *   
        206 TAAAAATGGAATTTTTGGAAGATT-TAGGG
          1 TAAAAATGG-ATTTTTGGAAG-TTCTGGGG

              *                       *    
        235 TCGAAAATGAGATTTTTGGAA-TGTCGGGGG
          1 T-AAAAATG-GATTTTTGGAAGT-TCTGGGG

                           **       *     
        265 TAAAAATGGAATTATAAGG-AGTTTTGGGG
          1 TAAAAATGG-ATT-TTTGGAAGTTCTGGGG

                              *      *    
        294 TCAAAAATGAGATTTTTGAAAGTTCGGGGG
          1 T-AAAAATG-GATTTTTGGAAGTTCTGGGG

                    *              * *   
        324 TAAAAATGAATTTTTTGGAAGTTTTTGGG
          1 TAAAAATGGA-TTTTTGGAAGTTCTGGGG

                              *            
        353 TCAAAAATGGGATTTTTGAAAGTTC-GAGGG
          1 T-AAAAAT-GGATTTTTGGAAGTTCTG-GGG

                         *    *    *     
        383 TAAAAATGGAATTCTTGGGAGTTTTGGGG
          1 TAAAAATGG-ATTTTTGGAAGTTCTGGGG

             *              **      *    
        412 TCAAAATGGGATTTTTAAAAGTTCGGGGG
          1 TAAAAAT-GGATTTTTGGAAGTTCTGGGG

                     *        *      *   
        441 TAAAAATAGAATTTTTGGGAGTT-TAGGG
          1 TAAAAAT-GGATTTTTGGAAGTTCTGGGG

             *                             
        469 TTAAAATGGGATTTTTGGAAGTT-TGGGGGG
          1 TAAAAAT-GGATTTTTGGAAGTTCT--GGGG

                         *    *    * *   
        499 TAAAAATGGAATTCTTGGGAGTTTTAGGG
          1 TAAAAATGG-ATTTTTGGAAGTTCTGGGG

                                     **   
        528 TCAAAAATGGGATTTTTGGAAGTTCAAGGG
          1 T-AAAAAT-GGATTTTTGGAAGTTCTGGGG

                              *    *     
        558 TAAAAATGGAATTTTTGGGAGTTTTGGGG
          1 TAAAAATGG-ATTTTTGGAAGTTCTGGGG

                              *      *    
        587 TTAAAAATGAGATTTTTGAAAGTTCCGGGG
          1 -TAAAAATG-GATTTTTGGAAGTTCTGGGG

                  
        617 TAAAAA
          1 TAAAAA

        623 CAGAATTTTT


Statistics
Matches: 324,  Mismatches: 64, Indels: 58
        0.73            0.14        0.13

Matches are distributed among these distances:
  28   32  0.10
  29  150  0.46
  30  134  0.41
  31    8  0.02

ACGTcount: A:0.33, C:0.03, G:0.31, T:0.33


Consensus pattern (28 bp):   
TAAAAATGGATTTTTGGAAGTTCTGGGG

Found at i:1580 original size:17 final size:17

Alignment explanation


    Indices: 1560--1597  Score: 51
    Period size: 17  Copynumber: 2.2  Consensus size: 17

       1550 ATTTTCCTTT

                              
       1560 TATTATTAT-TTTATTAA
          1 TATTATTATATTTATT-A

                   *         
       1577 TATTATTGTATTTATTA
          1 TATTATTATATTTATTA

                
       1594 TATT
          1 TATT

       1598 TATTGTTATT


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  17   13  0.68
  18    6  0.32

ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66


Consensus pattern (17 bp):   
TATTATTATATTTATTA
Done.