Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010256.1 Kokia drynarioides strain JFW-HI SEQ_125093, 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, 727

Length: 1212
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.31


Found at i:752 original size:29 final size:29

Alignment explanation


    Indices: 720--783  Score: 76
    Period size: 30  Copynumber: 2.2  Consensus size: 29

        710 TAAAAGGGTA

                                *         
        720 ATTTT-GAAGGTTTTAAGGTTAAAAATGGG
          1 ATTTTAGAA-GTTTTAAGGTCAAAAATGGG

                           **             
        749 ATTTTTAGAAGTTTTGGGGTCAAAAATGGG
          1 A-TTTTAGAAGTTTTAAGGTCAAAAATGGG

                 
        779 ATTTT
          1 ATTTT

        784 TGGAAGTTCA


Statistics
Matches: 30,  Mismatches: 3, Indels: 4
        0.81            0.08        0.11

Matches are distributed among these distances:
  29    5  0.17
  30   22  0.73
  31    3  0.10

ACGTcount: A:0.31, C:0.02, G:0.27, T:0.41


Consensus pattern (29 bp):   
ATTTTAGAAGTTTTAAGGTCAAAAATGGG

Found at i:774 original size:30 final size:29

Alignment explanation


    Indices: 739--1057  Score: 299
    Period size: 30  Copynumber: 10.8  Consensus size: 29

        729 GTTTTAAGGT

                            *            
        739 TAAAAATGGGATTTTTAGAAGTTTTGGGG
          1 TAAAAATGGGATTTTTGGAAGTTTTGGGG

                                    **    
        768 TCAAAAATGGGATTTTTGGAAGTTCAGGGG
          1 T-AAAAATGGGATTTTTGGAAGTTTTGGGG

                 *                    *   
        798 TAAAAGT-GGATTTTTTGGAAGTTTTTGGG
          1 TAAAAATGGGA-TTTTTGGAAGTTTTGGGG

                  *     *            *     
        827 TCAAAAGTGGGAATTTTGGAAG-TTCGGGAG
          1 T-AAAAATGGGATTTTTGGAAGTTTTGGG-G

                     *     *             
        857 TAAAAATGGAATTTTGGGAAGTTTTGGGG
          1 TAAAAATGGGATTTTTGGAAGTTTTGGGG

                             *             
        886 TTAAAAATGGGATTTTTAGAAG-TTTGAGGG
          1 -TAAAAATGGGATTTTTGGAAGTTTTG-GGG

                      *                   
        916 T-AAAATGGTAATTTTTGGAAGTTTTGGGG
          1 TAAAAATGG-GATTTTTGGAAGTTTTGGGG

                                    ***   
        945 TTAAAAATGGGATTTTTGGAAGTTCAAGGG
          1 -TAAAAATGGGATTTTTGGAAGTTTTGGGG

                     **                   
        975 T-AAAATGATAATTTTTGGAAGTTTTGGGG
          1 TAAAAATG-GGATTTTTGGAAGTTTTGGGG

                         *           *     
       1004 TCAAAAATGGGATCTTTGGAAG-TTCGAGGG
          1 T-AAAAATGGGATTTTTGGAAGTTTTG-GGG

                 *  **              
       1034 TAAAATTGTAATTTTTGGAAGTTT
          1 TAAAAATGGGATTTTTGGAAGTTT

       1058 AGGGACCTAC


Statistics
Matches: 236,  Mismatches: 37, Indels: 33
        0.77            0.12        0.11

Matches are distributed among these distances:
  28   16  0.07
  29   98  0.42
  30  106  0.45
  31   16  0.07

ACGTcount: A:0.30, C:0.03, G:0.31, T:0.36


Consensus pattern (29 bp):   
TAAAAATGGGATTTTTGGAAGTTTTGGGG

Found at i:783 original size:59 final size:59

Alignment explanation


    Indices: 731--1057  Score: 390
    Period size: 59  Copynumber: 5.5  Consensus size: 59

        721 TTTTGAAGGT

                   *         *      *                                  
        731 TTTAAGGTTAAAAATGGGATTTTTAGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG
          1 TTTAAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG

              * *        *    *              *         *     *         
        790 TTCAGGGGTAAAAGTGGATTTTTTGGAAGTTTTTGGGTCAAAAGTGGGAATTTTGGAAG
          1 TTTAAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG

               **                   *              *               *    
        849 -TTCGGGAGTAAAAATGGAATTTTGGGAAGTTTTGGGGTTAAAAATGGGATTTTTAGAAG
          1 TTTAAGG-GTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG

               *                                   *                    
        908 TTTGAGGGT-AAAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAG
          1 TTTAAGGGTAAAAATGG-AATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG

              *              *                                 *        
        967 TTCAAGGGT-AAAATGATAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATCTTTGGAAG
          1 TTTAAGGGTAAAAATG-GAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG

              **         *  *               
       1026 TTCGAGGGTAAAATTGTAATTTTTGGAAGTTT
          1 TTTAAGGGTAAAAATGGAATTTTTGGAAGTTT

       1058 AGGGACCTAC


Statistics
Matches: 232,  Mismatches: 31, Indels: 10
        0.85            0.11        0.04

Matches are distributed among these distances:
  58   11  0.05
  59  212  0.91
  60    9  0.04

ACGTcount: A:0.30, C:0.02, G:0.31, T:0.37


Consensus pattern (59 bp):   
TTTAAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG

Done.