Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001529.1 Kokia drynarioides strain JFW-HI SEQ_113095, 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: 3538
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37


Found at i:49 original size:27 final size:29

Alignment explanation


    Indices: 17--70  Score: 76
    Period size: 29  Copynumber: 1.9  Consensus size: 29

          7 AAAGGGTCGA

                             *           
         17 AAAATG-GA-GTTTGGAGAGTTTAGGGTC
          1 AAAATGTGATGTTTGGAAAGTTTAGGGTC

                      *                
         44 AAAATGTGATTTTTGGAAAGTTTAGGG
          1 AAAATGTGATGTTTGGAAAGTTTAGGG

         71 GTTAAAATAT


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  27    6  0.26
  28    2  0.09
  29   15  0.65

ACGTcount: A:0.31, C:0.02, G:0.33, T:0.33


Consensus pattern (29 bp):   
AAAATGTGATGTTTGGAAAGTTTAGGGTC

Found at i:86 original size:30 final size:30

Alignment explanation


    Indices: 26--149  Score: 106
    Period size: 30  Copynumber: 4.1  Consensus size: 30

         16 AAAAATGGAG

                  *                 * *   
         26 TTTGGAGAGTTTA-GGGTCAAAATGTGATT
          1 TTTGGAAAGTTTAGGGGTCAAAATATAATT

                              *            
         55 TTTGGAAAGTTTAGGGGTTAAAATATAATTT
          1 TTTGGAAAGTTTAGGGGTCAAAATATAA-TT

               *          *  * *           
         86 TTTTGAGAAGTTTATGGATAAAAATATAATT
          1 TTTGGA-AAGTTTAGGGGTCAAAATATAATT

               **       *         * *     
        117 TTTACAAAGTTTGGGGGTCAAAGTGTAATT
          1 TTTGGAAAGTTTAGGGGTCAAAATATAATT

               
        147 TTT
          1 TTT

        150 AAAGAAAATA


Statistics
Matches: 76,  Mismatches: 16, Indels: 5
        0.78            0.16        0.05

Matches are distributed among these distances:
  29   12  0.16
  30   32  0.42
  31   13  0.17
  32   19  0.25

ACGTcount: A:0.33, C:0.02, G:0.23, T:0.41


Consensus pattern (30 bp):   
TTTGGAAAGTTTAGGGGTCAAAATATAATT

Found at i:97 original size:32 final size:31

Alignment explanation


    Indices: 26--119  Score: 93
    Period size: 32  Copynumber: 3.1  Consensus size: 31

         16 AAAAATGGAG

                  *           *     * *    
         26 TTTGGAGAGTTTAGGG-TCAAAATGTGA-TT
          1 TTTGGAAAGTTTAGGGATAAAAATATAATTT

                            * *            
         55 TTTGGAAAGTTTAGGGGTTAAAATATAATTT
          1 TTTGGAAAGTTTAGGGATAAAAATATAATTT

               *          *                 
         86 TTTTGAGAAGTTTATGGATAAAAATATAATTT
          1 TTTGGA-AAGTTTAGGGATAAAAATATAATTT

              
        118 TT
          1 TT

        120 ACAAAGTTTG


Statistics
Matches: 54,  Mismatches: 8, Indels: 3
        0.83            0.12        0.05

Matches are distributed among these distances:
  29   15  0.28
  30    8  0.15
  31    7  0.13
  32   24  0.44

ACGTcount: A:0.34, C:0.01, G:0.22, T:0.43


Consensus pattern (31 bp):   
TTTGGAAAGTTTAGGGATAAAAATATAATTT

Found at i:2570 original size:22 final size:22

Alignment explanation


    Indices: 2542--2593  Score: 79
    Period size: 21  Copynumber: 2.4  Consensus size: 22

       2532 ATTTAATTTC

                       *          
       2542 AAAAAAAATTAGTAATT-AAAT
          1 AAAAAAAATTAATAATTCAAAT

                                  
       2563 AAAAAAAATTAATAATTCAAAT
          1 AAAAAAAATTAATAATTCAAAT

               *     
       2585 AAATAAAAT
          1 AAAAAAAAT

       2594 AGAACGAAGA


Statistics
Matches: 28,  Mismatches: 2, Indels: 1
        0.90            0.06        0.03

Matches are distributed among these distances:
  21   16  0.57
  22   12  0.43

ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27


Consensus pattern (22 bp):   
AAAAAAAATTAATAATTCAAAT
Done.