Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003279.1 Kokia drynarioides strain JFW-HI SEQ_115940, 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: 5022
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Found at i:612 original size:23 final size:25

Alignment explanation


    Indices: 550--613  Score: 69
    Period size: 27  Copynumber: 2.5  Consensus size: 25

        540 TTTTTTTACT

                  *                   *
        550 TATATTATAATAATATTATTAAAATAT
          1 TATATTTTAAT-A-ATTATTAAAATAA

                                      
        577 TATATTTTAAATAATTATT-AAATAA
          1 TATATTTT-AATAATTATTAAAATAA

                         
        602 TA-ATTTTAATAA
          1 TATATTTTAATAA

        614 AAAAAATCAA


Statistics
Matches: 34,  Mismatches: 2, Indels: 6
        0.81            0.05        0.14

Matches are distributed among these distances:
  23    5  0.15
  24    5  0.15
  25    7  0.21
  26    6  0.18
  27    8  0.24
  28    3  0.09

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (25 bp):   
TATATTTTAATAATTATTAAAATAA

Found at i:2457 original size:85 final size:85

Alignment explanation


    Indices: 2362--2533  Score: 317
    Period size: 85  Copynumber: 2.0  Consensus size: 85

       2352 TTTGAGGGTC

                          *                                                  
       2362 AAAGTGCAATTTTATCATTATTAATTTAAAATTTTATAAAGGTTAAATTACACCAACAGTCACTC
          1 AAAGTGCAATTTTACCATTATTAATTTAAAATTTTATAAAGGTTAAATTACACCAACAGTCACTC

                   *       *    
       2427 AATTTTGGGATAACTGACAA
         66 AATTTTGAGATAACTAACAA

                                                                             
       2447 AAAGTGCAATTTTACCATTATTAATTTAAAATTTTATAAAGGTTAAATTACACCAACAGTCACTC
          1 AAAGTGCAATTTTACCATTATTAATTTAAAATTTTATAAAGGTTAAATTACACCAACAGTCACTC

                                
       2512 AATTTTGAGATAACTAACAA
         66 AATTTTGAGATAACTAACAA

              
       2532 AA
          1 AA

       2534 CAATCACATT


Statistics
Matches: 84,  Mismatches: 3, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  85   84  1.00

ACGTcount: A:0.43, C:0.13, G:0.09, T:0.34


Consensus pattern (85 bp):   
AAAGTGCAATTTTACCATTATTAATTTAAAATTTTATAAAGGTTAAATTACACCAACAGTCACTC
AATTTTGAGATAACTAACAA

Found at i:2747 original size:17 final size:17

Alignment explanation


    Indices: 2723--2767  Score: 54
    Period size: 17  Copynumber: 2.6  Consensus size: 17

       2713 TTAGGATTTT

                             
       2723 AAGAAGAGAAAAAGAAG
          1 AAGAAGAGAAAAAGAAG

             *      * *      
       2740 ACGAAGAGGAGAAGAAG
          1 AAGAAGAGAAAAAGAAG

                       
       2757 AAGAAAGAGAA
          1 AAG-AAGAGAA

       2768 GAGAAAAAAT


Statistics
Matches: 22,  Mismatches: 5, Indels: 1
        0.79            0.18        0.04

Matches are distributed among these distances:
  17   16  0.73
  18    6  0.27

ACGTcount: A:0.64, C:0.02, G:0.33, T:0.00


Consensus pattern (17 bp):   
AAGAAGAGAAAAAGAAG

Found at i:2751 original size:20 final size:20

Alignment explanation


    Indices: 2723--2775  Score: 63
    Period size: 20  Copynumber: 2.6  Consensus size: 20

       2713 TTAGGATTTT

                                
       2723 AAGAAGAGAAAAAGAAGACG
          1 AAGAAGAGAAAAAGAAGACG

                *     *        *
       2743 AAGAGGAGAAGAAGAAGA-A
          1 AAGAAGAGAAAAAGAAGACG

                          
       2762 AGAGAAGAGAAAAA
          1 A-AGAAGAGAAAAA

       2776 ATGAGCTGCC


Statistics
Matches: 27,  Mismatches: 5, Indels: 2
        0.79            0.15        0.06

Matches are distributed among these distances:
  19    1  0.04
  20   26  0.96

ACGTcount: A:0.66, C:0.02, G:0.32, T:0.00


Consensus pattern (20 bp):   
AAGAAGAGAAAAAGAAGACG

Found at i:3199 original size:17 final size:16

Alignment explanation


    Indices: 3167--3198  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       3157 AAAAATGTGC

                 *          
       3167 AAAAATTCTTAATTTT
          1 AAAAAATCTTAATTTT

                            
       3183 AAAAAATCTTAATTTT
          1 AAAAAATCTTAATTTT

       3199 TGGATTTTGG


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47


Consensus pattern (16 bp):   
AAAAAATCTTAATTTT
Done.