Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005912.1 Kokia drynarioides strain JFW-HI SEQ_120272, 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: 6540
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34


Found at i:2515 original size:90 final size:89

Alignment explanation


    Indices: 2358--2584  Score: 267
    Period size: 90  Copynumber: 2.5  Consensus size: 89

       2348 AGAAATCGAG

                                  *               *       **    *   *     *  
       2358 GTCAAAATGTAATTTTGGAAAAATTTAAGGGTTAAAATGTAATTTTAAGAAAGTTTGAGGGTTAA
          1 GTCAAAATGTAATTTTGGAAAAGTTTAAGGGTTAAAATATAATTTTGGGAAAATTTAAGGGTCAA

                 *  *    *  *        
       2423 AATGTGATTTTGGGAAGGTTTGAGA
         66 AATGTAATGTTGGAAAAGTTT-AGA

                      *       *                                              
       2448 GTCAAAATGTGATTTTGGGAAAGTTTAAGGGTTAAAATATAATTTTGGGAAAATTTAAGGGTCAA
          1 GTCAAAATGTAATTTTGGAAAAGTTTAAGGGTTAAAATATAATTTTGGGAAAATTTAAGGGTCAA

                                   *
       2513 AATGTAATGTTGGAAAAGTTTAGG
         66 AATGTAATGTTGGAAAAGTTTAGA

                     *       *         *               *     
       2537 GAT-AAAATATAATTTTAGAAAAGTTTGAGGGTTAAAATATAAGTTTGG
          1 G-TCAAAATGTAATTTTGGAAAAGTTTAAGGGTTAAAATATAATTTTGG

       2585 ACAAGTTTGT


Statistics
Matches: 116,  Mismatches: 20, Indels: 3
        0.83            0.14        0.02

Matches are distributed among these distances:
  89   42  0.36
  90   74  0.64

ACGTcount: A:0.39, C:0.01, G:0.25, T:0.35


Consensus pattern (89 bp):   
GTCAAAATGTAATTTTGGAAAAGTTTAAGGGTTAAAATATAATTTTGGGAAAATTTAAGGGTCAA
AATGTAATGTTGGAAAAGTTTAGA

Found at i:2593 original size:30 final size:30

Alignment explanation


    Indices: 2361--2604  Score: 240
    Period size: 30  Copynumber: 8.2  Consensus size: 30

       2351 AATCGAGGTC

                           *   *   *      
       2361 AAAATGTAATTTTGGAAAAATTTAAGGGTT
          1 AAAATGTAATTTTGGGAAAGTTTGAGGGTT

                         **               
       2391 AAAATGTAATTTTAAGAAAGTTTGAGGGTT
          1 AAAATGTAATTTTGGGAAAGTTTGAGGGTT

                   *          *       *  *
       2421 AAAATGTGATTTTGGGAAGGTTTGAGAGTC
          1 AAAATGTAATTTTGGGAAAGTTTGAGGGTT

                   *               *      
       2451 AAAATGTGATTTTGGGAAAGTTTAAGGGTT
          1 AAAATGTAATTTTGGGAAAGTTTGAGGGTT

                 *             *   *     *
       2481 AAAATATAATTTTGGGAAAATTTAAGGGTC
          1 AAAATGTAATTTTGGGAAAGTTTGAGGGTT

                      *    *            * 
       2511 AAAATGTAATGTTGGAAAAGTTT-AGGGAT
          1 AAAATGTAATTTTGGGAAAGTTTGAGGGTT

                 *       * *              
       2540 AAAATATAATTTTAGAAAAGTTTGAGGGTT
          1 AAAATGTAATTTTGGGAAAGTTTGAGGGTT

                 *   *               **    
       2570 AAAATATAAGTTT-GGACAAGTTTGTTGGTT
          1 AAAATGTAATTTTGGGA-AAGTTTGAGGGTT

                 
       2600 AAAAT
          1 AAAAT

       2605 ATGATTTTTA


Statistics
Matches: 179,  Mismatches: 33, Indels: 4
        0.83            0.15        0.02

Matches are distributed among these distances:
  29   26  0.15
  30  153  0.85

ACGTcount: A:0.39, C:0.01, G:0.24, T:0.35


Consensus pattern (30 bp):   
AAAATGTAATTTTGGGAAAGTTTGAGGGTT

Found at i:4565 original size:20 final size:20

Alignment explanation


    Indices: 4540--4587  Score: 71
    Period size: 20  Copynumber: 2.4  Consensus size: 20

       4530 AAATAATTTT

                        *        
       4540 AATAATTTTAAATTTTAG-AA
          1 AATAATTTTAAAATTT-GTAA

                                
       4560 AATAATTTTAAAATTTGTAA
          1 AATAATTTTAAAATTTGTAA

                    
       4580 AATAATTT
          1 AATAATTT

       4588 GCTGACATGG


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  19    1  0.04
  20   25  0.96

ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46


Consensus pattern (20 bp):   
AATAATTTTAAAATTTGTAA

Found at i:4570 original size:29 final size:30

Alignment explanation


    Indices: 4506--4580  Score: 91
    Period size: 29  Copynumber: 2.5  Consensus size: 30

       4496 ATTAAAATTA

                          *                
       4506 TTTAATAATTTTATTATTTCAAAAAAATAAT
          1 TTTAATAATTTTA-AATTTCAAAAAAATAAT

                               * *        
       4537 TTTAATAATTTTAAATTT-TAGAAAATAAT
          1 TTTAATAATTTTAAATTTCAAAAAAATAAT

                            
       4566 TTTAA-AATTTGTAAA
          1 TTTAATAATTT-TAAA

       4581 ATAATTTGCT


Statistics
Matches: 40,  Mismatches: 3, Indels: 4
        0.85            0.06        0.09

Matches are distributed among these distances:
  28    5  0.12
  29   18  0.45
  30    4  0.10
  31   13  0.32

ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48


Consensus pattern (30 bp):   
TTTAATAATTTTAAATTTCAAAAAAATAAT
Done.