Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018399763.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3005.0, 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: 2751
ACGTcount: A:0.22, C:0.09, G:0.13, T:0.22

Warning! 952 characters in sequence are not A, C, G, or T


Found at i:2390 original size:22 final size:21

Alignment explanation


    Indices: 2316--2390  Score: 87
    Period size: 21  Copynumber: 3.5  Consensus size: 21

       2306 TACCCAAATA

                  *              
       2316 TTTTGAGAATGTACTTGGAGG
          1 TTTTGAAAATGTACTTGGAGG

                 *         * * **
       2337 TTTTGGAAATGTACTCGAAAA
          1 TTTTGAAAATGTACTTGGAGG

                                 
       2358 TTTTGAAAATGTACTTGGAGG
          1 TTTTGAAAATGTACTTGGAGG

                        
       2379 TTTTAGAAAATG
          1 TTTT-GAAAATG

       2391 CACCTAGAGA


Statistics
Matches: 42,  Mismatches: 11, Indels: 1
        0.78            0.20        0.02

Matches are distributed among these distances:
  21   35  0.83
  22    7  0.17

ACGTcount: A:0.32, C:0.05, G:0.25, T:0.37


Consensus pattern (21 bp):   
TTTTGAAAATGTACTTGGAGG

Found at i:2512 original size:21 final size:21

Alignment explanation


    Indices: 2486--2559  Score: 69
    Period size: 21  Copynumber: 3.5  Consensus size: 21

       2476 AGGTTTTATA

                                 
       2486 AGAATGTACTTGGAGGTTTTG
          1 AGAATGTACTTGGAGGTTTTG

                   * * *          
       2507 AGAATGTGCCTAGAGGTTTTAG
          1 AGAATGTACTTGGAGGTTTT-G

             *       *     *     
       2529 AAAATGTACATGGAGATTTT-
          1 AGAATGTACTTGGAGGTTTTG

                       
       2549 AGAGATGTACT
          1 AGA-ATGTACT

       2560 CGAAGCTTTT


Statistics
Matches: 41,  Mismatches: 10, Indels: 4
        0.75            0.18        0.07

Matches are distributed among these distances:
  20    2  0.05
  21   23  0.56
  22   16  0.39

ACGTcount: A:0.31, C:0.07, G:0.28, T:0.34


Consensus pattern (21 bp):   
AGAATGTACTTGGAGGTTTTG

Found at i:2548 original size:22 final size:22

Alignment explanation


    Indices: 2476--2551  Score: 73
    Period size: 22  Copynumber: 3.5  Consensus size: 22

       2466 AATTACTTGA

                    *          *   
       2476 AGGTTTTATAAGAATGTACTTGG
          1 AGGTTTTAGAA-AATGTACATGG

                      *     * * * 
       2499 AGGTTTT-GAGAATGTGCCTAG
          1 AGGTTTTAGAAAATGTACATGG

                                  
       2520 AGGTTTTAGAAAATGTACATGG
          1 AGGTTTTAGAAAATGTACATGG

              *       
       2542 AGATTTTAGA
          1 AGGTTTTAGA

       2552 GATGTACTCG


Statistics
Matches: 42,  Mismatches: 10, Indels: 3
        0.76            0.18        0.05

Matches are distributed among these distances:
  21   15  0.36
  22   20  0.48
  23    7  0.17

ACGTcount: A:0.32, C:0.05, G:0.28, T:0.36


Consensus pattern (22 bp):   
AGGTTTTAGAAAATGTACATGG
Done.