Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018397364.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1078.0, 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: 37762
ACGTcount: A:0.20, C:0.09, G:0.10, T:0.20

Warning! 15714 characters in sequence are not A, C, G, or T


Found at i:8058 original size:15 final size:17

Alignment explanation


    Indices: 8032--8064  Score: 52
    Period size: 16  Copynumber: 2.1  Consensus size: 17

       8022 CAAATTTTTA

                             
       8032 GTTTTATTTTTGT-AAT
          1 GTTTTATTTTTGTCAAT

                             
       8048 GTTTT-TTTTTGTCAAT
          1 GTTTTATTTTTGTCAAT

             
       8064 G
          1 G

       8065 CATTCTGGTT


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  15    7  0.44
  16    9  0.56

ACGTcount: A:0.15, C:0.03, G:0.15, T:0.67


Consensus pattern (17 bp):   
GTTTTATTTTTGTCAAT

Found at i:11574 original size:28 final size:28

Alignment explanation


    Indices: 11490--11576  Score: 86
    Period size: 28  Copynumber: 3.1  Consensus size: 28

      11480 TATATTTTAT

                                       *
      11490 TTTTTTATAGCTTTATCTTTTTTCTTTT
          1 TTTTTTATAGCTTTATCTTTTTTCTTTC

                  *  **      * ** *  *  
      11518 TTTTTTGTAAATTT-TCCTACTGCTATC
          1 TTTTTTATAGCTTTATCTTTTTTCTTTC

                                        
      11545 TTTTTTATAGCTTTATCTTTTTTCTTTC
          1 TTTTTTATAGCTTTATCTTTTTTCTTTC

                
      11573 TTTT
          1 TTTT

      11577 ATTTTTTATA


Statistics
Matches: 41,  Mismatches: 17, Indels: 2
        0.68            0.28        0.03

Matches are distributed among these distances:
  27   18  0.44
  28   23  0.56

ACGTcount: A:0.13, C:0.14, G:0.05, T:0.69


Consensus pattern (28 bp):   
TTTTTTATAGCTTTATCTTTTTTCTTTC

Found at i:13432 original size:11 final size:12

Alignment explanation


    Indices: 13416--13444  Score: 51
    Period size: 12  Copynumber: 2.5  Consensus size: 12

      13406 CTAGGCTGGT

                        
      13416 TTTATTTG-ATA
          1 TTTATTTGAATA

                        
      13427 TTTATTTGAATA
          1 TTTATTTGAATA

                  
      13439 TTTATT
          1 TTTATT

      13445 ATTTTTATTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  11    8  0.47
  12    9  0.53

ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66


Consensus pattern (12 bp):   
TTTATTTGAATA

Found at i:15787 original size:66 final size:66

Alignment explanation


    Indices: 15678--15810  Score: 257
    Period size: 66  Copynumber: 2.0  Consensus size: 66

      15668 NNNNNNNNNN

                                                                             
      15678 TAACAATAATAATGGCAATAATGCCATTAATTTGGTTCCCAAAGCAAATAGAGCCCTACGAGATG
          1 TAACAATAATAATGGCAATAATGCCATTAATTTGGTTCCCAAAGCAAATAGAGCCCTACGAGATG

             
      15743 A
         66 A

                                                  *                          
      15744 TAACAATAATAATGGCAATAATGCCATTAATTTGGTTCTCAAAGCAAATAGAGCCCTACGAGATG
          1 TAACAATAATAATGGCAATAATGCCATTAATTTGGTTCCCAAAGCAAATAGAGCCCTACGAGATG

             
      15809 A
         66 A

             
      15810 T
          1 T

      15811 GCTATTCCTC


Statistics
Matches: 66,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  66   66  1.00

ACGTcount: A:0.41, C:0.17, G:0.17, T:0.26


Consensus pattern (66 bp):   
TAACAATAATAATGGCAATAATGCCATTAATTTGGTTCCCAAAGCAAATAGAGCCCTACGAGATG
A

Found at i:20359 original size:37 final size:37

Alignment explanation


    Indices: 20318--20401  Score: 143
    Period size: 37  Copynumber: 2.3  Consensus size: 37

      20308 TTCCTGTGGG

                                                 
      20318 ATCGATACTTTACTTGTTAATATACTGTATATTCGAT
          1 ATCGATACTTTACTTGTTAATATACTGTATATTCGAT

                                    *            
      20355 ATCGATACTTTACTTGTTAATATATTGTATATTCGAT
          1 ATCGATACTTTACTTGTTAATATACTGTATATTCGAT

                       
      20392 A-CGTATACTT
          1 ATCG-ATACTT

      20402 GTATAGTAAA


Statistics
Matches: 45,  Mismatches: 1, Indels: 2
        0.94            0.02        0.04

Matches are distributed among these distances:
  36    2  0.04
  37   43  0.96

ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46


Consensus pattern (37 bp):   
ATCGATACTTTACTTGTTAATATACTGTATATTCGAT

Found at i:35546 original size:32 final size:32

Alignment explanation


    Indices: 35485--35546  Score: 97
    Period size: 32  Copynumber: 1.9  Consensus size: 32

      35475 CCAAATCAAA

                                  *         
      35485 AAAATAGTTTATGAAGTATTTATGCGATATGG
          1 AAAATAGTTTATGAAGTATTTAGGCGATATGG

                           *        *     
      35517 AAAATAGTTTATGAATTATTTAGGTGATAT
          1 AAAATAGTTTATGAAGTATTTAGGCGATAT

      35547 AAATTATTCC


Statistics
Matches: 27,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  32   27  1.00

ACGTcount: A:0.39, C:0.02, G:0.19, T:0.40


Consensus pattern (32 bp):   
AAAATAGTTTATGAAGTATTTAGGCGATATGG
Done.