Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018400858.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4027.0, 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: 3417
ACGTcount: A:0.22, C:0.08, G:0.09, T:0.22

Warning! 1341 characters in sequence are not A, C, G, or T


Found at i:586 original size:22 final size:22

Alignment explanation


    Indices: 558--614  Score: 105
    Period size: 22  Copynumber: 2.6  Consensus size: 22

        548 TATAGTCTGT

                                  
        558 TTTAACCAAAAATGTAAAAAAC
          1 TTTAACCAAAAATGTAAAAAAC

                                  
        580 TTTAACCAAAAATGTAAAAAAC
          1 TTTAACCAAAAATGTAAAAAAC

              *          
        602 TTCAACCAAAAAT
          1 TTTAACCAAAAAT

        615 AAATTATGGC


Statistics
Matches: 34,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  22   34  1.00

ACGTcount: A:0.58, C:0.16, G:0.04, T:0.23


Consensus pattern (22 bp):   
TTTAACCAAAAATGTAAAAAAC

Found at i:2741 original size:172 final size:168

Alignment explanation


    Indices: 2355--2882  Score: 581
    Period size: 172  Copynumber: 3.1  Consensus size: 168

       2345 NNNNNNNNNN

                             *     *             *     *          *      *   
       2355 ACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATTGTTTTATAATCTCAAAGTTGATTTAAA
          1 ACCCATTCCTTCAAAAGTCTTATGACTCACTTTAAATGGTTTTGTAATCTCAAAATTGATTAAAA

                   *        *                                        *   *   
       2420 TTTGAATACTTTGTACTTTTTTAGTTAAAATAGATTATAATTGAATGTCAACCTCAAAAAACATG
         66 TTTGAATTCTTTGTACATTTTTAGTTAAAA-AGATTATAATTGAATGTCAACCTCAAGAAATATG

                     *        *       *        *    
       2485 AAGAAAAAGGTTCATTGGTAAGAAAATTTCATTTACAGTC
        130 AAG-AAAAGATTCATTGGCAAGAAAAGTTCATTTATAGTC

                      *             *                            **********  
       2525 ACCCATTCCTCCAAAAGTCTTATGGCTCACTTTAAATGGTTTTGTAATCTCAANNNNNNNNNNAA
          1 ACCCATTCCTTCAAAAGTCTTATGACTCACTTTAAATGGTTTTGTAATCTCAAAATTGATTAAAA

                                                      *      *            *  
       2590 TTTGAATTCTTTGTACATTTTTAGTTACAAAAGATTATAATTCAATGTCGACCTCAAGAAATGTG
         66 TTTGAATTCTTTGTACATTTTTAGTTA-AAAAGATTATAATTGAATGTCAACCTCAAGAAATATG

                                               *      
       2655 AAGGTAAAAGCATTCATTGGCAAGAAAAGTTCATTAATAGTC
        130 AA-G-AAAAG-ATTCATTGGCAAGAAAAGTTCATTTATAGTC

                    *                   *       *                            
       2697 ACCCATTCGTTCAAAAGTCTTAAT-ACTTACTTTAATTGGTTTTGTAATCTCAAAATTGATTAAA
          1 ACCCATTCCTTCAAAAGTCTT-ATGACTCACTTTAAATGGTTTTGTAATCTCAAAATTGATTAAA

                           *    *  *             *              **           
       2761 ATTTGAATTCTTTGTTCATTATTGGTTAAAAAAGATTTTAATTGAATGTCAATGTCAAGAAATAT
         65 ATTTGAATTCTTTGTACATTTTTAGTT-AAAAAGATTATAATTGAATGTCAACCTCAAGAAATAT

              *                            *           
       2826 GGCAGAAAAGGTATTCATTGGCAAGAAAAGTCCATTTATAGTC
        129 -GAAGAAAA-G-ATTCATTGGCAAGAAAAGTTCATTTATAGTC

                          
       2869 ACCCATTCCTTCAA
          1 ACCCATTCCTTCAA

       2883 NNNNNNNNNN


Statistics
Matches: 293,  Mismatches: 58, Indels: 12
        0.81            0.16        0.03

Matches are distributed among these distances:
 170  105  0.36
 171   13  0.04
 172  170  0.58
 173    5  0.02

ACGTcount: A:0.35, C:0.14, G:0.12, T:0.36


Consensus pattern (168 bp):   
ACCCATTCCTTCAAAAGTCTTATGACTCACTTTAAATGGTTTTGTAATCTCAAAATTGATTAAAA
TTTGAATTCTTTGTACATTTTTAGTTAAAAAGATTATAATTGAATGTCAACCTCAAGAAATATGA
AGAAAAGATTCATTGGCAAGAAAAGTTCATTTATAGTC
Done.