Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018401975.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5072.0, 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, 937

Length: 1563
ACGTcount: A:0.24, C:0.10, G:0.08, T:0.24

Warning! 526 characters in sequence are not A, C, G, or T


Found at i:388 original size:171 final size:170

Alignment explanation


    Indices: 61--475  Score: 471
    Period size: 171  Copynumber: 2.4  Consensus size: 170

         51 CATTGATCGG

                       *          *  *                      *                
         61 CAAGAAAAGTCCATTTATAGCCACCCATTCCTTCAAAAGTCTTATTACACGCTTTAAATAGTTTT
          1 CAAGAAAAGTCTATTTATAGCCTCCTATTCCTTCAAAAGTCTTATTACTCG-TTTAAATAGTTTT

                *    *            *             *              *             
        126 -TAAACTAATAATTGATTTTAAGTTGAAATTTTTTACATTTTCCATTAAAATAGACTATAATTGA
         65 ATAATCTAAGAATTGATTTTAACTTGAAATTTTTTAAATTTTCCATTAAAACAGACTATAATTGA

                              *                  *   
        190 ACGTCTGCCTTAACAAACGTAAAGAAAAAAGCATTCATTGA
        130 ACGTCTGCCTTAACAAACATAAAGAAAAAAGCATTCACTGA

            * *                                  *      *                    
        231 TATGAAAAGTCTATTTATAGCCTCCTATTCCTTC-AACGTCCTTTTTACTCGTTCTAAATAGTTT
          1 CAAGAAAAGTCTATTTATAGCCTCCTATTCCTTCAAAAGT-CTTATTACTCGTT-TAAATAGTTT

                    *                 *  *             *                     
        295 TATAATCTCAGAATTGATTTTAACTTTAATTTTTTTAAATTTTTCATTAAAACAGACTATAATTG
         64 TATAATCTAAGAATTGATTTTAACTTGAAATTTTTTAAATTTTCCATTAAAACAGACTATAATTG

                  *       *    *   *                   *
        360 -ACTGTTTGCCTT-GCGAAGCATGAAGAAAAAAGCATTCACTGG
        129 AAC-GTCTGCCTTAAC-AAACATAAAGAAAAAAGCATTCACTGA

                             *  *              *                *       *    
        402 CAAGAAAAGTCTATTTACAGTCT-CTCATTCCTTCGAAAGTCTTATTACTCACTTTAAATGGTTT
          1 CAAGAAAAGTCTATTTATAGCCTCCT-ATTCCTTCAAAAGTCTTATTACTC-GTTTAAATAGTTT

                      
        466 TATAATCTAA
         64 TATAATCTAA

        476 TNNNNNNNNN


Statistics
Matches: 204,  Mismatches: 33, Indels: 15
        0.81            0.13        0.06

Matches are distributed among these distances:
 169    6  0.03
 170   54  0.26
 171  138  0.68
 172    6  0.03

ACGTcount: A:0.35, C:0.17, G:0.11, T:0.38


Consensus pattern (170 bp):   
CAAGAAAAGTCTATTTATAGCCTCCTATTCCTTCAAAAGTCTTATTACTCGTTTAAATAGTTTTA
TAATCTAAGAATTGATTTTAACTTGAAATTTTTTAAATTTTCCATTAAAACAGACTATAATTGAA
CGTCTGCCTTAACAAACATAAAGAAAAAAGCATTCACTGA

Found at i:557 original size:171 final size:157

Alignment explanation


    Indices: 322--637  Score: 267
    Period size: 171  Copynumber: 1.9  Consensus size: 157

        312 TTTTAACTTT

                                         *         * * * *         *         
        322 AATTTTTTTAAATTTTTCATTAAAACAGACTATAATTGACTGTTTGCCTTGCGAAGCATGAAGAA
          1 AATTTTTTTAAATTTTTCATTAAAACAGAATATAATTGAATATCTACCTTGCGAAACATGAAGAA

                          *           *           *           *    *  *     *
        387 AAAAGCATTCACTGGCAAGAAAAGTCTATTTACAGTC-TCTCATTCCTTCGAAAGTCTTATTACT
         66 AAAAGCATTCACTGACAAGAAAAGTCCATTTACAGTCACCT-ATTCCTTCAAAAGCCTAATTACA

                      *                               
        451 CACTTTAAATGGTTTTATAATCTAATNNNNNNNNNNNNNNTG
        130 CACTTTAAATAGTTTTATAATCTAAT--------------TG

                      *      *                            *           *      
        493 AATTTTTTTACATTTTTGATTAAAACAGAATATAATTGAATATCTATCTATG-GAAACGTGAAGA
          1 AATTTTTTTAAATTTTTCATTAAAACAGAATATAATTGAATATCTACCT-TGCGAAACATGAAGA

               *        *      *             **                              
        557 AAAGAGCATTCATTGACAATAAAAGTCCATTTATGGTCACCTATTCCTTCAAAAGCCTAATTACA
         65 AAAAAGCATTCACTGACAAGAAAAGTCCATTTACAGTCACCTATTCCTTCAAAAGCCTAATTACA

                            
        622 CACTTTAAATAGTTTT
        130 CACTTTAAATAGTTTT

        638 TCAATCTCNN


Statistics
Matches: 120,  Mismatches: 23, Indels: 4
        0.82            0.16        0.03

Matches are distributed among these distances:
 171  116  0.97
 172    4  0.03

ACGTcount: A:0.34, C:0.15, G:0.11, T:0.35


Consensus pattern (157 bp):   
AATTTTTTTAAATTTTTCATTAAAACAGAATATAATTGAATATCTACCTTGCGAAACATGAAGAA
AAAAGCATTCACTGACAAGAAAAGTCCATTTACAGTCACCTATTCCTTCAAAAGCCTAATTACAC
ACTTTAAATAGTTTTATAATCTAATTG
Done.