Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018398431.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1731.0, 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: 7485
ACGTcount: A:0.22, C:0.07, G:0.08, T:0.21

Warning! 3115 characters in sequence are not A, C, G, or T


Found at i:5096 original size:59 final size:59

Alignment explanation


    Indices: 5004--5122  Score: 229
    Period size: 59  Copynumber: 2.0  Consensus size: 59

       4994 AAATGGACTT

                                                       *               
       5004 TTGTTGCCAGTGAATGCCCTTTTCTTCATGTTTCTCACTATAACCATTCAATTATAATA
          1 TTGTTGCCAGTGAATGCCCTTTTCTTCATGTTTCTCACTATAAACATTCAATTATAATA

                                                                       
       5063 TTGTTGCCAGTGAATGCCCTTTTCTTCATGTTTCTCACTATAAACATTCAATTATAATA
          1 TTGTTGCCAGTGAATGCCCTTTTCTTCATGTTTCTCACTATAAACATTCAATTATAATA

             
       5122 T
          1 T

       5123 GTTTTAACTA


Statistics
Matches: 59,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  59   59  1.00

ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43


Consensus pattern (59 bp):   
TTGTTGCCAGTGAATGCCCTTTTCTTCATGTTTCTCACTATAAACATTCAATTATAATA

Found at i:6115 original size:172 final size:162

Alignment explanation


    Indices: 5875--6200  Score: 314
    Period size: 172  Copynumber: 2.0  Consensus size: 162

       5865 AAGGCTTCTG

                   *              *      *             *        *  ** * *    
       5875 AAGGAATTGGTGACTATAAATGTACTTTTGTTGCCAATGAATGTCTTTTTCTTCATGTTTGATGA
          1 AAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGACTTTTTCTACACCTATCATGA

                   *              *            *              *              
       5940 GGTAGACGTTCAATCATAATCTGTTCTAATGAAAATTGTAAA-AAGAATTGAACTTAAAATCAAT
         66 GGTAGACATTCAATCATAATCTATTCTAATGAAAAATGTAAACAA-AATTCAACTTAAAATCAAT

             * * *         * *               
       6004 TTTGAGATTATAAAATCGTTTAAAGTGACTAAT
        130 TATAAAATTATAAAACCATTTAAAGTGACTAAT

                                                                             
       6037 AANNNNNNNNNNGGAATGGGTGACTATAAATGGACTTTTCTT-CTCAATGAATGACTTTTTCTAC
          1 AA----------GGAATGGGTGACTATAAATGGACTTTTCTTGC-CAATGAATGACTTTTTCTAC

                   *        *        *  *       *                            
       6101 ACCTATCCTGAGGTAGGCATTCAATTATTATCTATTTTAATGAAAAATGTAAACAAAATTCAACT
         55 ACCTATCATGAGGTAGACATTCAATCATAATCTATTCTAATGAAAAATGTAAACAAAATTCAACT

                  *                            
       6166 TAAAATGAATTATAAAATTATAAAACCATTTAAAG
        120 TAAAATCAATTATAAAATTATAAAACCATTTAAAG

       6201 CGAGTAATNN


Statistics
Matches: 128,  Mismatches: 24, Indels: 14
        0.77            0.14        0.08

Matches are distributed among these distances:
 162    2  0.02
 171    1  0.01
 172  123  0.96
 173    2  0.02

ACGTcount: A:0.37, C:0.11, G:0.14, T:0.35


Consensus pattern (162 bp):   
AAGGAATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGACTTTTTCTACACCTATCATGA
GGTAGACATTCAATCATAATCTATTCTAATGAAAAATGTAAACAAAATTCAACTTAAAATCAATT
ATAAAATTATAAAACCATTTAAAGTGACTAAT
Done.