Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018401218.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4365.0, 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: 2122
ACGTcount: A:0.25, C:0.07, G:0.09, T:0.24

Warning! 730 characters in sequence are not A, C, G, or T


Found at i:795 original size:171 final size:161

Alignment explanation


    Indices: 496--807  Score: 304
    Period size: 171  Copynumber: 1.9  Consensus size: 161

        486 ACTATAAATG

                        *                   *                                
        496 GACTTTTCTTACTAATGAATCTCTTTTTCTTCTTGTTTCTCTAGGTAAACATTCAATTATAGTCT
          1 GACTTTTCTTACCAATGAATCTCTTTTTCTTCATGTTTCTCTAGGTAAACATTCAATTATAGTCT

            *      *              *            * * *      *         *       *
        561 GTTTTAATAAAAAATGTAAAACCATTCAACTTAAAGTTACTGATGAGATAAAAAAATCATTTAAG
         66 ATTTTAACAAAAAATGTAAAACAATTCAACTTAAAATCAATGATGAAATAAAAAAACCATTTAAA

             *                                       
        626 GTGAGTAATAAGGTTTTTAAAGGAATGGNNNNNNNNNNATA
        131 GCGAGTAATAAGGTTTTTAAAGGAATGG----------ATA

                      *  *                                   *               
        667 GACTTTTCTTGCCGATGAATACTC-TTTTCTTCATGTTTCT-TAAGGTAGACATTCAATTATAGT
          1 GACTTTTCTTACCAATGAAT-CTCTTTTTCTTCATGTTTCTCT-AGGTAAACATTCAATTATAGT

                   *       *       *    *              *       * *           
        730 CTATTTTCACAAAAATTGTAAAAGAATTGAACTTAAAATCAATTATGAAATTATAAAACCATTTA
         64 CTATTTTAACAAAAAATGTAAAACAATTCAACTTAAAATCAATGATGAAATAAAAAAACCATTTA

                         
        795 AAGCGAGTAATAA
        129 AAGCGAGTAATAA

        808 NNNNNNNNNN


Statistics
Matches: 117,  Mismatches: 22, Indels: 4
        0.82            0.15        0.03

Matches are distributed among these distances:
 170    1  0.01
 171  113  0.97
 172    3  0.03

ACGTcount: A:0.36, C:0.12, G:0.12, T:0.37


Consensus pattern (161 bp):   
GACTTTTCTTACCAATGAATCTCTTTTTCTTCATGTTTCTCTAGGTAAACATTCAATTATAGTCT
ATTTTAACAAAAAATGTAAAACAATTCAACTTAAAATCAATGATGAAATAAAAAAACCATTTAAA
GCGAGTAATAAGGTTTTTAAAGGAATGGATA

Found at i:1665 original size:171 final size:172

Alignment explanation


    Indices: 1360--1676  Score: 456
    Period size: 171  Copynumber: 1.8  Consensus size: 172

       1350 NNNNNNNNNN

                                                *             *            * 
       1360 TATGAGATTATAAAACCATTCAAAGCGAGTAATAAGGCTTTCGAAGGAATGGGTGACTATAAATG
          1 TATGAGATTATAAAACCATTCAAAGCGAGTAATAAGCCTTTCGAAGGAATAGGTGACTATAAAGG

               *    *                         *        *    **            *  
       1425 GATTTTTTTTTGCCAATGAATACCTTTTTCTTCATATTTCTTGGGGTAGGCATTCAATTATAGTC
         66 GATCTTTTCTTGCCAATGAATACCTTTTTCTTCACATTTCTTGAGGTAAACATTCAATTATAATC

                   *                                  
       1490 TATTTTATCCAAAAATACAAAAAAATTCAACTTTAAATTAGT
        131 TATTTTAACCAAAAATACAAAAAAATTCAACTTTAAATTAGT

                            *   *                    *  *                    
       1532 TATGAGATTATAAAACTATTTAAAGCGAGTAATAAGCCTTTTGATGGAATAGGTGACTATAAAGG
          1 TATGAGATTATAAAACCATTCAAAGCGAGTAATAAGCCTTTCGAAGGAATAGGTGACTATAAAGG

                                 * *           *                             
       1597 GA-CTTTTCTTGCCAATGAATGCTTTTTTCTTCACGTTTCTTGAGGTAAACATTCAATTATAATC
         66 GATCTTTTCTTGCCAATGAATACCTTTTTCTTCACATTTCTTGAGGTAAACATTCAATTATAATC

                     *      
       1661 TATTTTAACTAAAAAT
        131 TATTTTAACCAAAAAT

       1677 GTANNNNNNN


Statistics
Matches: 126,  Mismatches: 19, Indels: 1
        0.86            0.13        0.01

Matches are distributed among these distances:
 171   66  0.52
 172   60  0.48

ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37


Consensus pattern (172 bp):   
TATGAGATTATAAAACCATTCAAAGCGAGTAATAAGCCTTTCGAAGGAATAGGTGACTATAAAGG
GATCTTTTCTTGCCAATGAATACCTTTTTCTTCACATTTCTTGAGGTAAACATTCAATTATAATC
TATTTTAACCAAAAATACAAAAAAATTCAACTTTAAATTAGT
Done.