Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018399001.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2280.1, 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: 1863
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.28

Warning! 390 characters in sequence are not A, C, G, or T


Found at i:1756 original size:174 final size:170

Alignment explanation


    Indices: 1173--1863  Score: 645
    Period size: 169  Copynumber: 4.1  Consensus size: 170

       1163 NNNNNNNNNN

                                                     *          *            
       1173 ATTATGAGATTATAAAACTATTTAAAGAGAGTAATAAGGCTGTTGAAGGCTTAGGTGACTATAAA
          1 ATTATGAGATTATAAAACTATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAA

                  *               **                               *         
       1238 T-GGCTTTTCTTGCCAATGAATGGGTTTTTCTTCATGTTTCTCAATGCAAACATTTAATTATAAT
         66 TGGGCTCTTCTTGCCAATGAATTAGTTTTTCTTCATGTTTCTCAATGCAAACATTCAATTATAAT

            *                       *    *            
       1302 GTGTTTTAACAAAAAATGTAAAAACCATTTAACTTAAAATCA
        131 CTGTTTTAA-AAAAAATGTAAAAAACA-TCAACTTAAAATCA

             *  * *  ** *     *        *        *                            
       1344 AATACGGGAAAACAAAACCATTTAAAGTGAGTAATAGGGCTTTTGAAGGCTTGGGTGACTATAAA
          1 ATTATGAGATTATAAAACTATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAA

             *          *                               * * *      *         
       1409 TTGGCTCTTCTTACCAATGAA-TAGGTTTTTCTTCATGTTTCTCTAGGTAAACATGCAATT-TGA
         66 TGGGCTCTTCTTGCCAATGAATTA-GTTTTTCTTCATGTTTCTCAATGCAAACATTCAATTAT-A

                                 *                    
       1472 ATCTGTTTT-AAAAAAATGTACAAAACATCAACTTAAAATCA
        129 ATCTGTTTTAAAAAAAATGTAAAAAACATCAACTTAAAATCA

                         **********    *                      *              
       1513 ATTATGAGATTATNNNNNNNNNNAAAGCGAGTAATAAGGCTTTTGAAGGCCTGGGTGACTATAAA
          1 ATTATGAGATTATAAAACTATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAA

                  *      *          *                   *                    
       1578 TGGGCTTTTCTTGTCAATGAATTAATTTTTCTTCATGTTTCGT-GATGCAAACATTCAATTATAA
         66 TGGGCTCTTCTTGCCAATGAATTAGTTTTTCTTCATGTTTC-TCAATGCAAACATTCAATTATAA

                                               *         
       1642 TCTGTTTTAAATAAAAATGTAAAAAAACAACTCAATTTAAAATCA
        130 TCTGTTTTAAA-AAAAATGT-AAAAAAC-A-TCAACTTAAAATCA

               * *           *        *                         *     *   *  
       1687 ATTTTTAGATTATAAAAATATTTAAAAAGAGTAATAAGGCTTTTGAAGGCTTCGGTGATTATGAA
          1 ATTATGAGATTATAAAACTATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAA

                         *           **              *   * *   *      *      
       1752 TGGGCTCTTCTTGTCAATGAA-T-GGGTTT-TT-A----TCCCAAGGAAAATATTCAAATATAAT
         66 TGGGCTCTTCTTGCCAATGAATTAGTTTTTCTTCATGTTTCTCAATGCAAACATTCAATTATAAT

            *         *                             * 
       1809 TTGTTTTAACTAAAAATGTAAAAAA-ATTCAACTTAAAATAA
        131 CTGTTTTAA-AAAAAATGTAAAAAACA-TCAACTTAAAATCA

                          
       1850 ATTATGAGATTATA
          1 ATTATGAGATTATA


Statistics
Matches: 418,  Mismatches: 89, Indels: 34
        0.77            0.16        0.06

Matches are distributed among these distances:
 163   25  0.06
 165    6  0.01
 166   35  0.08
 169  115  0.28
 170   22  0.05
 171   67  0.16
 172   66  0.16
 173    2  0.00
 174   80  0.19

ACGTcount: A:0.37, C:0.11, G:0.15, T:0.35


Consensus pattern (170 bp):   
ATTATGAGATTATAAAACTATTTAAAGAGAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAA
TGGGCTCTTCTTGCCAATGAATTAGTTTTTCTTCATGTTTCTCAATGCAAACATTCAATTATAAT
CTGTTTTAAAAAAAATGTAAAAAACATCAACTTAAAATCA
Done.