Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018398443.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1742.0, 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: 2236
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.27

Warning! 642 characters in sequence are not A, C, G, or T


Found at i:1134 original size:171 final size:170

Alignment explanation


    Indices: 640--1368  Score: 514
    Period size: 171  Copynumber: 4.3  Consensus size: 170

        630 NNNNNNNNNN

                     *         *   *                *         * * *    *     
        640 ATAAATAGACTTTTCTTGCTAATAGATATCTTTTTCTTCACGTTTCTCAAGGTATACAGGT-AAT
          1 ATAAATAGAATTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCTCAAAGCAAACA-TTCAAT

                *   *         *                   *      **              *   
        704 TATATTCTATTTTAATAATAAATATAAAAAGAGTTCAACTTAAAAGGAATTATGAGATTAATAAA
         65 TATAATCTGTTTTAATAACAAATATAAAAA-AGTTCAAATTAAAACTAATTATGAGATTAAAAAA

            *                   *     **********       
        769 CTATTTAAAGCGAGTAATAAAGCTTNNNNNNNNNNGGGTGACT
        129 GTATTTAAAGCGAGTAATAAGGCTT-TTGAAGGATCGGTGACT

                  * **     * * *   **    *     *  * *      *      * *        
        812 ATAAATGGGCTTTTCCTACTAATAAATATATTTTTATTTACGTTTCTTAAAGCAGATATTCAATT
          1 ATAAATAGAATTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCTCAAAGCAAACATTCAATT

                       *                       *        *         *   *      
        877 ATAATCTGTTTCAATAACAAATATAAAAAAGTTCAGATTAAAACAAATTATGAGGTTATAAAA-T
         66 ATAATCTGTTTTAATAACAAATATAAAAAAGTTCAAATTAAAACTAATTATGAGATTAAAAAAGT

                  **********                          
        941 CATTTANNNNNNNNNNTAAGGCTTTTGAAGGCATCGGTGACT
        131 -ATTTAAAGCGAGTAATAAGGCTTTTGAAGG-ATCGGTGACT

                          *    *                               * *           
        983 ATAAATAGAATTTTTTTGCTAATGGATATCTTTTTCTTCATGTTTCTTC-AGGTAAACATGT-AA
          1 ATAAATAGAATTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTC-TCAAAGCAAACAT-TCAA

                               **   *             *      *          *********
       1046 TTATAATCTGTTTTAATAATGAATGTAAAAAAGTTCAACTTAAAAGTAATTATGAGNNNNNNNNN
         64 TTATAATCTGTTTTAATAACAAATATAAAAAAGTTCAAATTAAAACTAATTATGAGATTAAAAAA

            *                                *         
       1111 NTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAACGGGTGACT
        129 GTATTTAAAGCGAGTAATAAGGCTTTTGAAGGATC-GGTGACT

                    **       *               *    * *             *          
       1154 ATAAATAGGCTTTTCTTACCAATGGATATCTTTCTCTTTACGTTTCTCAAAGCAGACATTCAATT
          1 ATAAATAGAATTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCTCAAAGCAAACATTCAATT

              *                              *                               
       1219 ATTATCTGTTTTAATAACAAATATAAAAAAGTTTAAATTAAAACTAATTATGAGATTAAAAAAGT
         66 ATAATCTGTTTTAATAACAAATATAAAAAAGTTCAAATTAAAACTAATTATGAGATTAAAAAAGT

                 *         *        *     *  *       
       1284 ATTTAGAGCGAGTAAGAAGGCTTTCGAAGATATGGGTGACT
        131 ATTTAAAGCGAGTAATAAGGCTTTTGAAG-GATCGGTGACT

                                                         
       1325 ATAAATA-AACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTT
          1 ATAAATAGAA-TTTTCTTGCCAATGGATATCTTTTTCTTCATGTT

       1369 NNNNNNNNNN


Statistics
Matches: 415,  Mismatches: 131, Indels: 23
        0.73            0.23        0.04

Matches are distributed among these distances:
 170    6  0.01
 171  331  0.80
 172   78  0.19

ACGTcount: A:0.36, C:0.10, G:0.13, T:0.36


Consensus pattern (170 bp):   
ATAAATAGAATTTTCTTGCCAATGGATATCTTTTTCTTCATGTTTCTCAAAGCAAACATTCAATT
ATAATCTGTTTTAATAACAAATATAAAAAAGTTCAAATTAAAACTAATTATGAGATTAAAAAAGT
ATTTAAAGCGAGTAATAAGGCTTTTGAAGGATCGGTGACT

Found at i:1306 original size:342 final size:343

Alignment explanation


    Indices: 640--1368  Score: 818
    Period size: 342  Copynumber: 2.1  Consensus size: 343

        630 NNNNNNNNNN

                     *             *                *             *          
        640 ATAAATAGACTTTTCTTGCTAATAGATATCTTTTTCTTCACGTTTCTCAAGGTATACAGGTAATT
          1 ATAAATAGAATTTTCTTGCTAATGGATATCTTTTTCTTCATGTTTCTCAAGGTAAACAGGTAATT

               *                                                             
        705 ATATTCTATTTTAATAATAAATATAAAAAGAGTTCAACTTAAAAGGAATTATGAGATTAATAAAC
         66 ATAATCTATTTTAATAATAAATATAAAAAGAGTTCAACTTAAAAGGAATTATGAGATTAATAAAC

                                    **********              *            *   
        770 TATTTAAAGCGAGTAATAAAGCTTNNNNNNNNNNGGGTGACTATAAATGGGCTTTTCCTACTAAT
        131 TATTTAAAGCGAGTAATAAAGCTTTTGAAGGAACGGGTGACTATAAATAGGCTTTTCCTACCAAT

                      *             *        *                               
        835 AAATATATTTTTATTTACGTTTCTTAAAGCAGATATTCAATTATAATCTGTTTCAATAACAAATA
        196 AAATATATTTCTATTTACGTTTCTCAAAGCAGACATTCAATTATAATCTGTTTCAATAACAAATA

                        *                  *   *           ***********       
        900 TAAAAAAGTTCAGATTAAAACAAATTATGAGGTTATAAAATCATTTANNNNNNNNNNTAAGGCTT
        261 TAAAAAAGTTCAAATTAAAACAAATTATGAGATTAAAAAATCATTTAGAGCGAGTAAGAAGGCTT

             *    *           
        965 TTGAAGGCATCGGTGACT
        326 TCGAAGACATCGGTGACT

                          *                                            *     
        983 ATAAATAGAATTTTTTTGCTAATGGATATCTTTTTCTTCATGTTTCTTC-AGGTAAACATGTAAT
          1 ATAAATAGAATTTTCTTGCTAATGGATATCTTTTTCTTCATGTTTC-TCAAGGTAAACAGGTAAT

                    *          *   *                      *         *********
       1047 TATAATCTGTTTTAATAATGAATGTAAAAA-AGTTCAACTTAAAAGTAATTATGAGNNNNNNNNN
         65 TATAATCTATTTTAATAATAAATATAAAAAGAGTTCAACTTAAAAGGAATTATGAGATTAATAAA

            *                   *                                     *      
       1111 NTATTTAAAGCGAGTAATAAGGCTTTTGAAGGAACGGGTGACTATAAATAGGCTTTTCTTACCAA
        130 CTATTTAAAGCGAGTAATAAAGCTTTTGAAGGAACGGGTGACTATAAATAGGCTTTTCCTACCAA

             **    *     *                               *        *          
       1176 TGGATATCTTTCTCTTTACGTTTCTCAAAGCAGACATTCAATTATTATCTGTTTTAATAACAAAT
        195 TAAATATATTTCTATTTACGTTTCTCAAAGCAGACATTCAATTATAATCTGTTTCAATAACAAAT

                       *          *                                          
       1241 ATAAAAAAGTTTAAATTAAAACTAATTATGAGATTAAAAAAGT-ATTTAGAGCGAGTAAGAAGGC
        260 ATAAAAAAGTTCAAATTAAAACAAATTATGAGATTAAAAAA-TCATTTAGAGCGAGTAAGAAGGC

                     *  *       
       1305 TTTCGAAGATATGGGTGACT
        324 TTTCGAAGACATCGGTGACT

                                *                        
       1325 ATAAATA-AACTTTTCTTGCCAATGGATATCTTTTTCTTCATGTT
          1 ATAAATAGAA-TTTTCTTGCTAATGGATATCTTTTTCTTCATGTT

       1369 NNNNNNNNNN


Statistics
Matches: 317,  Mismatches: 66, Indels: 7
        0.81            0.17        0.02

Matches are distributed among these distances:
 341    2  0.01
 342  231  0.73
 343   82  0.26
 344    2  0.01

ACGTcount: A:0.36, C:0.10, G:0.13, T:0.36


Consensus pattern (343 bp):   
ATAAATAGAATTTTCTTGCTAATGGATATCTTTTTCTTCATGTTTCTCAAGGTAAACAGGTAATT
ATAATCTATTTTAATAATAAATATAAAAAGAGTTCAACTTAAAAGGAATTATGAGATTAATAAAC
TATTTAAAGCGAGTAATAAAGCTTTTGAAGGAACGGGTGACTATAAATAGGCTTTTCCTACCAAT
AAATATATTTCTATTTACGTTTCTCAAAGCAGACATTCAATTATAATCTGTTTCAATAACAAATA
TAAAAAAGTTCAAATTAAAACAAATTATGAGATTAAAAAATCATTTAGAGCGAGTAAGAAGGCTT
TCGAAGACATCGGTGACT
Done.