Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018400694.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3878.0, 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: 1964
ACGTcount: A:0.23, C:0.07, G:0.08, T:0.21

Warning! 805 characters in sequence are not A, C, G, or T


Found at i:1073 original size:171 final size:170

Alignment explanation


    Indices: 891--1244  Score: 444
    Period size: 170  Copynumber: 2.1  Consensus size: 170

        881 NNTTCAAAGG

                *             **   *                           *  *          
        891 CATGGGTGACTATAAATGGGCTTTTCATA-TCGAT-GAATATCTTTTTCTTTACGTTTCTCAAGG
          1 CATGAGTGACTATAAATGAACTTATCATAGT-GATAG-ATATCTTTTTCTTCACATTTCTCAAGG

                           *     *              *     *              *     **
        954 AAAATATTCAATTATTATCTATTTTAA-ACAAAAATGTAAAACAATTCAACTTAAAATCAATTGT
         64 AAAATATTCAATTATAATCT-GTTTAATA-AAAAATATAAAAAAATTCAACTTAAAACCAATTAA

              *                 *                       
       1018 GATATTATAAAAATATTTAAGGCGAGTAATAAGGCTTTCGAAGA
        127 GAAATTATAAAAATATTTAAAGCGAGTAATAAGGCTTTCGAAGA

                                      *                        *       *   * 
       1062 CATGAGTGACTATAAATGAACTTATCCTAGTGATAGATATCTTTTTCTTCATATTTCTCGAGGTA
          1 CATGAGTGACTATAAATGAACTTATCATAGTGATAGATATCTTTTTCTTCACATTTCTCAAGGAA

                                                       *                     
       1127 AATATTCAATTATAATCTGTTTAATAAAAAATATAAAAAAATTTAACTTAAAACCAATTAAGAAA
         66 AATATTCAATTATAATCTGTTTAATAAAAAATATAAAAAAATTCAACTTAAAACCAATTAAGAAA

                    *         *                    *
       1192 TTATAAAACTATTTAAAGTGAGTAATAAGGCTTTCGAAGG
        131 TTATAAAAATATTTAAAGCGAGTAATAAGGCTTTCGAAGA

                         
       1232 CATGAGTGACTAT
          1 CATGAGTGACTAT

       1245 NNNNNNNNNN


Statistics
Matches: 157,  Mismatches: 23, Indels: 7
        0.84            0.12        0.04

Matches are distributed among these distances:
 170   86  0.55
 171   69  0.44
 172    2  0.01

ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36


Consensus pattern (170 bp):   
CATGAGTGACTATAAATGAACTTATCATAGTGATAGATATCTTTTTCTTCACATTTCTCAAGGAA
AATATTCAATTATAATCTGTTTAATAAAAAATATAAAAAAATTCAACTTAAAACCAATTAAGAAA
TTATAAAAATATTTAAAGCGAGTAATAAGGCTTTCGAAGA

Found at i:1225 original size:170 final size:171

Alignment explanation


    Indices: 927--1244  Score: 451
    Period size: 170  Copynumber: 1.9  Consensus size: 171

        917 ATATCGATGA

                         *  *                         *     *             *  
        927 ATATCTTTTTCTTTACGTTTCTCAAGGAAAATATTCAATTATTATCTATTTTAAACAAAAATGTA
          1 ATATCTTTTTCTTCACATTTCTCAAGGAAAATATTCAATTATAATCTAGTTTAAACAAAAATATA

               *              *     **  *                 *                  
        992 AAACAATTCAACTTAAAATCAATTGTGATATTATAAAAATATTTAAGGCGAGTAATAAGGCTTTC
         66 AAAAAATTCAACTTAAAACCAATTAAGAAATTATAAAAATATTTAAAGCGAGTAATAAGGCTTTC

                                                     
       1057 GAAGACATGAGTGACTATAAATGAACTTATCCTAGTGATAG
        131 GAAGACATGAGTGACTATAAATGAACTTATCCTAGTGATAG

                           *       *   *                                     
       1098 ATATCTTTTTCTTCATATTTCTCGAGGTAAATATTCAATTATAATCT-GTTTAATA-AAAAATAT
          1 ATATCTTTTTCTTCACATTTCTCAAGGAAAATATTCAATTATAATCTAGTTTAA-ACAAAAATAT

                     *                             *         *               
       1161 AAAAAAATTTAACTTAAAACCAATTAAGAAATTATAAAACTATTTAAAGTGAGTAATAAGGCTTT
         65 AAAAAAATTCAACTTAAAACCAATTAAGAAATTATAAAAATATTTAAAGCGAGTAATAAGGCTTT

                 *             
       1226 CGAAGGCATGAGTGACTAT
        130 CGAAGACATGAGTGACTAT

       1245 NNNNNNNNNN


Statistics
Matches: 128,  Mismatches: 18, Indels: 3
        0.86            0.12        0.02

Matches are distributed among these distances:
 170   86  0.67
 171   42  0.33

ACGTcount: A:0.42, C:0.11, G:0.12, T:0.36


Consensus pattern (171 bp):   
ATATCTTTTTCTTCACATTTCTCAAGGAAAATATTCAATTATAATCTAGTTTAAACAAAAATATA
AAAAAATTCAACTTAAAACCAATTAAGAAATTATAAAAATATTTAAAGCGAGTAATAAGGCTTTC
GAAGACATGAGTGACTATAAATGAACTTATCCTAGTGATAG
Done.