Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018399407.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2673.0, 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: 4168
ACGTcount: A:0.19, C:0.07, G:0.06, T:0.18

Warning! 2094 characters in sequence are not A, C, G, or T


Found at i:1228 original size:170 final size:161

Alignment explanation


    Indices: 1042--1354  Score: 328
    Period size: 171  Copynumber: 1.9  Consensus size: 161

       1032 AAGGCTTTTG

                *                                                          * 
       1042 AAGGAATGGCTGACTATAAAAAAACTTTTCTTCTCAATGAATGG-CTTTTCTACACGTTTCTCGA
          1 AAGGCATGGCTGACTATAAAAAAACTTTTCTTCTCAATGAATGGTCTTTTCTACACGTTTCTCAA

            * *           *                **                  *   *         
       1106 TATAGACATTCAATTATAG-CT-TATTCTAATTAAAAATGTAATAA-AATTTAACTTAAAATCAA
         66 GACAGACATTCAATCATAGTCTGT-TT-TAACCAAAAATGTAA-AACAATTCAACGTAAAATCAA

                                              
       1168 TTATGAGACTATAAAATAATTTAATGTGAGTAAT
        128 TTATGAGACTATAAAATAATTTAATGTGAGTAAT

                               *          * *                      *       **
       1202 AAGGCNNNNNNNNNNATGGGTGACTATAAATATACTTTTCTTCTCAATGAATGGTGTTTTCTATG
          1 AAGGC----------ATGGCTGACTATAAAAAAACTTTTCTTCTCAATGAATGGTCTTTTCTACA

                       *                                                     
       1267 CGTTTCTCAAGGCAGACATTCAATCATAGTCTGTTTTAACCAAAAATGTAAAACAATTCAACGTA
         56 CGTTTCTCAAGACAGACATTCAATCATAGTCTGTTTTAACCAAAAATGTAAAACAATTCAACGTA

                           *       
       1332 AAATCAATTATGAGATTATAAAA
        121 AAATCAATTATGAGACTATAAAA

       1355 CAATAAAAAG


Statistics
Matches: 122,  Mismatches: 17, Indels: 17
        0.78            0.11        0.11

Matches are distributed among these distances:
 160    4  0.03
 170   38  0.31
 171   75  0.61
 172    4  0.03
 173    1  0.01

ACGTcount: A:0.38, C:0.13, G:0.12, T:0.34


Consensus pattern (161 bp):   
AAGGCATGGCTGACTATAAAAAAACTTTTCTTCTCAATGAATGGTCTTTTCTACACGTTTCTCAA
GACAGACATTCAATCATAGTCTGTTTTAACCAAAAATGTAAAACAATTCAACGTAAAATCAATTA
TGAGACTATAAAATAATTTAATGTGAGTAAT

Found at i:1505 original size:169 final size:169

Alignment explanation


    Indices: 1269--1580  Score: 412
    Period size: 169  Copynumber: 1.8  Consensus size: 169

       1259 TTTCTATGCG

                                          *                                  
       1269 TTTCTCAAGGCAGACATTCAATCATAGTCTGTTTTAACCAAAAATGTAAAACAATTCAACGTAAA
          1 TTTCTCAAGGCAGACATTCAATCATAGTCTATTTTAACCAAAAATGTAAAACAATTCAACGTAAA

                  *  *                                 *  *         **       
       1334 ATCAATTATGAGATTATAAAACAATAAAAAGCAAGTAATAAAGTTTTTGAAGGAATGGGTGACTA
         66 ATCAATCATAAGATTATAAAACAATAAAAAGCAAGTAATAAAGCTTCTGAAGGAATAAGTGACTA

                                                   
       1399 TAAATAAACTTTTTGCTAATGAATTCCTTTTTCTTCATA
        131 TAAATAAACTTTTTGCTAATGAATTCCTTTTTCTTCATA

                      *   *       *                   *                *  *  
       1438 TTTCTCAAGGTAGATATTCAATTATAG-CATATTTTAACCAACAATGTAAAACAAATT-GACTTA
          1 TTTCTCAAGGCAGACATTCAATCATAGTC-TATTTTAACCAAAAATGTAAAAC-AATTCAACGTA

                               *       **    **        *                     
       1501 AAATCAATCATAAGATTATGAAACAATTTAAAGGGAGTAATAAGGCTTCTGAAGGAATAAGTGAC
         64 AAATCAATCATAAGATTATAAAACAATAAAAAGCAAGTAATAAAGCTTCTGAAGGAATAAGTGAC

                    *      
       1566 TATAAATAGACTTTT
        129 TATAAATAAACTTTT

       1581 CTTCTTAACG


Statistics
Matches: 121,  Mismatches: 20, Indels: 4
        0.83            0.14        0.03

Matches are distributed among these distances:
 168    1  0.01
 169  116  0.96
 170    4  0.03

ACGTcount: A:0.42, C:0.12, G:0.13, T:0.32


Consensus pattern (169 bp):   
TTTCTCAAGGCAGACATTCAATCATAGTCTATTTTAACCAAAAATGTAAAACAATTCAACGTAAA
ATCAATCATAAGATTATAAAACAATAAAAAGCAAGTAATAAAGCTTCTGAAGGAATAAGTGACTA
TAAATAAACTTTTTGCTAATGAATTCCTTTTTCTTCATA
Done.