Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018403277.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_952.0, 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: 4269
ACGTcount: A:0.22, C:0.06, G:0.08, T:0.20

Warning! 1840 characters in sequence are not A, C, G, or T


Found at i:1180 original size:171 final size:172

Alignment explanation


    Indices: 877--1193  Score: 435
    Period size: 171  Copynumber: 1.8  Consensus size: 172

        867 TTTTTGCATG

                                                                         *   
        877 TTTCTCAAGGCAGACATTCAATTAAAGTCTGTTTTAACAAAAAAATGTAAAAAAATTCAACTTAA
          1 TTTCTCAAGGCAGACATTCAATTAAAGTCTGTTTTAACAAAAAAATGTAAAAAAATTCAACGTAA

                  *    *           **                    *                   
        942 AATCAATTATGCGATTATAAAACTGTTTAAAGCGAGTAATAAGCTTTTTGAAGGAAAGGATGACT
         66 AATCAACTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGCTATTTGAAGGAAAGGATGACT

                                                      
       1007 CTAAATAGACTTTTCTTCTTAATGAATGACTTTTTCTGTACA
        131 CTAAATAGACTTTTCTTCTTAATGAATGACTTTTTCTGTACA

                  *   *              *                     *   *      *      
       1049 TTTCTCGAGGTAGACGA-TCAATTACAGTCTGTTTTAAC-AAAAAATTTAAGAAAATTGAACGTA
          1 TTTCTCAAGGCAGAC-ATTCAATTAAAGTCTGTTTTAACAAAAAAATGTAAAAAAATTCAACGTA

                                                         *             *  *  
       1112 AAA-CTAACTATGAGATTATAAAACAATTTAAAGCGAGTAAT-AGGTCATTTGAAGGAATGGGTG
         65 AAATC-AACTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGCT-ATTTGAAGGAAAGGATG

                     *         
       1175 ACTCTAAATGGACTTTTCT
        128 ACTCTAAATAGACTTTTCT

       1194 NNNNNNNNNN


Statistics
Matches: 126,  Mismatches: 16, Indels: 7
        0.85            0.11        0.05

Matches are distributed among these distances:
 170    4  0.03
 171   88  0.70
 172   33  0.26
 173    1  0.01

ACGTcount: A:0.39, C:0.12, G:0.15, T:0.33


Consensus pattern (172 bp):   
TTTCTCAAGGCAGACATTCAATTAAAGTCTGTTTTAACAAAAAAATGTAAAAAAATTCAACGTAA
AATCAACTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGCTATTTGAAGGAAAGGATGACT
CTAAATAGACTTTTCTTCTTAATGAATGACTTTTTCTGTACA

Found at i:2597 original size:173 final size:173

Alignment explanation


    Indices: 2259--2573  Score: 427
    Period size: 173  Copynumber: 1.8  Consensus size: 173

       2249 NNNNNNNTTT

                                 *                            **    *        
       2259 AAAGTGAGTAATAAGCCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTGTTCTTAATGAATA
          1 AAAGTGAGTAATAAGCCTTTTCAAGGAATGAGTGACTATAAATAGACTTTCCTTCTCAATGAATA

                      *  *    * *      * * * *                               
       2324 AGCTTTTTCTGCATGTTTTTTAAGATAGGTATTGAATTATAGTCTATTTTAACAAAAAAATAAAA
         66 AGCTTTTTCTACACGTTTCTCAAGATAAGCAATCAATTATAGTCTATTTTAACAAAAAAATAAAA

                                                       
       2389 AAAATTCAACTTAAAATCAATTATGAAATTATAAAAACAATTA
        131 AAAATTCAACTTAAAATCAATTATGAAATTATAAAAACAATTA

                  *         *                          *                    *
       2432 AAAGTGGGTAATAAGCTTTTTCAAGGAATGAGTGACTATAAATGGACTTTCCTTCTCAATGAATG
          1 AAAGTGAGTAATAAGCCTTTTCAAGGAATGAGTGACTATAAATAGACTTTCCTTCTCAATGAATA

                                    *                    *                 * 
       2497 A-CTTTTTCTACACGTTTCTCAAGGTAAGCAATCAATTATAGTCTGTTTTGAAC-AAAAAATGTA
         66 AGCTTTTTCTACACGTTTCTCAAGATAAGCAATCAATTATAGTCTATTTT-AACAAAAAAAT-AA

                          
       2560 AAAAAATTCAACTT
        129 AAAAAATTCAACTT

       2574 NNNNNNNNNN


Statistics
Matches: 121,  Mismatches: 19, Indels: 4
        0.84            0.13        0.03

Matches are distributed among these distances:
 172   45  0.37
 173   76  0.63

ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35


Consensus pattern (173 bp):   
AAAGTGAGTAATAAGCCTTTTCAAGGAATGAGTGACTATAAATAGACTTTCCTTCTCAATGAATA
AGCTTTTTCTACACGTTTCTCAAGATAAGCAATCAATTATAGTCTATTTTAACAAAAAAATAAAA
AAAATTCAACTTAAAATCAATTATGAAATTATAAAAACAATTA
Done.