Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018401939.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5039.0, 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: 3804
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.19

Warning! 1918 characters in sequence are not A, C, G, or T


Found at i:324 original size:170 final size:160

Alignment explanation


    Indices: 135--454  Score: 340
    Period size: 170  Copynumber: 1.9  Consensus size: 160

        125 GGCTTATTAC

                                                                             
        135 TTTAAATGGTTTTATAATCTCATAATAGATTTTAAG-TAGAATTTTTTTAT-ATTTTTCATTAAA
          1 TTTAAATGGTTTTATAATCTCATAATAGATTTTAAGTTA-AA-TTTTTTATCATTTTTCATTAAA

             **                **            *                     *         
        198 ATGGACTATAACTGAATATTTACCTCAAGAAACGTG-AACAAAAAGCATTCAATGGTAAGAAAAG
         64 ACAGACTATAACTGAATATCCACCTCAAGAAACATGAAAC-AAAAGCATTCAATGATAAGAAAAG

                                                       
        262 TCCATTTATAGTCACCCATTNNNNNNNNNNCCTTGTTACCCAT
        128 TCCATTTATAGTCACCCATT----------CCTTGTTACCCAT

                                      *                             *        
        305 TTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTATCATTTTTTATTAAAAC
          1 TTTAAATGGTTTTATAATCTCATAATAGATTTTAAGTTAAATTTTTTATCATTTTTCATTAAAAC

                     *   * *       **                 * *     *              
        370 AGACTATAATTGATTGTCCACCTTGAGAAACATGAAATCAAAGGTATTCATTGATAAGAAAAGTC
         66 AGACTATAACTGAATATCCACCTCAAGAAACATGAAA-CAAAAGCATTCAATGATAAGAAAAGTC

                          *     
        435 CATTTATAGTCACCGATTCC
        130 CATTTATAGTCACCCATTCC

        455 CTCAAAAGCC


Statistics
Matches: 129,  Mismatches: 17, Indels: 17
        0.79            0.10        0.10

Matches are distributed among these distances:
 161    2  0.02
 169    8  0.06
 170   75  0.58
 171   43  0.33
 172    1  0.01

ACGTcount: A:0.35, C:0.13, G:0.11, T:0.38


Consensus pattern (160 bp):   
TTTAAATGGTTTTATAATCTCATAATAGATTTTAAGTTAAATTTTTTATCATTTTTCATTAAAAC
AGACTATAACTGAATATCCACCTCAAGAAACATGAAACAAAAGCATTCAATGATAAGAAAAGTCC
ATTTATAGTCACCCATTCCTTGTTACCCAT

Found at i:3729 original size:17 final size:17

Alignment explanation


    Indices: 3700--3732  Score: 50
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       3690 NNNAGACTAT

                             
       3700 AAATAGAATTGTTTTCC
          1 AAATAGAATTGTTTTCC

                             
       3717 AAATA-AATGTGTTTTC
          1 AAATAGAAT-TGTTTTC

       3733 TCATACGTTT


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  16    3  0.20
  17   12  0.80

ACGTcount: A:0.36, C:0.09, G:0.12, T:0.42


Consensus pattern (17 bp):   
AAATAGAATTGTTTTCC
Done.