Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018402488.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5562.0, 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: 3945
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.30

Warning! 851 characters in sequence are not A, C, G, or T


Found at i:767 original size:171 final size:162

Alignment explanation


    Indices: 580--909  Score: 315
    Period size: 171  Copynumber: 2.0  Consensus size: 162

        570 GGAGAAACGC

                                                                          *  
        580 GAAGAGAAAAGCATTCATCGGCAAAAAAAGTCCATTTATAGCCACCCATTCTTTCAAAAGCCTTA
          1 GAAGAGAAAAGCATTCATCGGCAAAAAAAGTCCATTTATAGCCACCCATTCTTTCAAAAGCCATA

                                  *   *   *                    *     *       
        645 TTACACACTTTAAATAGTTTTATAAAGTCATAATTCATTTTAAGTTGAATTGTTTG-GCATTTTT
         66 TTACACACTTTAAATAGTTTTAGAAACTCAAAATTCATTTTAAGTTGAATTCTTTGTACATTTTT

                     *                                 
        709 GATT-AAAATAGACTATAATTGAATGTCTNNNNNNNNNNATGT
        131 -ATTCAAAACAGACTATAATTGAATGTCT----------ATGT

                               ** *  *       *        *    *                 
        751 GAAGA-AAAAGGCATTCATTTGTAAGAAAAGTCTATTTATAGTCACCTATTCTTTCAAAAGCCAT
          1 GAAGAGAAAA-GCATTCATCGGCAAAAAAAGTCCATTTATAGCCACCCATTCTTTCAAAAGCCAT

            *    * *     *  *         *         *                            
        815 GTTACTCGCTTTATATGGTTTTAGAATCTCAAAATTGATTTTAAGTTGAATTCTTTGTACATTTT
         65 ATTACACACTTTAAATAGTTTTAGAAACTCAAAATTCATTTTAAGTTGAATTCTTTGTACATTTT

                 *       *           *    
        880 TATTCTAAACAGATTATAATTGAATATCTA
        130 TATTCAAAACAGACTATAATTGAATGTCTA

        910 CCTAGAGAAA


Statistics
Matches: 132,  Mismatches: 24, Indels: 15
        0.77            0.14        0.09

Matches are distributed among these distances:
 162    1  0.01
 170    4  0.03
 171  100  0.76
 172   27  0.20

ACGTcount: A:0.35, C:0.13, G:0.12, T:0.37


Consensus pattern (162 bp):   
GAAGAGAAAAGCATTCATCGGCAAAAAAAGTCCATTTATAGCCACCCATTCTTTCAAAAGCCATA
TTACACACTTTAAATAGTTTTAGAAACTCAAAATTCATTTTAAGTTGAATTCTTTGTACATTTTT
ATTCAAAACAGACTATAATTGAATGTCTATGT

Found at i:3322 original size:172 final size:171

Alignment explanation


    Indices: 3027--3340  Score: 459
    Period size: 172  Copynumber: 1.8  Consensus size: 171

       3017 NNNNNNNNNN

                                                                  *          
       3027 CTCACTTTAAATAGTTTATAATCTCAAAACTGATTTCAATTTGAATTCTTTGCATATTTTTGGTT
          1 CTCACTTTAAATAGTTTATAATCTCAAAACTGATTTCAATTTGAATTCTTTGCACATTTTTGGTT

                  *                                        *   *         *   
       3092 AAAACAGATTATAATTGAATGTCTACCTCAAGAAAAATGAAGAAAAATGCATTCATTGGCAGGAA
         66 AAAACAAATTATAATTGAATGTCTACCTCAAGAAAAATGAAGAAAAAAGCAATCATTGGCAAGAA

              *                                      
       3157 AAGTCCATTTATAGTCACTCATTCCTTTAAAAGCCTTTTTA
        131 AACTCCATTTATAGTCACTCATTCCTTTAAAAGCCTTTTTA

                                           * *    * *             *        * 
       3198 CTCACTTTAAATAGTTTTATAATCT-AAAAGTTTATTTTAGTTTGAATTCTTTGTACATTTTTTG
          1 CTCACTTTAAATAG-TTTATAATCTCAAAA-CTGATTTCAATTTGAATTCTTTGCACATTTTTGG

                          *                *     *                           
       3262 TTAAAACAAATTATTATTGAATGTCTACCTCGAGAAACATGAAGAAAAAAGCAATCATTGGCAAG
         64 TTAAAACAAATTATAATTGAATGTCTACCTCAAGAAAAATGAAGAAAAAAGCAATCATTGGCAAG

             *            
       3327 ACAACTCCATTTAT
        129 AAAACTCCATTTAT

       3341 TGACNNNNNN


Statistics
Matches: 125,  Mismatches: 16, Indels: 3
        0.87            0.11        0.02

Matches are distributed among these distances:
 171   18  0.14
 172  107  0.86

ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38


Consensus pattern (171 bp):   
CTCACTTTAAATAGTTTATAATCTCAAAACTGATTTCAATTTGAATTCTTTGCACATTTTTGGTT
AAAACAAATTATAATTGAATGTCTACCTCAAGAAAAATGAAGAAAAAAGCAATCATTGGCAAGAA
AACTCCATTTATAGTCACTCATTCCTTTAAAAGCCTTTTTA
Done.