Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018399327.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2596.0, 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: 6155
ACGTcount: A:0.21, C:0.08, G:0.07, T:0.22

Warning! 2630 characters in sequence are not A, C, G, or T


Found at i:3197 original size:170 final size:162

Alignment explanation


    Indices: 2872--3199  Score: 356
    Period size: 170  Copynumber: 2.0  Consensus size: 162

       2862 TCAATTTATT

                *               * *     *       *   *                        
       2872 TTACTTTTTTCATTAAAACATATTATAATTGAATGTTTACGTTGAGAAACTTGAAGAAAAGAAGC
          1 TTACATTTTTCATTAAAACAGACTATAAATGAATGTCTACATTGAGAAACTTGAAGAAAAGAAGC

            *                   *      *        * *                     *    
       2937 GTTCATTGGCAAGAAAAGTCTATTTATTGTCACCCATTCCTTCAAAAGCCATATTACTCACTTCA
         66 ATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCAATACTTCAAAAGCCATATTACTCAATTCA

                        *     *             
       3002 AATAGTTTTATAGTCTCATAATTGATTTTAAG
        131 AATAGTTTTATAATCTCAAAATTGATTTTAAG

                                        *                                    
       3034 TNNNNNNNNNNTACATTTTTCATTAAAATAGACTATAAATGAATGTCTACATTGAGAAA-TGTGA
          1 T----------TACATTTTTCATTAAAACAGACTATAAATGAATGTCTACATTGAGAAACT-TGA

                    *           *                                        *   
       3098 AGAAAAG-CGCATTCATTGGTAAGAAAAGTCCA-TTATAGTCACCCAATACTTCAAAAGCCTTAT
         55 AGAAAAGAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCAATACTTCAAAAGCCATAT

                     *    *                        
       3161 TACTCAATTTAAATGGTTTTATAATCTCAAAATTGATTT
        120 TACTCAATTCAAATAGTTTTATAATCTCAAAATTGATTT

       3200 NNNNNNNNNN


Statistics
Matches: 135,  Mismatches: 20, Indels: 14
        0.80            0.12        0.08

Matches are distributed among these distances:
 162    1  0.01
 170   61  0.45
 171   22  0.16
 172   51  0.38

ACGTcount: A:0.36, C:0.14, G:0.12, T:0.35


Consensus pattern (162 bp):   
TTACATTTTTCATTAAAACAGACTATAAATGAATGTCTACATTGAGAAACTTGAAGAAAAGAAGC
ATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCAATACTTCAAAAGCCATATTACTCAATTCA
AATAGTTTTATAATCTCAAAATTGATTTTAAG

Found at i:3564 original size:170 final size:161

Alignment explanation


    Indices: 3327--3646  Score: 299
    Period size: 170  Copynumber: 1.9  Consensus size: 161

       3317 CCTTCCAAAC

                      **                                           *         
       3327 CCTTATTACTTACTTTAAATGATTTTATAATCACATAATTTATTTGAAGTTGAATGTTTTAACAT
          1 CCTTATTACTCGCTTTAAATGATTTTATAATCACATAATTTATTTGAAGTTGAATATTTTAACAT

                                                                       *     
       3392 TTTTAATTAAAACAGACTATAATTAA-TG-TCTACCTCAAGAAACAT-TAAAAAAAAGGGATTCA
         66 TTTTAATTAAAACAGACTATAATTAATTGCT-TACCTCAAGAAACATGT-AAAAAAAGGCATTCA

             *    *                          
       3454 TTGAGATGAAAAGTCCATTTATAGCCACCCATT
        129 TGGAGAAGAAAAGTCCATTTATAGCCACCCATT

                                           *             *      *   *        
       3487 CCTTNNNNNNNNNNATTACTCGCTTTAAATGGTTTTATAATCTA-TTAATTTCTTTTAAG-TGAA
          1 CCTT----------ATTACTCGCTTTAAATGATTTTATAATC-ACATAATTTATTTGAAGTTG-A

                   *        **            *     *       *   * *          *   
       3550 ATATTTTTACATTTTTTGTTAAAACAGACTCTAATTGATTGCTTGCCTTAGGAAACATGTAGAAA
         54 ATATTTTAACATTTTTAATTAAAACAGACTATAATTAATTGCTTACCTCAAGAAACATGTAAAAA

               *                            
       3615 AAGTCATTCATGGAGAAGAAAAGTCCATTTAT
        119 AAGGCATTCATGGAGAAGAAAAGTCCATTTAT

       3647 TGTCACCTAT


Statistics
Matches: 125,  Mismatches: 20, Indels: 19
        0.76            0.12        0.12

Matches are distributed among these distances:
 160    4  0.03
 169    2  0.02
 170   70  0.56
 171   47  0.38
 172    2  0.02

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


Consensus pattern (161 bp):   
CCTTATTACTCGCTTTAAATGATTTTATAATCACATAATTTATTTGAAGTTGAATATTTTAACAT
TTTTAATTAAAACAGACTATAATTAATTGCTTACCTCAAGAAACATGTAAAAAAAGGCATTCATG
GAGAAGAAAAGTCCATTTATAGCCACCCATT
Done.