Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018398703.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_199.0, 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: 6627
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.20

Warning! 3081 characters in sequence are not A, C, G, or T


Found at i:2267 original size:171 final size:161

Alignment explanation


    Indices: 2058--2371  Score: 328
    Period size: 171  Copynumber: 1.9  Consensus size: 161

       2048 NNNNNNNNNN

                            *        *  *                                    
       2058 GAGTAATAAGCCTTTTGAAGGAATGGGTGACCATAAATGAACTTTTCTTACCAATGAATGC-TTT
          1 GAGTAATAAGCCTTTTAAAGGAATGCGTAACCATAAATGAACTTTTCTTACCAATGAATGCTTTT

                                  *                     *                 ** 
       2122 TTCTTCAAATTTCTC-ATGGTAGACATTCAATTATAATCCGTTTTAACCACAAAA-GTACAATGA
         66 TTCTTCAAATTTCTCGA-GGTAAACATTCAATTATAATCCGTTTGAACCA-AAAATGTA-AAAAA

                                                        
       2185 ATTCAAATTAAAATCAATTTTGAGATTATANNNNNNNNNNAAGT
        128 ATTCAAATTAAAATCAATTTTGAGATTATA----------AAGT

                   *  *                    *       *                 *       
       2229 GAGTAATCAGGCTTTTAAAGGAATGCGTAACTATAAATGGACTTTTCTTACCAATGAGTGCTTTT
          1 GAGTAATAAGCCTTTTAAAGGAATGCGTAACCATAAATGAACTTTTCTTACCAATGAATGCTTTT

                 * **                             *        *                 
       2294 TTCTTTACCTTTCTCGAGGTAAACATTCAATTATAATCTGTTTGAACTAAAAATGTAAAAAAATT
         66 TTCTTCAAATTTCTCGAGGTAAACATTCAATTATAATCCGTTTGAACCAAAAATGTAAAAAAATT

               *         
       2359 CAACTTAAAATCA
        131 CAAATTAAAATCA

       2372 NNNNNNNNNN


Statistics
Matches: 122,  Mismatches: 18, Indels: 6
        0.84            0.12        0.04

Matches are distributed among these distances:
 171   75  0.61
 172   46  0.38
 173    1  0.01

ACGTcount: A:0.36, C:0.14, G:0.13, T:0.34


Consensus pattern (161 bp):   
GAGTAATAAGCCTTTTAAAGGAATGCGTAACCATAAATGAACTTTTCTTACCAATGAATGCTTTT
TTCTTCAAATTTCTCGAGGTAAACATTCAATTATAATCCGTTTGAACCAAAAATGTAAAAAAATT
CAAATTAAAATCAATTTTGAGATTATAAAGT

Found at i:2428 original size:21 final size:21

Alignment explanation


    Indices: 2390--2429  Score: 55
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       2380 NNTATAAAAC

                        *        
       2390 CTTTTAAAGTGAGTAATAAGG
          1 CTTTTAAAGTGAATAATAAGG

                                
       2411 CTTTTAAAG-GAATGAATAA
          1 CTTTTAAAGTGAAT-AATAA

       2430 CTATAAATAC


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20    3  0.18
  21   14  0.82

ACGTcount: A:0.42, C:0.05, G:0.20, T:0.33


Consensus pattern (21 bp):   
CTTTTAAAGTGAATAATAAGG

Found at i:3933 original size:171 final size:170

Alignment explanation


    Indices: 3756--4080  Score: 377
    Period size: 170  Copynumber: 1.9  Consensus size: 170

       3746 NNNNTTTGGT

                     *                                   *                   
       3756 TAAAACAGAGTATAATTGAATG-TCTACC-TGTAGAAACATGAAGGGAAAAACATTCATCAAGA-
          1 TAAAACAGACTATAATTGAATGCT-TACCTTG-AGAAACATGAAGAGAAAAACATTCATCAAGAT

                     *                   *          *        *      *        
       3818 AGAAAAGTCTATTTATAGTCACCTATTCCCTCAAAAGCCTTATCACTCGTTTTAAATGATTTTAT
         64 A-AAAAGTCCATTTATAGT-ACCTATTCCATCAAAAGCCTCATCACTCGCTTTAAACGATTTTAT

                                   *                    
       3883 AATCTCATAATTGATTTGAAGTTTAATTGTTTTACATTTTTTGC
        127 AATCTCATAATTGATTTGAAGTTGAATTGTTTTACATTTTTTGC

                                     **    *        *   *    *       ***     
       3927 TAAAACAGACTATAATTGAATGCTTGTCTTGGGAAACATGTAGATAAAACCATTCATTTGGATAA
          1 TAAAACAGACTATAATTGAATGCTTACCTTGAGAAACATGAAGAGAAAAACATTCATCAAGATAA

             *           *  ***                    *                         
       3992 ACAGTCCATTTATTGTTTTTATTCCATCAAAAGCCTCATTACTCGCTTTAAACGATTTTATAATC
         66 AAAGTCCATTTATAGTACCTATTCCATCAAAAGCCTCATCACTCGCTTTAAACGATTTTATAATC

                         *          
       4057 TCATAATTGATTTTAAGTTGAATT
        131 TCATAATTGATTTGAAGTTGAATT

       4081 TTNNNNNNNN


Statistics
Matches: 127,  Mismatches: 24, Indels: 7
        0.80            0.15        0.04

Matches are distributed among these distances:
 170   63  0.50
 171   60  0.47
 172    4  0.03

ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37


Consensus pattern (170 bp):   
TAAAACAGACTATAATTGAATGCTTACCTTGAGAAACATGAAGAGAAAAACATTCATCAAGATAA
AAAGTCCATTTATAGTACCTATTCCATCAAAAGCCTCATCACTCGCTTTAAACGATTTTATAATC
TCATAATTGATTTGAAGTTGAATTGTTTTACATTTTTTGC
Done.