Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018403189.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_856.0, 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: 5858
ACGTcount: A:0.18, C:0.06, G:0.05, T:0.19

Warning! 2998 characters in sequence are not A, C, G, or T


Found at i:3141 original size:171 final size:169

Alignment explanation


    Indices: 2735--3155  Score: 450
    Period size: 169  Copynumber: 2.5  Consensus size: 169

       2725 NNNNNNNNNN

                               *  *    *                          *          
       2735 ATAGATTATAATTGAATGTTTACCTCAGGAAACATGAAGAAAAAGATATCCATTAGCAAGAAAAG
          1 ATAGATTATAATTGAATGTCTAGCTCAAGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAG

                *              *                                        *    
       2800 TCCAATTATAGTCACCCATGCCTTCAAAAGCTTTATTACTAGCTTTAAATGATTTGATAAGCTCA
         66 TCCATTTATAGTCACCCATACCTTCAAAAGCTTTATTACTAGCTTTAAATGATTTGATAACCTCA

                 * *                         *     
       2865 TAATTTATTTTAGATTGAATTTTATTATATTTTTTTAAA
        131 TAATTGAATTTAGATTGAATTTTATTATATTTTATTAAA

               *         *            **            *          *     *       
       2904 ATAAATTATAATTAAATGTCT-GCCTTGAGAAACATGAAGGAAAAGATATCTATTGGTAAGAAAA
          1 ATAGATTATAATTGAATGTCTAG-CTCAAGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAA

                      *                *  **************            **       
       2968 GTCCATTTATTGTCACCCATACCTTCAGAANNNNNNNNNNNNNNTTTAAATGATTTTTTAACCTC
         65 GTCCATTTATAGTCACCCATACCTTCAAAAGCTTTATTACTAGCTTTAAATGATTTGATAACCTC

                                     *                 
       3033 ATAATTGAATTTA-ATTTGAATTTTTTTATAATTGTTATTAAA
        130 ATAATTGAATTTAGA-TTGAATTTTATTAT-ATT-TTATTAAA

                             *                            *                  
       3075 ATAGATTATAATTGAATATCTAGCTCAAGAAACATGAAGAAAAAGACATCCATTGGCAAGAAAAG
          1 ATAGATTATAATTGAATGTCTAGCTCAAGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAG

                            
       3140 TCCATTTATAGTCACC
         66 TCCATTTATAGTCACC

       3156 NNNNNNNNNN


Statistics
Matches: 201,  Mismatches: 46, Indels: 8
        0.79            0.18        0.03

Matches are distributed among these distances:
 168    1  0.00
 169  120  0.60
 170    3  0.01
 171   76  0.38
 172    1  0.00

ACGTcount: A:0.38, C:0.12, G:0.12, T:0.34


Consensus pattern (169 bp):   
ATAGATTATAATTGAATGTCTAGCTCAAGAAACATGAAGAAAAAGATATCCATTGGCAAGAAAAG
TCCATTTATAGTCACCCATACCTTCAAAAGCTTTATTACTAGCTTTAAATGATTTGATAACCTCA
TAATTGAATTTAGATTGAATTTTATTATATTTTATTAAA

Found at i:5850 original size:170 final size:170

Alignment explanation


    Indices: 5533--5855  Score: 407
    Period size: 170  Copynumber: 1.9  Consensus size: 170

       5523 NNNNNNNNNN

                                                                     *       
       5533 CTTTAAATGATTTTATAACCTCATAATTGATTTTAATTTGAATTTTTTTATTTATTTTTTAAAAC
          1 CTTTAAATGATTTTATAACCTCATAATTGATTTTAATTTGAATTTTTTTATTTATTTATTAAAAC

                             *      *        *                               
       5598 AGATTATAATTGAATGTTTACATCGAGAAACATGAAGAAAAAGATATCCATTCGAAAGAAAAGTC
         66 AGATTATAATTGAATGTCTACATCAAGAAACATAAAGAAAAAGATATCCATTCGAAAGAAAAGTC

             **********                             
       5663 CNNNNNNNNNNACCCATGCCTTTAAAAGCTTTATTACTCG
        131 CATTTATAGTAACCCATGCCTTTAAAAGCTTTATTACTCG

                            *    *                   *                     * 
       5703 CTTTAAATGATTTTATGACCTTATAATTGATTTTAATTTGACTTTTTTCATATTT-TTTATTATA
          1 CTTTAAATGATTTTATAACCTCATAATTGATTTTAATTTGAATTTTTT--TATTTATTTATTAAA

                                 * * *                            * *        
       5767 ACAGATTATAATTGAATGTCTGCCTTAAGAAACATAAAG-AAAAGATATCCATTGGCAAGAAAAG
         64 ACAGATTATAATTGAATGTCTACATCAAGAAACATAAAGAAAAAGATATCCATTCGAAAGAAAAG

                                     
       5831 TCCATTTATAGTAACCCATGCCTTT
        129 TCCATTTATAGTAACCCATGCCTTT

       5856 GAA


Statistics
Matches: 128,  Mismatches: 23, Indels: 4
        0.83            0.15        0.03

Matches are distributed among these distances:
 170   83  0.65
 171   40  0.31
 172    5  0.04

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


Consensus pattern (170 bp):   
CTTTAAATGATTTTATAACCTCATAATTGATTTTAATTTGAATTTTTTTATTTATTTATTAAAAC
AGATTATAATTGAATGTCTACATCAAGAAACATAAAGAAAAAGATATCCATTCGAAAGAAAAGTC
CATTTATAGTAACCCATGCCTTTAAAAGCTTTATTACTCG
Done.