Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018402271.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5354.0, 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, 723

Length: 1206
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.34

Warning! 141 characters in sequence are not A, C, G, or T


Found at i:823 original size:173 final size:162

Alignment explanation


    Indices: 637--965  Score: 329
    Period size: 172  Copynumber: 2.0  Consensus size: 162

        627 CATTGATATA

                  *        *          *                                  * * 
        637 AAAAGTCCATTTATAGTCACCCATGCTTTCAAAAGCCTTATTACTCACTTAAAATAGTTTTGTTA
          1 AAAAGTACATTTATAATCACCCATGCCTTCAAAAGCCTTATTACTCACTTAAAATA-TTTTATAA

                     **      *   **         *   *                  *         
        702 TCTCAAAATTGATTTTATGTTTTAT-TTTATTTTACGTTTTTGC-TTAAAACAGATTATAATTGA
         65 TCTCAAAATCAATTTTAAGTTAAATGTTT-TTATACATTTTT-CATTAAAACAGACTATAATTGA

                         *                               
        765 ATGTCTACCTCAAGAAATGTAAAGAAAAAGGNNNNNNNNNNCAAG
        128 ATGTCTACCTCAAAAAATGTAAAGAAAAAGG----------CAAG

                                    *                      *  *              
        810 AAAAGTACATTTATAATCACCCATTCCTTCAAAAGCCTTATTACTCATTTTAAATATTTTATAAT
          1 AAAAGTACATTTATAATCACCCATGCCTTCAAAAGCCTTATTACTCACTTAAAATATTTTATAAT

                *                            *              *                
        875 CTCATAATCAATTTTAAGTTAAATGTTTTTATATATTTTTCATTAAAATAGACTATAATTGAATG
         66 CTCAAAATCAATTTTAAGTTAAATGTTTTTATACATTTTTCATTAAAACAGACTATAATTGAATG

                *            *        
        940 TCTATCTCAAAAAATGTGAAGAAAAA
        131 TCTACCTCAAAAAATGTAAAGAAAAA

        966 AGCATTCATT


Statistics
Matches: 132,  Mismatches: 22, Indels: 5
        0.83            0.14        0.03

Matches are distributed among these distances:
 171    1  0.01
 172   78  0.59
 173   53  0.40

ACGTcount: A:0.37, C:0.13, G:0.09, T:0.38


Consensus pattern (162 bp):   
AAAAGTACATTTATAATCACCCATGCCTTCAAAAGCCTTATTACTCACTTAAAATATTTTATAAT
CTCAAAATCAATTTTAAGTTAAATGTTTTTATACATTTTTCATTAAAACAGACTATAATTGAATG
TCTACCTCAAAAAATGTAAAGAAAAAGGCAAG

Found at i:995 original size:172 final size:171

Alignment explanation


    Indices: 464--1206  Score: 593
    Period size: 173  Copynumber: 4.3  Consensus size: 171

        454 TGTTACTAAA

                   *          * *              *                *    *       
        464 AAAAGTCTATTTATAGTCTCTCATTCTTTCAAAAGTCTTATTACTCACTTTATATGACTTTATAA
          1 AAAAGTCCATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTCACTTTAAAT-ATTTTATAA

                             *   *             *      *       *           *  
        529 TCTCATAATTGATTTTAGGTTCAATTGTTTT-TACTTTGTTTTGTTAAAAAAGATTATAATTCAA
         65 TCTCATAATTGATTTTATGTTAAATT-TTTTATACATT-TTTCGTTAAAATAGATTATAATTGAA

             *     * ** *   *      *                *    
        593 TTTCTACGTGGAGAAACGTGAAGGAAAAAGCATTCATTGATATA-
        128 TGTCTACATCAAAAAATGTGAAGAAAAAAGCATTCATTGACA-AG

                                    *                         *          * * 
        637 AAAAGTCCATTTATAGTCACCCATGCTTTCAAAAGCCTTATTACTCACTTAAAATAGTTTTGTTA
          1 AAAAGTCCATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTCACTTTAAATA-TTTTATAA

                 *               **        *   *              *              
        702 TCTCAAAATTGATTTTATGTTTTATTTTATTTTACGTTTTT-GCTTAAAACAGATTATAATTGAA
         65 TCTCATAATTGATTTTATGTTAAATTTT-TTATACATTTTTCG-TTAAAATAGATTATAATTGAA

                   *    *      *        * **********    
        766 TGTCTACCTCAAGAAATGTAAAGAAAAAGGNNNNNNNNNNCAAG
        128 TGTCTACATCAAAAAATGTGAAGAAAAAAGCATTCATTGACAAG

                  *        *          *                    *                 
        810 AAAAGTACATTTATAATCACCCATTCCTTCAAAAGCCTTATTACTCATTTTAAATATTTTATAAT
          1 AAAAGTCCATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTCACTTTAAATATTTTATAAT

                    **      *                *       *          *            
        875 CTCATAATCAATTTTAAGTTAAATGTTTTTATATATTTTTCATTAAAATAGACTATAATTGAATG
         66 CTCATAATTGATTTTATGTTAAAT-TTTTTATACATTTTTCGTTAAAATAGATTATAATTGAATG

                                                  *    
        940 TCTATC-TCAAAAAATGTGAAGAAAAAAGCATTCATTGCCAAG
        130 TCTA-CATCAAAAAATGTGAAGAAAAAAGCATTCATTGACAAG

                             ** *                          *   ********      
        982 AAAAGTCCATTTATAGTTTCTCATTCTTTCAAAAGCCTTATTACTC-GTNNNNNNNNNNTTTATA
          1 AAAAGTCCATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTCACT--TTAAATATTTTATA

                                  *         *     *  *                       
       1046 ATCTCATAATTGATTTTATGTTCAATTTTTT-CACATTATTGGTTAAAATAGATTATAATTGAAT
         64 ATCTCATAATTGATTTTATGTTAAATTTTTTATACATTTTTCGTTAAAATAGATTATAATTGAAT

              *            *                  *     *   *
       1110 GTGTACATCAAGAAACT-TGAAG-AAAAAGACATCCATTGGCAAA
        129 GTCTACATCAA-AAAATGTGAAGAAAAAAG-CATTCATTGACAAG

                   * *           *    *                           
       1153 AAAAGTCTACTTATAGTCACCTATTCCTTCAAAAGCCTTATTACTCACTTTAAA
          1 AAAAGTCCATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTCACTTTAAA


Statistics
Matches: 444,  Mismatches: 112, Indels: 31
        0.76            0.19        0.05

Matches are distributed among these distances:
 170    7  0.02
 171   91  0.20
 172  137  0.31
 173  204  0.46
 174    5  0.01

ACGTcount: A:0.35, C:0.14, G:0.10, T:0.38


Consensus pattern (171 bp):   
AAAAGTCCATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTCACTTTAAATATTTTATAAT
CTCATAATTGATTTTATGTTAAATTTTTTATACATTTTTCGTTAAAATAGATTATAATTGAATGT
CTACATCAAAAAATGTGAAGAAAAAAGCATTCATTGACAAG
Done.