Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018397670.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3650.0, 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, 985

Length: 1643
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38

Warning! 10 characters in sequence are not A, C, G, or T


Found at i:942 original size:172 final size:171

Alignment explanation


    Indices: 113--1516  Score: 1289
    Period size: 171  Copynumber: 8.2  Consensus size: 171

        103 AGAGTTATCA

                   *              *       *   * *    *       *               
        113 ATTACTCACTTTAAATGGTTTTGTAATCTCGTAAATGATTTCAAGTTGATTTTTTTTACATTTTT
          1 ATTACTCGCTTTAAATGGTTTTATAATCTCATAATTCATTTTAAGTTGAATTTTTTTACATTTTT

             *        *                 **    *                              
        178 GATTAAAACAAATTATAATTGAATGTCTACCTTAAGAAACGTAAAGAAAAAGCCATTCATTGGA-
         66 GGTTAAAACAGATTATAATTGAATGTCTGTCTTAGGAAACGTAAAGAAAAAGCCATTCATT-GAC

            *         *        *    *  *               
        242 AAGAAAAGTCTATTTATAGCCACCTATTCC-TCGAAAAGCCTT
        130 TAGAAAAGTCCATTTATAGTCACCCATGCCTTCG-AAAGCCTT

                            *     *               *                 *        
        284 ATTACTCGCTTTAAATAGTTTTGTAATCTCATAATTCAGTTTAAGTTGAATTTTTTCACATTTTT
          1 ATTACTCGCTTTAAATGGTTTTATAATCTCATAATTCATTTTAAGTTGAATTTTTTTACATTTTT

            *          ** **        *       * **    * *         **          *
        349 CGTTAAAACAGGCTGCAATTGAATATCTGTCTCAAAAAACATTAAGAAAAAGGAATTCATTGACG
         66 GGTTAAAACAGATTATAATTGAATGTCTGTCTTAGGAAACGTAAAGAAAAAGCCATTCATTGACT

                                   *  *               
        414 AGAAAAGTCCATTTATAGTCACCTATCCCTTC-AAATGCCTT
        131 AGAAAAGTCCATTTATAGTCACCCATGCCTTCGAAA-GCCTT

                            *            *                               *   
        455 ATTACTCGCTTTAAATAGTTTTATAATCTAATAATTCATTTTAAGTTGAATTTTTTTACATATTT
          1 ATTACTCGCTTTAAATGGTTTTATAATCTCATAATTCATTTTAAGTTGAATTTTTTTACATTTTT

            *           *                **          *  *                    
        520 AGTTAAAACAGACTATAATT-AAGTGTCTACCTT-GAGAAATGTGAAGAAACAAG-CATTCATTG
         66 GGTTAAAACAGATTATAATTGAA-TGTCTGTCTTAG-GAAACGTAAAGAAA-AAGCCATTCATTG

             *                         *  *     *   **   
        582 -GTAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAATCTT
        128 ACT-AGAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTT

                   *                            *                    *       
        626 ATTACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTCCATTTTT
          1 ATTACTCGCTTTAAATGGTTTTATAATCTCATAATTCATTTTAAGTTGAATTTTTTTACATTTTT

                                 *                               * *         
        691 GGTTAAAACAG-TATATAATTAAATGTCTG--TTAGGAGAAACGTAAAGAAAACGACATTCATTG
         66 GGTTAAAACAGAT-TATAATTGAATGTCTGTCTTA-G-GAAACGTAAAGAAAAAGCCATTCATTG

            *                           *       *    *  
        753 CCTAGAAAAGTCCATTTATAGTCACCCAAGCCTTCGTAAGCGTT
        128 ACTAGAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTT

               *            *             *             *  *          *      
        797 ATTGCTCGCTTTAAATAGTTTTATAATCTCGTAATTCATTTTAAATTTAATTTTTTTTTCATTTT
          1 ATTACTCGCTTTAAATGGTTTTATAATCTCATAATTCATTTTAAGTTGAA-TTTTTTTACATTTT

                     *      *      *         *      *  *                     
        862 TGGTTAAAATAGATTACAATTGATTGTCTGTCTCAGGAAATGTGAAGAAAAAGCCATTCATTGAC
         65 TGGTTAAAACAGATTATAATTGAATGTCTGTCTTAGGAAACGTAAAGAAAAAGCCATTCATTGAC

                    *                                 
        927 TAGAAAAGCCCATTTATAGTCACCCATGCCTTCGAAAGCCTT
        130 TAGAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTT

                   **                           *         *      *           
        969 ATTACTCATTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTAGAATTTCTTTACAATTTT
          1 ATTACTCGCTTTAAATGGTTTTATAATCTCATAATTCATTTTAAGTTGAATTTTTTTAC-ATTTT

                     * *         *                   **    *      ***        
       1034 T-GTTAAAAAAAATTATAATTCAATGTCT-TCGTTAGGAAATATAAACAAAAAGTTGTTCATTGA
         65 TGGTTAAAACAGATTATAATTGAATGTCTGTC-TTAGGAAACGTAAAGAAAAAGCCATTCATTGA

            **        **          *      ***  **   *    
       1097 AAAGAAAA-TTTATTTATAG-CCCCCTATTTTTTTAAAACCCTT
        129 CTAGAAAAGTCCATTTATAGTCACCC-ATGCCTTCGAAAGCCTT

                             *    *       *     * *                  *  *    
       1139 ATTACTCGCTTTAAATGATTTTGTAATCTCGTAATTGAGTTTAAGTT--ATATTTTTGACCTTTT
          1 ATTACTCGCTTTAAATGGTTTTATAATCTCATAATTCATTTTAAGTTGAAT-TTTTTTACATTTT

             *    *                 *   *        *     * *         *    *    
       1202 TAGTTACAACATGA-TATAATTGACTGTTTGTCTTA-AAGAACATTAAGAAAAAGGCATTTATTG
         65 TGGTTAAAACA-GATTATAATTGAATGTCTGTCTTAGGA-AACGTAAAGAAAAAGCCATTCATTG

                        *              *  *     *        
       1265 -CTAAGAAAAGTTCATTTATAGTCACCTATTCCTTCAAAAGCCTT
        128 ACT-AGAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTT

                                                           *                 
       1309 ATTACTCGCTTTAAATGGTTTTATAATCTCATAATTCATTTTAAGTTAAATTTTTTTTACATTTT
          1 ATTACTCGCTTTAAATGGTTTTATAATCTCATAATTCATTTTAAGTTGAA-TTTTTTTACATTTT

                          * *             *   *   *  * *         *           
       1374 TGGTTAAAACAGATAACAATTGAATGTCTGCCTTGGGAGACATGAAGAAAAAGTCATTCATTGAC
         65 TGGTTAAAACAGATTATAATTGAATGTCTGTCTTAGGAAACGTAAAGAAAAAGCCATTCATTGAC

                    *    *   *    *                   
       1439 TAGAAAAGCCCATATATTGTCATCCATGCCTTCGAAAGCCTT
        130 TAGAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTT

                                       *  *     
       1481 ATTACTCGCTTTAAATGGTTTTATAATATCGTAATT
          1 ATTACTCGCTTTAAATGGTTTTATAATCTCATAATT

       1517 GATNNNNNNN


Statistics
Matches: 1004,  Mismatches: 194, Indels: 69
        0.79            0.15        0.05

Matches are distributed among these distances:
 168    8  0.01
 169   58  0.06
 170  138  0.14
 171  511  0.51
 172  281  0.28
 173    6  0.01
 174    2  0.00

ACGTcount: A:0.34, C:0.14, G:0.12, T:0.39


Consensus pattern (171 bp):   
ATTACTCGCTTTAAATGGTTTTATAATCTCATAATTCATTTTAAGTTGAATTTTTTTACATTTTT
GGTTAAAACAGATTATAATTGAATGTCTGTCTTAGGAAACGTAAAGAAAAAGCCATTCATTGACT
AGAAAAGTCCATTTATAGTCACCCATGCCTTCGAAAGCCTT
Done.