Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018400590.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3783.0, 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, 894

Length: 1490
ACGTcount: A:0.25, C:0.11, G:0.08, T:0.25

Warning! 464 characters in sequence are not A, C, G, or T


Found at i:1054 original size:172 final size:170

Alignment explanation


    Indices: 701--1372  Score: 650
    Period size: 172  Copynumber: 3.9  Consensus size: 170

        691 NNNNNNNNCG

                        *                *       **       *               *  
        701 TTTATAGTCACCTATTCCTTCAAAAGCCTCATTACTCGTTTTAAATGGTTTTGTAATGC-CATAA
          1 TTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTGTAAT-CTCAAAA

                  *** *   * * *                *       *                     
        765 TTGATTTTTAGTTGCAGTATTTTACATTTTTGGTTTAAACAGACTATAATTGAATGTCAATCTCA
         65 TTGATTGAAATTTGAATTCTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCAA-CTCA

                    *         *     *    *           *
        830 AGAAACATAAAGAAAAAGACATTTGTTGGCAAGAAAAGTCCC
        129 AGAAACATGAAGAAAAAGGCATTTATTGGTAAGAAAAGTCCA

                                           *                        *        
        872 TTTATAGTCACCCATTCCTTCAAAAGCCTTAGTACTCACTTTAAATAGTTTTGTAAACTCAAAAT
          1 TTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTGTAATCTCAAAAT

              *                      *             *          *      *       
        937 TGCTTGAAATTTGAATTCTTTATACTTTTTTGGTTAAAAAAGATTATAATGGAATGTGAACATCA
         66 TGATTGAAATTTGAATTCTTT-TACATTTTTGGTTAAAACAGATTATAATTGAATGTCAAC-TCA

            *           *                             
       1002 GGAAACATGAAGGAAAAGGCATTTATTGGTAAGAAAAGTCCA
        129 AGAAACATGAAGAAAAAGGCATTTATTGGTAAGAAAAGTCCA

                                    *          *     *          *            
       1044 TTTATAGTCACCCATTCCTTCAAATGCCTTATTACACACTTGAAATAGTTTTATAATCTCAAAAT
          1 TTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTGTAATCTCAAAAT

             *   **********                          *             *         
       1109 TAATTNNNNNNNNNNTTCTTTGTACATTTTTGGTTAAAACATATTATAATTGAATATCAACCTCA
         66 TGATTGAAATTTGAATTCTTT-TACATTTTTGGTTAAAACAGATTATAATTGAATGTCAA-CTCA

                       *           *                  
       1174 AGAAACATGAATAAAAAGG--TTCATTGGTAAGAAAAGTCCA
        129 AGAAACATGAAGAAAAAGGCATTTATTGGTAAGAAAAGTCCA

                * *     *      *                         *                 * 
       1214 TTTACAATCACCTATTCCTCCAAAAGCCTTATTACTCACTTTAAACAGTTTTGTAATCTCAAACT
          1 TTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTGTAATCTCAAAAT

                        *         *          *      *           *   *        
       1279 TGATTGAAATTTCAATTCTTTGCACATTTTAT-ATTAAAAGAGATTATAATTCAATATCAATCTC
         66 TGATTGAAATTTGAATTCTTT-TACATTTT-TGGTTAAAACAGATTATAATTGAATGTCAA-CTC

                  **     **         *     
       1343 AAGAAATGTGAAGGTAAAGGCATTCATTGG
        128 AAGAAACATGAAGAAAAAGGCATTTATTGG

       1373 CAAGNNNNNN


Statistics
Matches: 404,  Mismatches: 90, Indels: 13
        0.80            0.18        0.03

Matches are distributed among these distances:
 170  136  0.34
 171   70  0.17
 172  197  0.49
 173    1  0.00

ACGTcount: A:0.36, C:0.15, G:0.12, T:0.35


Consensus pattern (170 bp):   
TTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTGTAATCTCAAAAT
TGATTGAAATTTGAATTCTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCAACTCAAG
AAACATGAAGAAAAAGGCATTTATTGGTAAGAAAAGTCCA

Found at i:1487 original size:342 final size:342

Alignment explanation


    Indices: 704--1490  Score: 778
    Period size: 342  Copynumber: 2.3  Consensus size: 342

        694 NNNNNCGTTT

                     *                *                       *              
        704 ATAGTCACCTATTCCTTCAAAAGCCTCATTACTCGT-TTTAAATGGTTTTGTAATGCCATAATTG
          1 ATAGTCACCCATTCCTTCAAAAGCCTTATTACTC-TATTTAAATGGTTTTATAATGCCATAATTG

                 *     * * *                *                   *    *       
        768 ATTTTTAGTTGCAGTATTTTACATTTTTGGTTTAAACAGACTATAATTGAATGTCAATCTCAAGA
         65 ATTTTAAGTTGAACTTTTTTACATTTTTGGTTAAAACAGACTATAATTGAATATCAACCTCAAGA

                                **                *    * *            *      
        833 AACATAAAGAAAAAGACATTTGTTGGCAAGAAAAGTCCCTTTATAGTCACCCATTCCTTCAAAAG
        130 AACATAAAGAAAAAGA-ATTCATTGGCAAGAAAAGTCCATTTACAATCACCCATTCCTCCAAAAG

                               *                     *         *         *   
        898 CCTTAGTACTCACTTTAAATAGTTTTGTAAACTCAAAATTGCTTGAAATTTGAATTCTTTATACT
        194 CCTTAGTACTCACTTTAAACAGTTTTGTAAACTCAAAATTGATTGAAATTTCAATTCTTTACACT

               *  *                  *   * *       *                      *  
        963 TTTTTGGTTAAAAAAGATTATAATGGAATGTGAACATCAGGAAACATGAAGGAAAAGGCATTTAT
        259 TTTATGATTAAAAAAGATTATAATGCAATATCAACATCAAGAAACATGAAGGAAAAGGCATTCAT

               *              *
       1028 TGGTAAGAAAAGTCCATTT
        324 TGGCAAGAAAAGTCCATTA

                                 *          *      *    *               *    
       1047 ATAGTCACCCATTCCTTCAAATGCCTTATTACAC-ACTTGAAATAGTTTTATAAT-CTCAAAATT
          1 ATAGTCACCCATTCCTTCAAAAGCCTTATTACTCTA-TTTAAATGGTTTTATAATGC-CATAATT

              *  **********                          * *                     
       1110 -AATTNNNNNNNNNNTTCTTTGTACATTTTTGGTTAAAACATATTATAATTGAATATCAACCTCA
         64 GATTTTAAGTTGAACTT-TTT-TACATTTTTGGTTAAAACAGACTATAATTGAATATCAACCTCA

                    *  *       *        *                        *           
       1174 AGAAACATGAATAAAAAG-GTTCATTGGTAAGAAAAGTCCATTTACAATCACCTATTCCTCCAAA
        127 AGAAACATAAAGAAAAAGAATTCATTGGCAAGAAAAGTCCATTTACAATCACCCATTCCTCCAAA

                   *                        *      *                      *  
       1238 AGCCTTATTACTCACTTTAAACAGTTTTGTAATCTCAAACTTGATTGAAATTTCAATTCTTTGCA
        192 AGCCTTAGTACTCACTTTAAACAGTTTTGTAAACTCAAAATTGATTGAAATTTCAATTCTTTACA

                            *          *                    **      *        
       1303 CATTTTAT-ATTAAAAGAGATTATAATTCAATATCAATC-TCAAGAAATGTGAAGGTAAAGGCAT
        257 C-TTTTATGATTAAAAAAGATTATAATGCAATATCAA-CATCAAGAAACATGAAGGAAAAGGCAT

                       **********  
       1366 TCATTGGCAAGNNNNNNNNNNTA
        320 TCATTGGCAAGAAAAGTCCATTA

                                                     *     *                 
       1389 ATAGTCACCCATTCCTTCAAAAAGCCTTATTACTCTATTTACATGGTCTTATAATGCCATAATTG
          1 ATAGTCACCCATTCCTTC-AAAAGCCTTATTACTCTATTTAAATGGTTTTATAATGCCATAATTG

                                      *          
       1454 ATTTTAAGTTGAACTTTTTTACATTTATGGTTAAAAC
         65 ATTTTAAGTTGAACTTTTTTACATTTTTGGTTAAAAC


Statistics
Matches: 346,  Mismatches: 87, Indels: 23
        0.76            0.19        0.05

Matches are distributed among these distances:
 342  188  0.54
 343   97  0.28
 344   61  0.18

ACGTcount: A:0.35, C:0.15, G:0.12, T:0.35


Consensus pattern (342 bp):   
ATAGTCACCCATTCCTTCAAAAGCCTTATTACTCTATTTAAATGGTTTTATAATGCCATAATTGA
TTTTAAGTTGAACTTTTTTACATTTTTGGTTAAAACAGACTATAATTGAATATCAACCTCAAGAA
ACATAAAGAAAAAGAATTCATTGGCAAGAAAAGTCCATTTACAATCACCCATTCCTCCAAAAGCC
TTAGTACTCACTTTAAACAGTTTTGTAAACTCAAAATTGATTGAAATTTCAATTCTTTACACTTT
TATGATTAAAAAAGATTATAATGCAATATCAACATCAAGAAACATGAAGGAAAAGGCATTCATTG
GCAAGAAAAGTCCATTA
Done.