Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018399178.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2450.0, 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, 933

Length: 1556
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.32

Warning! 213 characters in sequence are not A, C, G, or T


Found at i:833 original size:170 final size:169

Alignment explanation


    Indices: 342--953  Score: 697
    Period size: 171  Copynumber: 3.6  Consensus size: 169

        332 NNNNNNNNNN

                            *                 *                      *      *
        342 AAAGCCTTATTACTCTTTTTAAATGGTTTTATAATCTCAAAATTGATTTTAGGTTGAGTTTTTTA
          1 AAAGCCTTATTACTCTCTTTAAATGGTTTTATAACCTCAAAATTGATTTTAGGTTGAATTTTTTT

             *    *                                                      **  
        407 ACATTTGTGGTTAAAACAGATTATAATTGAATGTTTAGCTCATGAAACAT-AAAGAAAAACTAAT
         66 ATATTTTTGGTTAAAACAGATTATAATTGAATG-TTAGC-CATGAAACATGAAA-AAAAACCCAT

               *                          *          *
        471 TCACTGGCAAGAAAAGCCCATTTATAGTCAGCCAAGCCTTCG
        128 TCATTGGCAAGAAAAGCCCATTTATAGTCACCCAAGCCTTCA

                     *       *           *    * *  *    *            *       
        513 AAAGCCTTACTACTCTCCTTAAATGGTTTAATAATCGCATAATTTATTTTAGGTTGAGTTTTTTT
          1 AAAGCCTTATTACTCTCTTTAAATGGTTTTATAACCTCAAAATTGATTTTAGGTTGAATTTTTTT

                              *          *     *      *    *     *    *      
        578 ATATTTTTGGTTAAAACATATTATAATTGCATGTTTGCCAAGGGAAATATGAAGAAAACCCCATT
         66 ATATTTTTGGTTAAAACAGATTATAATTGAATGTTAGCC-A-TGAAACATGAAAAAAAACCCATT

                         *                    * *  * 
        643 CATTGGCAAGAAATGCCCATTTATAGTCACCCAAACTTTTA
        129 CATTGGCAAGAAAAGCCCATTTATAGTCACCCAAGCCTTCA

                                    **       *   *             *   *         
        684 AAAGCCTTATTACTCTCTTTAAATTATTTTATAGCCTTAAAATTGATTTTAAGTTTAATTTTTTT
          1 AAAGCCTTATTACTCTCTTTAAATGGTTTTATAACCTCAAAATTGATTTTAGGTTGAATTTTTTT

                    *                          *   *                         
        749 -TATTTTTTGTTAAAACAGATTATAATTGAATGTTCGCCTTGTAAAACATGAAAAAAAACCCATT
         66 ATATTTTTGGTTAAAACAGATTATAATTGAATGTTAGCCATG--AAACATGAAAAAAAACCCATT

            *                             **         
        813 TATTGGCAAGAAAAGCCCATTTATAGTCACTTAAGCCTTCA
        129 CATTGGCAAGAAAAGCCCATTTATAGTCACCCAAGCCTTCA

            *    *       *                   *   *                 *         
        854 GAAGCATTATTACCCTCTTTAAATGGTTTTATAGCCTTAAAATTGATTTTAGGTTTAATTGTTTT
          1 AAAGCCTTATTACTCTCTTTAAATGGTTTTATAACCTCAAAATTGATTTTAGGTTGAATT-TTTT

                     *                         
        919 TATATTTTTAGTTAAAACAGATTATAATTGAATGT
         65 TATATTTTTGGTTAAAACAGATTATAATTGAATGT

        954 NNNNNNNNNN


Statistics
Matches: 371,  Mismatches: 63, Indels: 13
        0.83            0.14        0.03

Matches are distributed among these distances:
 168    1  0.00
 169    1  0.00
 170  145  0.39
 171  190  0.51
 172   34  0.09

ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39


Consensus pattern (169 bp):   
AAAGCCTTATTACTCTCTTTAAATGGTTTTATAACCTCAAAATTGATTTTAGGTTGAATTTTTTT
ATATTTTTGGTTAAAACAGATTATAATTGAATGTTAGCCATGAAACATGAAAAAAAACCCATTCA
TTGGCAAGAAAAGCCCATTTATAGTCACCCAAGCCTTCA

Found at i:1491 original size:172 final size:170

Alignment explanation


    Indices: 1141--1556  Score: 462
    Period size: 172  Copynumber: 2.4  Consensus size: 170

       1131 NNNNNNACAG

                                  *                  *        *        *     
       1141 ATTATAATTGAATGTTTGCCTTTGGAAACATGAAGAAAAACACATTCATTTGCAAGAAAGGCCCA
          1 ATTATAATTGAATGTTTGCCTTAGGAAACATGAAG-AAAACCCATTCATTGGCAAGAAAAGCCCA

                                          *       *      *      *   **       
       1206 TTTATAGTCACCCAAGCCTTCAAAAGCCCTGTTACTCGCTTTAAATGGTTTTGTAGTGCCATAAT
         65 TTTATAGTCACCCAAGCCTTCAAAAGCCCTATTACTCGATTTAAAAGGTTTTATAGACCCATAAT

               *                 *             *     *
       1271 TGATTTTAAGCTGAATGGTTTTTACATTTTTAGTTCAAACAG
        130 TGACTTTAAGCTGAA-GGTTTCTACATTTTTAGTTAAAACAA

                              ** * *       *    *                            
       1313 ATTATAATTGAATGTTTGGATCAAGAAACATTAAGTGAAACCCATTCATTGGCAAGAAAAGCCCA
          1 ATTATAATTGAATGTTTGCCTTAGGAAACATGAAG-AAAACCCATTCATTGGCAAGAAAAGCCCA

                  *                      *        *                          
       1378 TTTATATTCACCCAAGCCTTCGAAAAGCCTTATTACTCTATTTAAAAGGTTTTATA-ACCTCATA
         65 TTTATAGTCACCCAAGCCTTC-AAAAGCCCTATTACTCGATTTAAAAGGTTTTATAGACC-CATA

                      *                        *          
       1442 ATTGACTTTACG-TAGAA-GTTTCTA-ATGTTTTTGGTTAAAACAA
        128 ATTGACTTTAAGCT-GAAGGTTTCTACA--TTTTTAGTTAAAACAA

                         *   *    *                            *             
       1485 ATTATAATTGAATCTTTTCCTTGGGAAACATGAAGAAACACCCATTCATTGACAAGAAAAGCCCA
          1 ATTATAATTGAATGTTTGCCTTAGGAAACATGAAGAAA-ACCCATTCATTGGCAAGAAAAGCCCA

                   
       1550 TTTATAG
         65 TTTATAG


Statistics
Matches: 201,  Mismatches: 37, Indels: 12
        0.80            0.15        0.05

Matches are distributed among these distances:
 170    1  0.00
 171    8  0.04
 172  147  0.73
 173   45  0.22

ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34


Consensus pattern (170 bp):   
ATTATAATTGAATGTTTGCCTTAGGAAACATGAAGAAAACCCATTCATTGGCAAGAAAAGCCCAT
TTATAGTCACCCAAGCCTTCAAAAGCCCTATTACTCGATTTAAAAGGTTTTATAGACCCATAATT
GACTTTAAGCTGAAGGTTTCTACATTTTTAGTTAAAACAA
Done.