Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018399755.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2999.0, 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: 2900
ACGTcount: A:0.22, C:0.08, G:0.07, T:0.23

Warning! 1189 characters in sequence are not A, C, G, or T


Found at i:1717 original size:171 final size:162

Alignment explanation


    Indices: 1498--1826  Score: 317
    Period size: 172  Copynumber: 2.0  Consensus size: 162

       1488 TAATTTTTTT

                      *       * *               *                            
       1498 ACATTTTTGGTTAAAACAGATTATAATTGAATGTCTGCCGAAAGAAACAT-ATAGAAAAAA-CCA
          1 ACATTTTTGGCTAAAACAAACTATAATTGAATGTCTACCGAAAGAAACATGA-AGAAAAAATCCA

                     *                 *   *                        *        
       1561 TTC-ATTGAGAAGAAAAGCCCATTTATGGTCTTTCATTCCTTCAAAAGCCTTATTATTCACTTTA
         65 TTCAATT-ACAAGAAAAGCCCATTTATAGTCATTCATTCCTTCAAAAGCCTTATTACTCACTTTA

                              *                         
       1625 AATAATTTTATAATCTCATAATTGATNNNNNNNNNNATTTTCTA
        129 AATAATTTTATAATCTCAAAATTGAT----------ATTTTCTA

                                          *        ***                   *   
       1669 ACATTTTTGGCTAAAACAAACTATAATTGATTGTCTACCTTGAGAAACATGAAGAAAAAATGCAT
          1 ACATTTTTGGCTAAAACAAACTATAATTGAATGTCTACCGAAAGAAACATGAAGAAAAAATCCAT

                  *       * * *                                       *   *  
       1734 TCAATTCCAAGAAAGGTCTATTTATAGTCATTCATTCCTTCAAAAGCCTTATTACTCATTTTGAA
         66 TCAATTACAAGAAAAGCCCATTTATAGTCATTCATTCCTTCAAAAGCCTTATTACTCACTTTAAA

              *      *                    
       1799 TAGTTTTATTATCTCAAAATT--TATTTTC
        131 TAATTTTATAATCTCAAAATTGATATTTTC

       1827 AATTCAATTT


Statistics
Matches: 133,  Mismatches: 22, Indels: 17
        0.77            0.13        0.10

Matches are distributed among these distances:
 160    6  0.05
 170    1  0.01
 171   50  0.38
 172   73  0.55
 173    3  0.02

ACGTcount: A:0.36, C:0.15, G:0.10, T:0.36


Consensus pattern (162 bp):   
ACATTTTTGGCTAAAACAAACTATAATTGAATGTCTACCGAAAGAAACATGAAGAAAAAATCCAT
TCAATTACAAGAAAAGCCCATTTATAGTCATTCATTCCTTCAAAAGCCTTATTACTCACTTTAAA
TAATTTTATAATCTCAAAATTGATATTTTCTA

Found at i:1927 original size:172 final size:171

Alignment explanation


    Indices: 1428--1928  Score: 549
    Period size: 171  Copynumber: 2.9  Consensus size: 171

       1418 NNNNNNNNTT

                                         *                           *  *    
       1428 CTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTATTATCTCAAAATTGATATTCAGTTTAATT
          1 CTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATTATCTCAAAATTGATATTCAATTCAATT

                                   *                    **                   
       1493 TTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTGCCGAAAGAAACAT-ATAGAAAAA
         66 TTTTTACATTTTTGGTTAAAACAAATTATAATTGAATGTCTGCCTTAAGAAACATGA-AGAAAAA

             *                    * *      *   *       
       1557 ACCATTCATTGAG-AAGAAAAGCCCATTTATGGTCTTTCATTC
        130 AGCATTCATT-AGCAAGAAAAGTCTATTTATAGTCATTCATTC

                             *            *      *      *       **********   
       1599 CTTCAAAAGCCTTATTATTCACTTTAAATAATTTTATAATCTCATAATTGATNNNNNNNNNNATT
          1 CTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATTATCTCAAAATTGATATTCAATTCAATT

              * *          *         *         *     *    *                  
       1664 TTCTAACATTTTTGGCTAAAACAAACTATAATTGATTGTCTACCTTGAGAAACATGAAGAAAAAA
         66 TTTTTACATTTTTGGTTAAAACAAATTATAATTGAATGTCTGCCTTAAGAAACATGAAGAAAAAA

                        *       *                      
       1729 TGCATTCAATT-CCAAGAAAGGTCTATTTATAGTCATTCATTC
        131 -GCATTC-ATTAGCAAGAAAAGTCTATTTATAGTCATTCATTC

                                 *   *                       *  *            
       1771 CTTCAAAAGCCTTATTACTCATTTTGAATAGTTTTATTATCTCAAAATTTATTTTCAATTCAATT
          1 CTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATTATCTCAAAATTGATATTCAATTCAA-T

                          *         *            **                          
       1836 TTTTTTACATTTTTAGTTAAAACATATTATAATTGAACATCTGCCTTAAGAAACATGAAGAAAAA
         65 TTTTTTACATTTTTGGTTAAAACAAATTATAATTGAATGTCTGCCTTAAGAAACATGAAGAAAAA

            *                           
       1901 GGCATTCATTAGCAAGAAAAGTCTATTT
        130 AGCATTCATTAGCAAGAAAAGTCTATTT

       1929 NNNNNNNNNN


Statistics
Matches: 261,  Mismatches: 63, Indels: 11
        0.78            0.19        0.03

Matches are distributed among these distances:
 171  106  0.41
 172   97  0.37
 173   58  0.22

ACGTcount: A:0.36, C:0.14, G:0.10, T:0.38


Consensus pattern (171 bp):   
CTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATTATCTCAAAATTGATATTCAATTCAATT
TTTTTACATTTTTGGTTAAAACAAATTATAATTGAATGTCTGCCTTAAGAAACATGAAGAAAAAA
GCATTCATTAGCAAGAAAAGTCTATTTATAGTCATTCATTC
Done.