Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018397771.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_107.0, 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: 19573
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.21

Warning! 8488 characters in sequence are not A, C, G, or T


Found at i:12399 original size:171 final size:169

Alignment explanation


    Indices: 12008--12410  Score: 413
    Period size: 170  Copynumber: 2.4  Consensus size: 169

      11998 NNNNNNNNNT

                                       *          *     *                    
      12008 CACCCATTCTTTCAAAAGCCTTATTACCCGCTTTAATTAGTTTTGTAATCTCATAATTCATTATA
          1 CACCCATTCTTTCAAAAGCCTTATTACACGCTTTAATTGGTTTTATAATCTCATAATT-ATT-TA

                               *   *        *  *            * *   *        * 
      12073 AGTTGAAATTTTTTACAATTTTATTTAAAACAGACTATAATTGAATGTTTCCCTTGAGAAACGTG
         64 AGTTGAAATTTTTTACAATATTAGTTAAAACAAACAATAATTGAATGTCTACCTCGAGAAACGAG

            *       *       *                        
      12138 TAGAAAAAGCCATTCATTGAGAAAAAAAGTCCATTTATAGC
        129 AAGAAAAAACCATTCAATGAGAAAAAAAGTCCATTTATAGC

                             **        *       *                             
      12179 CACCCATT-TTTCAAAATTCTTATTACTCGCTTTACTTGGTTTTATAATCTCATAATTGATTTCA
          1 CACCCATTCTTTCAAAAGCCTTATTACACGCTTTAATTGGTTTTATAATCTCATAATT-ATTT-A

                    *        *         *                                     
      12243 AGTTGAATTTTTTTTA-TATATTAGTTCAAACAAACAATAATT-AATTGTCTACCTCGAGAAACG
         64 AGTTGAA-ATTTTTTACAATATTAGTTAAAACAAACAATAATTGAA-TGTCTACCTCGAGAAACG

                                       **      *      * *
      12306 AGAAGAAAAATACC-TTCAATG-GCAAGCAAAGTCTATTTATCGT
        127 AGAAGAAAAA-ACCATTCAATGAG-AAAAAAAGTCCATTTATAGC

            *   *                                *                *        
      12349 TACCTACTTCTTT-AAAAGCCTTATTACACGCTTTAAATGGTTTTATAATCTCAAAATTATTT
          1 CACCCA-TTCTTTCAAAAGCCTTATTACACGCTTTAATTGGTTTTATAATCTCATAATTATTT

      12411 TTNNNNNNNN


Statistics
Matches: 191,  Mismatches: 34, Indels: 15
        0.80            0.14        0.06

Matches are distributed among these distances:
 169    4  0.02
 170  126  0.66
 171   58  0.30
 172    3  0.02

ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38


Consensus pattern (169 bp):   
CACCCATTCTTTCAAAAGCCTTATTACACGCTTTAATTGGTTTTATAATCTCATAATTATTTAAG
TTGAAATTTTTTACAATATTAGTTAAAACAAACAATAATTGAATGTCTACCTCGAGAAACGAGAA
GAAAAAACCATTCAATGAGAAAAAAAGTCCATTTATAGC

Found at i:15234 original size:171 final size:160

Alignment explanation


    Indices: 14912--15238  Score: 318
    Period size: 171  Copynumber: 2.0  Consensus size: 160

      14902 NNNNNNNNNN

                *                             *                         *    
      14912 AGTTGAATTTTTTTACATTTTTGGATTAAAAAAAGTATAATTAAATGTCTACCTAAAGAACCATG
          1 AGTTAAATTTTTTTACATTTTTGGATTAAAAAAACTATAATTAAATGTCTACCTAAAGAAACATG

                                *   *  *                     *   *           
      14977 AAGAAAAAGACATTCATTGGCAAGCAAGGTCCATTTATAGTCGGTCATTTCTTTAAAAACCTAGT
         66 AAGAAAAAGACATTCATTGGAAAGAAAAGTCCATTTATAGTC-GTCATTCCTTCAAAAACCTAGT

                  *      *                 
      15042 TACTAGCTTTAAATAGTTTTATAATCTCATA
        130 TACTAGATTTAAACAGTTTTATAATCTCATA

                                                                 *     *     
      15073 NNNNNNNNNNAGTTAAATTTTTTTACATTTTTGGA-TAAAAAAGACTATAATTGAATGTTTACCT
          1 ----------AGTTAAATTTTTTTACATTTTTGGATTAAAAAA-ACTATAATTAAATGTCTACCT

            **                 * *                         *                 
      15137 TGAGAAACATGAAGAAAAATATATTCATTGGAAAGAAAAGTCCATTTGTAGTC-TCCTATTCCTT
         55 AAAGAAACATGAAGAAAAAGACATTCATTGGAAAGAAAAGTCCATTTATAGTCGT-C-ATTCCTT

                             *       * *           
      15201 CAAAAACCTTA-TTACTTGATTTAAGCGGTTTTATAATC
        118 CAAAAACC-TAGTTACTAGATTTAAACAGTTTTATAATC

      15239 ACAAAATTGA


Statistics
Matches: 132,  Mismatches: 20, Indels: 8
        0.82            0.12        0.05

Matches are distributed among these distances:
 169    1  0.01
 170    8  0.06
 171  121  0.92
 172    2  0.02

ACGTcount: A:0.36, C:0.12, G:0.13, T:0.36


Consensus pattern (160 bp):   
AGTTAAATTTTTTTACATTTTTGGATTAAAAAAACTATAATTAAATGTCTACCTAAAGAAACATG
AAGAAAAAGACATTCATTGGAAAGAAAAGTCCATTTATAGTCGTCATTCCTTCAAAAACCTAGTT
ACTAGATTTAAACAGTTTTATAATCTCATA
Done.