Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018398547.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1839.0, 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: 7564
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.16

Warning! 4293 characters in sequence are not A, C, G, or T


Found at i:2042 original size:169 final size:160

Alignment explanation


    Indices: 1813--2134  Score: 290
    Period size: 169  Copynumber: 2.0  Consensus size: 160

       1803 AAGTTAAATG

                             *  *  *          *   *                         *
       1813 TTTTTTACATTTTTATTCAACCATATTATAATTGGATGTCTATCCCAGGAAACATGAAGAAAAAG
          1 TTTTTTACATTTTTATTAAAACAGATTATAATTGAATGCCTATCCCAGGAAACATGAAGAAAAAA

                      *                 *                          *     **  
       1878 GCATTCATTGGCAAGAAAAGCCT-ATTTGTAGTCACCAAAGCCTTCAAAAGCCTTTTTACTTGCT
         66 GCATTCATTGACAAG-AAAGCCTAATTTATAGTCACCAAAGCCTTCAAAAGCCTTATTACTCCCT

                   *     *                           
       1942 CTAAATGGTTTTATAATCTCATNNNNNNNNNNAAGTTGATT
        130 CTAAATGATTTTACAATCTCAT----------AAGTTGATT

                    *                                     *      **          
       1983 TTTTTTA-TTTTTTATTAAAACAGATTATAATTGAATGCCTA-CCTTAGGAAATGTGAAGAAAAA
          1 TTTTTTACATTTTTATTAAAACAGATTATAATTGAATGCCTATCC-CAGGAAACATGAAGAAAAA

                  *             **         *     * *         *               
       2046 AGCATTTATTGACAAGAAAGGGTAATTTATATTCACCCATGCCTTCAAATGCCTTATTACTCCCT
         65 AGCATTCATTGACAAGAAAGCCTAATTTATAGTCACCAAAGCCTTCAAAAGCCTTATTACTCCCT

            *                       
       2111 TTAAATGATTTTACAATCTCATAA
        130 CTAAATGATTTTACAATCTCATAA

       2135 TTAATTTAAA


Statistics
Matches: 125,  Mismatches: 25, Indels: 15
        0.76            0.15        0.09

Matches are distributed among these distances:
 159    2  0.02
 168    7  0.06
 169  109  0.87
 170    7  0.06

ACGTcount: A:0.34, C:0.16, G:0.12, T:0.36


Consensus pattern (160 bp):   
TTTTTTACATTTTTATTAAAACAGATTATAATTGAATGCCTATCCCAGGAAACATGAAGAAAAAA
GCATTCATTGACAAGAAAGCCTAATTTATAGTCACCAAAGCCTTCAAAAGCCTTATTACTCCCTC
TAAATGATTTTACAATCTCATAAGTTGATT

Found at i:4100 original size:171 final size:171

Alignment explanation


    Indices: 3817--4294  Score: 557
    Period size: 171  Copynumber: 2.8  Consensus size: 171

       3807 TGTAAAACAT

                   *    *            *     **        **                      
       3817 TCAACTTTAAATTAATTATGAGATTGTAAAATAATTTAAAGGGAGTAATAAGGCTTTTGAAGGCA
          1 TCAACTTCAAATCAATTATGAGATTATAAAACCATTTAAAGAAAGTAATAAGGCTTTTGAAGGCA

             *             * *         *    *     *          *              *
       3882 TGGGTGAATATAAATTGCCTTTTCTTGTCAATAAATGCTTTTTTCTTCACGTTTCCTAAGGTAGG
         66 TAGGTGAATATAAATAGGCTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCCTAAGGTAGA

                          *  *  *                    
       3947 CATTCAATTATAATCTGTTTTAATAAAAA-CTAAAAA-AAA
        131 CATTCAATTATAATATGGTTGAATAAAAATCTAAAAACAAA

                               *                  *  *      *                
       3986 TCAACTTCAAATCAATTATAAGATTATAAAACCATTTAGAGCAAGTAAAAAGGCTTTTTTGAAGG
          1 TCAACTTCAAATCAATTATGAGATTATAAAACCATTTAAAGAAAGTAATAAGGC--TTTTGAAGG

             * *     *                                                       
       4051 CTTTGGTGACTATAAATAGGCTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCCT-AGGAT
         64 CATAGGTGAATATAAATAGGCTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCCTAAGG-T

                                             *         *
       4115 AGACATTCAATTATAATATGGTTGAATAAAAATGTAAAAACAAT
        128 AGACATTCAATTATAATATGGTTGAATAAAAATCTAAAAACAAA

             *                        *             *                     *  
       4159 TTAACTTCAAATCAATTATGAGATTACAAAACCATTTAAAAAAAGTAATAAGGCTTTTGAAGACA
          1 TCAACTTCAAATCAATTATGAGATTATAAAACCATTTAAAGAAAGTAATAAGGCTTTTGAAGGCA

                **               *      * *      *  *    *                   
       4224 TAGGCAAATATAAATAGGCTTCTCTTGCTAGTGAATGGCTATTTCATCATGTTTCCTAAGGTAGA
         66 TAGGTGAATATAAATAGGCTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCCTAAGGTAGA

                  
       4289 CATTCA
        131 CATTCA

       4295 NNNNNNNNNN


Statistics
Matches: 259,  Mismatches: 44, Indels: 10
        0.83            0.14        0.03

Matches are distributed among these distances:
 169   44  0.17
 170    3  0.01
 171  154  0.59
 172    9  0.03
 173   49  0.19

ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35


Consensus pattern (171 bp):   
TCAACTTCAAATCAATTATGAGATTATAAAACCATTTAAAGAAAGTAATAAGGCTTTTGAAGGCA
TAGGTGAATATAAATAGGCTTTTCTTGCCAATGAATGCCTTTTTCTTCATGTTTCCTAAGGTAGA
CATTCAATTATAATATGGTTGAATAAAAATCTAAAAACAAA
Done.