Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018399836.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3073.0, 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: 3113
ACGTcount: A:0.22, C:0.08, G:0.07, T:0.22

Warning! 1282 characters in sequence are not A, C, G, or T


Found at i:436 original size:171 final size:172

Alignment explanation


    Indices: 1--474  Score: 461
    Period size: 171  Copynumber: 2.7  Consensus size: 172

                                            **  *      *                *    
          1 TTGAATTCTTTACACATTTTTGATTAAAACAGGCTAGAATTGATTGTCTACCTTTAAAAAAATGT
          1 TTGAATTCTTTACACATTTTTGATTAAAACAGATTATAATTGAATGTCTACC-TTAAAAACA--T

            *  *       *           *     *  *         *                      
         66 TAACAAAAAGGTATTCATTGGCATGAAAAATCTATTTATAGTAACCTATTCCTTTAAAAGCCTTA
         63 AAAGAAAAAGGAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATTCCTTTAAAAGCCTTA

                      **********   *             *     * 
        131 TTACTCACTTNNNNNNNNNNTATTATCTCAAAATTGATTTTAAGT
        128 TTACTCACTTATAAATGTTTTATAATCTCAAAATTGAATTTAAAT

             **        **         * *      *            *       *   *    *   
        176 TCAAATT-TTTTTACATTTTTGGTCAAAACATATTATAATTGAAAGTCTAGCTTTAGAAACGTAA
          1 TTGAATTCTTTACACATTTTTGATTAAAACAGATTATAATTGAATGTCTA-CCTTAAAAACATAA

            *        *   *    *                                        *     
        240 TGAAAAAGGCATTTATTGACAAGAAAAGTCCATTTATAGTCACCTATTCCTTTAAAAGCGTTATT
         65 AGAAAAAGGAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATTCCTTTAAAAGCCTTATT

                                                       
        305 ACTCACTT-TAAATGTTTTATAATCTCAAAATT-AATTTAAAT
        130 ACTCACTTATAAATGTTTTATAATCTCAAAATTGAATTTAAAT

                                                           *     *           
        346 TTGAATTCTTTACACATTTTTGATTAAAACAGATTATAATTGAATGTTTACCTCAACAAACATAA
          1 TTGAATTCTTTACACATTTTTGATTAAAACAGATTATAATTGAATGTCTACCTTAA-AAACATAA

                                                         *       *           
        411 AGAAAAAGGAATTCATTGGCAAGAAAAG-CCTATTTATAGTCACCCATTCCTTCAAAAGCCTTAT
         65 AGAAAAAGGAATTCATTGGCAAGAAAAGTCC-ATTTATAGTCACCTATTCCTTTAAAAGCCTTAT

        475 NNNNNNNNNN


Statistics
Matches: 236,  Mismatches: 59, Indels: 12
        0.77            0.19        0.04

Matches are distributed among these distances:
 170   17  0.07
 171  110  0.47
 172   65  0.28
 174   38  0.16
 175    6  0.03

ACGTcount: A:0.37, C:0.14, G:0.10, T:0.36


Consensus pattern (172 bp):   
TTGAATTCTTTACACATTTTTGATTAAAACAGATTATAATTGAATGTCTACCTTAAAAACATAAA
GAAAAAGGAATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATTCCTTTAAAAGCCTTATTA
CTCACTTATAAATGTTTTATAATCTCAAAATTGAATTTAAAT

Found at i:1962 original size:170 final size:169

Alignment explanation


    Indices: 1753--2059  Score: 404
    Period size: 170  Copynumber: 1.8  Consensus size: 169

       1743 TCATCGATAT

                *                                       *                    
       1753 GAAATGTCCATTTATAGTCACCCATTCCAGCAAAAGCCTTATTATTCACTTTAAATAGTTTTA-T
          1 GAAAAGTCCATTTATAGTCACCCATTCCAGCAAAAGCCTTATTACTCACTTTAAATAGTTTTATT

                                 * *                                *  *     
       1817 AA-TCACAAAATTGACTTAAATTTGAAT-TGTTTGTACATTTTTGGATAAAATAAATTATAATTG
         66 AACT-A-AAAATTGACTTAAAGTAGAATAT-TTT-TACATTTTTGGATAAAATAAAGTAGAATTG

                                                       
       1880 AATGTCTACCTCGACAAACGCAAAAAAAAGCCTTTATTGGTAA
        127 AATGTCTACCTCGACAAACGCAAAAAAAAGCCTTTATTGGTAA

                    *         *  *       *                          *        
       1923 GAAAAGTCTATTTATAGTTACTCATTCCATCAAAAGCCTTATTACTCACTTTAAATGGTTTTATT
          1 GAAAAGTCCATTTATAGTCACCCATTCCAGCAAAAGCCTTATTACTCACTTTAAATAGTTTTATT

                  *      *  *                         *    *  *              
       1988 AACTAATAATTGATTTTAAGTAGAATATTTTTACATTTTTGGTTAAAGTAGAGTAGAATTGAATG
         66 AACTAAAAATTGACTTAAAGTAGAATATTTTTACATTTTTGGATAAAATAAAGTAGAATTGAATG

                   
       2053 TCTACCT
        131 TCTACCT

       2060 TAAGAAAAAT


Statistics
Matches: 117,  Mismatches: 17, Indels: 7
        0.83            0.12        0.05

Matches are distributed among these distances:
 169   36  0.31
 170   75  0.64
 171    5  0.04
 172    1  0.01

ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38


Consensus pattern (169 bp):   
GAAAAGTCCATTTATAGTCACCCATTCCAGCAAAAGCCTTATTACTCACTTTAAATAGTTTTATT
AACTAAAAATTGACTTAAAGTAGAATATTTTTACATTTTTGGATAAAATAAAGTAGAATTGAATG
TCTACCTCGACAAACGCAAAAAAAAGCCTTTATTGGTAA
Done.