Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018401764.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4877.0, 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: 2276
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.24

Warning! 755 characters in sequence are not A, C, G, or T


Found at i:410 original size:172 final size:161

Alignment explanation


    Indices: 161--491  Score: 358
    Period size: 172  Copynumber: 2.0  Consensus size: 161

        151 ACGGCATTAC

                *                  **     *     *   *                  *    *
        161 AAAATCATTTAAAGCAAGTAATACTGCTTTTGAAGGTATGGGTGACCATAAATGGACTTTTCTTG
          1 AAAACCATTTAAAGCAAGTAATAAAGCTTTCGAAGGAATGAGTGACCATAAATGGACTTCTCTTC

            *             *                                         *        
        226 TCAATAAATGCCTTTTTCTTCATGATTCTCA-AGGTAGACATTCAATCTTAGTCTATTTTAACCA
         66 CCAATAAATGCCTTGTTCTTCATGATTCT-AGAGGTAGACATTCAATCTTAGTCT-GTTTAACCA

                 *  *   *          *                   
        290 AAAATGTACAAAGAATTCAAATTTAAATCAANNNNNNNNNNAT
        129 AAAATATAAAAAAAATTCAAATTAAAATCAA----------AT

                          **                              *                  
        333 AAAACCATTTAAAGTGAGTAATAAAGCTTTCGAAGGAATGAGTGACTATAAATGGACTTCTCTTC
          1 AAAACCATTTAAAGCAAGTAATAAAGCTTTCGAAGGAATGAGTGACCATAAATGGACTTCTCTTC

                 *              *                                            
        398 CCAATGAATGCCTTGTTCTTTATGATTCTAGAGGTAGACATTCAATCTTAGTCTGTTTAACCAAA
         66 CCAATAAATGCCTTGTTCTTCATGATTCTAGAGGTAGACATTCAATCTTAGTCTGTTTAACCAAA

                              *          
        463 AATATAAAAAAAATTCAACTTAAAATCAA
        131 AATATAAAAAAAATTCAAATTAAAATCAA

        492 TTATGGCANN


Statistics
Matches: 137,  Mismatches: 21, Indels: 3
        0.85            0.13        0.02

Matches are distributed among these distances:
 171   35  0.26
 172  102  0.74

ACGTcount: A:0.37, C:0.15, G:0.13, T:0.32


Consensus pattern (161 bp):   
AAAACCATTTAAAGCAAGTAATAAAGCTTTCGAAGGAATGAGTGACCATAAATGGACTTCTCTTC
CCAATAAATGCCTTGTTCTTCATGATTCTAGAGGTAGACATTCAATCTTAGTCTGTTTAACCAAA
AATATAAAAAAAATTCAAATTAAAATCAAAT

Found at i:2127 original size:17 final size:19

Alignment explanation


    Indices: 2107--2144  Score: 53
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       2097 GTACAAAGAA

                               
       2107 TTTAA-ATT-TAAAACAAT
          1 TTTAAGATTATAAAACAAT

                            *  
       2124 TTTAAGATTATAAAACCAT
          1 TTTAAGATTATAAAACAAT

              
       2143 TT
          1 TT

       2145 AAACCAAGTA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  17    5  0.28
  18    3  0.17
  19   10  0.56

ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42


Consensus pattern (19 bp):   
TTTAAGATTATAAAACAAT

Found at i:2270 original size:172 final size:172

Alignment explanation


    Indices: 1958--2271  Score: 380
    Period size: 172  Copynumber: 1.8  Consensus size: 172

       1948 TATTTATGGC

                              *              *      **  *                    
       1958 ATTACAAAACCATTTAAAGAGAGTAATAAGACTTTTGAAGTTATTGGTGACTATAAATGAACTTT
          1 ATTACAAAACCATTTAAACAGAGTAATAAGACTCTTGAAGGAATGGGTGACTATAAATGAACTTT

                            *          *          *        *    *            
       2023 TCTTGCCAATGAATACTTTTTTCTTCATATGTCTCAAGTTAGACATTGAATTCTAGTCAGTTTTA
         66 TCTTGCCAATGAATACCTTTTTCTTCACATGTCTCAAGGTAGACATTCAATTATAGTCAGTTTTA

                                                      
       2088 ACAAAAAATGTACAAAGAATTTAAATTTAAAACAATTTTAAG
        131 ACAAAAAATGTACAAAGAATTTAAATTTAAAACAATTTTAAG

                *                          **                 *         *    
       2130 ATTATAAAACCATTTAAACCA-AGTAATAAGGGTCTTGAAGGAATGGGTGTCTATAAATGGACTT
          1 ATTACAAAACCATTTAAA-CAGAGTAATAAGACTCTTGAAGGAATGGGTGACTATAAATGAACTT

                   *     * *          *  * *   *                             
       2194 TTCTTGCTAATGACTGCCTTTTTCTTTACGTTTCTTAAGGTAGACATTCAATTATAGTCTA-TTT
         65 TTCTTGCCAATGAATACCTTTTTCTTCACATGTCTCAAGGTAGACATTCAATTATAGTC-AGTTT

               * *        
       2258 TAATAGAAAATGTA
        129 TAACAAAAAATGTA

       2272 AAAAA


Statistics
Matches: 116,  Mismatches: 24, Indels: 4
        0.81            0.17        0.03

Matches are distributed among these distances:
 172  114  0.98
 173    2  0.02

ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37


Consensus pattern (172 bp):   
ATTACAAAACCATTTAAACAGAGTAATAAGACTCTTGAAGGAATGGGTGACTATAAATGAACTTT
TCTTGCCAATGAATACCTTTTTCTTCACATGTCTCAAGGTAGACATTCAATTATAGTCAGTTTTA
ACAAAAAATGTACAAAGAATTTAAATTTAAAACAATTTTAAG
Done.