Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018398509.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1802.0, 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, 957

Length: 1596
ACGTcount: A:0.25, C:0.10, G:0.12, T:0.26

Warning! 437 characters in sequence are not A, C, G, or T


Found at i:367 original size:170 final size:171

Alignment explanation


    Indices: 81--399  Score: 417
    Period size: 170  Copynumber: 1.9  Consensus size: 171

         71 ACATTCCCTA

                      **                          *   *                      
         81 ATGCAAACATTTAATTATGATAGGTTTTAACAAGAAAGGAAATAGATTTTGACTTAAACTCATTT
          1 ATGCAAACATCCAATTATGATAGGTTTTAACAAGAAAGCAAAAAGATTTTGACTTAAACTCATTT

                   **               **                                *      
        146 AAAAGATTCTAAAACCATTTAAAGTGAGTAATAAGGCTTTCGATAGCATGAGTGAATATAAATGG
         66 AAAAGATGATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGATAGCATGAGTGAATACAAATGG

                   *                                 
        211 ACTATTCTTGTCAATGGATAGCATCCACTTCATGTTTAACT
        131 ACTATTCCTGTCAATGGATAGCATCCACTTCATGTTTAACT

                                           *     *      *       *            
        252 ATGCAAACATCCAATTATGATAGGTTTTAACCA-AAATCAAAAATATTTTGATTTATAA-TCATT
          1 ATGCAAACATCCAATTATGATAGGTTTTAACAAGAAAGCAAAAAGATTTTGACTTA-AACTCATT

              *           *      *                       *        * *        
        315 TATAAGATGATAAAGCCATTTCAAGCAAGTAATAAGGCTTTCGATGGCATGAGTTACTACAAATG
         65 TAAAAGATGATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGATAGCATGAGTGAATACAAATG

              * *               
        380 GATTTTTCCTGTCAATGGAT
        130 GACTATTCCTGTCAATGGAT

        400 GATATTTTCT


Statistics
Matches: 125,  Mismatches: 22, Indels: 3
        0.83            0.15        0.02

Matches are distributed among these distances:
 170   93  0.74
 171   32  0.26

ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34


Consensus pattern (171 bp):   
ATGCAAACATCCAATTATGATAGGTTTTAACAAGAAAGCAAAAAGATTTTGACTTAAACTCATTT
AAAAGATGATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGATAGCATGAGTGAATACAAATGG
ACTATTCCTGTCAATGGATAGCATCCACTTCATGTTTAACT

Found at i:436 original size:170 final size:170

Alignment explanation


    Indices: 93--457  Score: 401
    Period size: 170  Copynumber: 2.1  Consensus size: 170

         83 GCAAACATTT

                                      *   *                             **   
         93 AATTATGATAGGTTTTAACAAGAAAGGAAATAGATTTTGACTTAAACTCATTTAAAAGATTCTAA
          1 AATTATGATAGGTTTTAACAA-AAAGCAAAAAGATTTTGACTTAAACTCATTTAAAAGATGATAA

                        **                                *             *    
        158 AACCATTTAAAGTGAGTAATAAGGCTTTCGATAGCATGAGTGAATATAAATGGACTATTCTTGTC
         65 AACCATTTAAAGCAAGTAATAAGGCTTTCGATAGCATGAGTGAATACAAATGGACTATTCCTGTC

                                 *  *   *   *        
        223 AATGGATAGCATCCACTTCATGTTTAACTATGCAAACATCC
        130 AATGGATAGCATCCACTTCATATTCAACAATGAAAACATCC

                               *    *      *       *              *          
        264 AATTATGATAGGTTTTAACCAAAATCAAAAATATTTTGATTTATAA-TCATTTATAAGATGATAA
          1 AATTATGATAGGTTTTAACAAAAAGCAAAAAGATTTTGACTTA-AACTCATTTAAAAGATGATAA

             *      *                       *        * *          * *        
        328 AGCCATTTCAAGCAAGTAATAAGGCTTTCGATGGCATGAGTTACTACAAATGGATTTTTCCTGTC
         65 AACCATTTAAAGCAAGTAATAAGGCTTTCGATAGCATGAGTGAATACAAATGGACTATTCCTGTC

                      *  ***   *      *          *    
        393 AATGGAT-GATATTTTCTTTATATTCCACAATGAAAATATCC
        130 AATGGATAG-CATCCACTTCATATTCAACAATGAAAACATCC

                        *           
        434 AATTATGATAGGCTTTAACAAAAA
          1 AATTATGATAGGTTTTAACAAAAA

        458 ATGAAAANNN


Statistics
Matches: 159,  Mismatches: 33, Indels: 5
        0.81            0.17        0.03

Matches are distributed among these distances:
 169    1  0.01
 170  136  0.86
 171   22  0.14

ACGTcount: A:0.39, C:0.13, G:0.15, T:0.34


Consensus pattern (170 bp):   
AATTATGATAGGTTTTAACAAAAAGCAAAAAGATTTTGACTTAAACTCATTTAAAAGATGATAAA
ACCATTTAAAGCAAGTAATAAGGCTTTCGATAGCATGAGTGAATACAAATGGACTATTCCTGTCA
ATGGATAGCATCCACTTCATATTCAACAATGAAAACATCC

Found at i:858 original size:103 final size:103

Alignment explanation


    Indices: 601--816  Score: 315
    Period size: 103  Copynumber: 2.1  Consensus size: 103

        591 NNNNNNNNNN

                                                          *                  
        601 TAAATGGATTTTTCTTGTCAATGGATGGCATTGGCTTCAGGTAGACTTGGCATAAATGAAAACTA
          1 TAAATGGATTTTTCTTGTCAATGGATGGCATTGGCTTCAGGTAGACCTGGCATAAATGAAAACTA

                           *                 *****
        666 TTAGCAAGTAAAAAGGCTTTTGATGGCATGAGTNNNNN
         66 TTAGCAAGTAAAAAGACTTTTGATGGCATGAGTTACTA

            *****                                                        *   
        704 NNNNNGGATTTTTCTTGTCAATGGATGGCATTGGCTTCAGGTAGACCTGGCATAAATGAAAGCTA
          1 TAAATGGATTTTTCTTGTCAATGGATGGCATTGGCTTCAGGTAGACCTGGCATAAATGAAAACTA

                                                  
        769 TTAGCAAGTAAAAAGACTTTTGATGGCATGAGTTACTA
         66 TTAGCAAGTAAAAAGACTTTTGATGGCATGAGTTACTA

                      
        807 TAAATGGATT
          1 TAAATGGATT

        817 NNNNNNNNNN


Statistics
Matches: 95,  Mismatches: 18, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
 103   95  1.00

ACGTcount: A:0.30, C:0.11, G:0.23, T:0.31


Consensus pattern (103 bp):   
TAAATGGATTTTTCTTGTCAATGGATGGCATTGGCTTCAGGTAGACCTGGCATAAATGAAAACTA
TTAGCAAGTAAAAAGACTTTTGATGGCATGAGTTACTA
Done.