Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018399725.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_297.0, 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: 5137
ACGTcount: A:0.22, C:0.07, G:0.08, T:0.22

Warning! 2075 characters in sequence are not A, C, G, or T


Found at i:4194 original size:171 final size:169

Alignment explanation


    Indices: 3906--4518  Score: 549
    Period size: 171  Copynumber: 3.6  Consensus size: 169

       3896 NNNNNNNNNN

                         *  *                              *                 
       3906 AAAATGTAAAAAATTTTAACTTAAAATCAATTATTAGATTAT-AAACTATTTAGAA-CGAGTAAT
          1 AAAATGTAAAAAAATTGAACTTAAAATCAATTATTAGATTATAAAACCATTTA-AAGCGAGTAAT

                        * *          *                                *******
       3969 -AAGACTTTTGATGAAATGAGTGACTATAAATGGACTTTTCTTGCTAATGAATGTGTTNNNNNNN
         65 AAAG-CTTTTGAAGGAATG-GTGACCATAAATGGACTTTTCTTGCTAATGAATGTGTTTTTCTTC

            ***     **                   *            
       4033 NNNTTTCTTTAGGTAGACATTCAATTATATTCTATTTTAATG
        128 ACATTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAATG

                                               * *                   *       
       4075 AAAATTGTAAAAAAATTGAACTTAAAATCAATTATAACATTATAAAACCATTTAAAGTGAGTAAT
          1 AAAA-TGTAAAAAAATTGAACTTAAAATCAATTATTAGATTATAAAACCATTTAAAGCGAGTAAT

                                                                            *
       4140 AAAGCTTTTGAAGGAATAGGTGACCATAAATGGACTTTTCTTGCTAATGAATGTGTTTTTCTTCN
         65 AAAGCTTTTGAAGGAAT-GGTGACCATAAATGGACTTTTCTTGCTAATGAATGTGTTTTTCTTCA

            *********                                
       4205 NNNNNNNNNAGGTAGACATTCAATTATAGTCTATTTTAATG
        129 CATTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAATG

                 *                                    *         *            
       4246 AAAA-ATAAAAAAATTCG-ACTTAAAATCAATTATTAGATTACAAAACCATTCAAAGCGAGTAAT
          1 AAAATGTAAAAAAATT-GAACTTAAAATCAATTATTAGATTATAAAACCATTTAAAGCGAGTAAT

              *      *         *            *         ** *                   
       4309 AAGGCTTTTTAAGGAAT-GAGAGCCTATAAATAGACTTTTCTCACCAATGAATGT-TATTTTCTT
         65 AAAGCTTTTGAAGGAATGGTGA-CC-ATAAATGGACTTTTCTTGCTAATGAATGTGT-TTTTCTT

            *            *  *              *  *        *
       4372 TACATTTCTCAAGTTAAACATTCAATTATAGCCTGTTTTAATTA
        127 CACATTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAA-TG

                        **                                    * *   **    *  
       4416 AAAATGTAAAAATTTTGAACTTAAAATCAATTATTAGATTATAAAACCATCTGAAGTTAGTATTA
          1 AAAATGTAAAAAAATTGAACTTAAAATCAATTATTAGATTATAAAACCATTTAAAGCGAGTAATA

            *                       *              
       4481 TAGCTTTTGAAGGAAAAT-GTGACTATAAATGGACTTTT
         66 AAGCTTTTGAAGG--AATGGTGACCATAAATGGACTTTT

       4519 NNNNNNNNNN


Statistics
Matches: 361,  Mismatches: 69, Indels: 26
        0.79            0.15        0.06

Matches are distributed among these distances:
 167    3  0.01
 168    3  0.01
 169  128  0.35
 170   43  0.12
 171  173  0.48
 172    5  0.01
 173    6  0.02

ACGTcount: A:0.39, C:0.10, G:0.12, T:0.36


Consensus pattern (169 bp):   
AAAATGTAAAAAAATTGAACTTAAAATCAATTATTAGATTATAAAACCATTTAAAGCGAGTAATA
AAGCTTTTGAAGGAATGGTGACCATAAATGGACTTTTCTTGCTAATGAATGTGTTTTTCTTCACA
TTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAATG

Found at i:4395 original size:169 final size:169

Alignment explanation


    Indices: 4043--4518  Score: 449
    Period size: 169  Copynumber: 2.8  Consensus size: 169

       4033 NNNTTTCTTT

                 *             *                  *                          
       4043 AGGTAGACATTCAATTATATTCTATTTTAATGAAAATTGTAAAAAAATTGAACTTAAAATCAATT
          1 AGGTAAACATTCAATTATAGTCTATTTTAATGAAAA--ATAAAAAAATTGAACTTAAAATCAATT

              * *              *    *                           *          * 
       4108 ATAACATTATAAAACCATTTAAAGTGAGTAATAAAGCTTTTGAAGGAATAGGTGACCATAAATGG
         64 ATTAGATTATAAAACCATTCAAAGCGAGTAATAAAGCTTTTGAAGGAATAGGAGACCATAAATAG

                    ** *                   **********
       4173 ACTTTTCTTGCTAATGAATGTGTTTTTCTTCNNNNNNNNNN
        129 ACTTTTCTCACCAATGAATGTGTTTTTCTTCACATTTCTCA

                 *                                                           
       4214 AGGTAGACATTCAATTATAGTCTATTTTAATGAAAAATAAAAAAATTCG-ACTTAAAATCAATTA
          1 AGGTAAACATTCAATTATAGTCTATTTTAATGAAAAATAAAAAAATT-GAACTTAAAATCAATTA

                    *                        *      *                        
       4278 TTAGATTACAAAACCATTCAAAGCGAGTAATAAGGCTTTTTAAGGAAT--GAGAGCCTATAAATA
         65 TTAGATTATAAAACCATTCAAAGCGAGTAATAAAGCTTTTGAAGGAATAGGAGA-CC-ATAAATA

                                            *          
       4341 GACTTTTCTCACCAATGAATGT-TATTTTCTTTACATTTCTCA
        128 GACTTTTCTCACCAATGAATGTGT-TTTTCTTCACATTTCTCA

              *                 *  *       *             **                  
       4383 AGTTAAACATTCAATTATAGCCTGTTTTAATTAAAAATGTAAAAATTTTGAACTTAAAATCAATT
          1 AGGTAAACATTCAATTATAGTCTATTTTAATGAAAAA--TAAAAAAATTGAACTTAAAATCAATT

                                 *   **    *  *              * * *   *      *
       4448 ATTAGATTATAAAACCA-TCTGAAGTTAGTATTATAGCTTTTGAAGGAAAATGTGACTATAAATG
         64 ATTAGATTATAAAACCATTC-AAAGCGAGTAATAAAGCTTTTGAAGGAATAGGAGACCATAAATA

                   
       4512 GACTTTT
        128 GACTTTT

       4519 NNNNNNNNNN


Statistics
Matches: 251,  Mismatches: 44, Indels: 20
        0.80            0.14        0.06

Matches are distributed among these distances:
 167    3  0.01
 168    3  0.01
 169  130  0.52
 170    4  0.02
 171  107  0.43
 172    1  0.00
 173    3  0.01

ACGTcount: A:0.39, C:0.11, G:0.12, T:0.35


Consensus pattern (169 bp):   
AGGTAAACATTCAATTATAGTCTATTTTAATGAAAAATAAAAAAATTGAACTTAAAATCAATTAT
TAGATTATAAAACCATTCAAAGCGAGTAATAAAGCTTTTGAAGGAATAGGAGACCATAAATAGAC
TTTTCTCACCAATGAATGTGTTTTTCTTCACATTTCTCA
Done.