Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018400196.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_341.0, 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: 2469
ACGTcount: A:0.23, C:0.07, G:0.09, T:0.23

Warning! 927 characters in sequence are not A, C, G, or T


Found at i:439 original size:171 final size:160

Alignment explanation


    Indices: 238--561  Score: 335
    Period size: 170  Copynumber: 2.0  Consensus size: 160

        228 ATAAGCCTTC

                                   *                        *                
        238 TGAAGGAATGAGTGACTATAAATGGACTTTTATTCTCAATTAATGATATTTTTTGCACGTTTCTC
          1 TGAAGGAATGAGTGACTATAAATAGACTTTTATTCTCAATTAAT-A-ACTTTTTGCACGTTTCTC

               **   **   *                  *         *                   *  
        303 AAGGTAAATGTTTTATTATAGTCT-GTTTTAATAAAAAATGTCAAAAAGTTCAACTTAAAATTAA
         64 AAGACAAACATTTAATTATAGTCTAGTTTTAACAAAAAATGTAAAAAAGTTCAACTTAAAATCAA

                                                      
        367 TTATGAGATTATAAAACTATTTAAAGTGGNNNNNNNNNNTTT
        129 TTATGAGATTATAAAACTATTTAAAGTGG----------TTT

                                           *          *  *                 * 
        409 TGAAGGAATGAGTGACTATAAATAGACTTTTCTTCTCAATTACTAGCTTTTTGCACGTTTCTCGA
          1 TGAAGGAATGAGTGACTATAAATAGACTTTTATTCTCAATTAATAACTTTTTGCACGTTTCTCAA

                *            *     *       *    *         *               *  
        474 GACAGACATTTAATTATTGTCTATTTTTAACGAAAATTGTAAAAAATTTCAACTTAAAATCATTT
         66 GACAAACATTTAATTATAGTCTAGTTTTAACAAAAAATGTAAAAAAGTTCAACTTAAAATCAATT

                          *        
        539 ATGAGATTATAAAATTATTTAAA
        131 ATGAGATTATAAAACTATTTAAA

        562 CCGAGTAATA


Statistics
Matches: 130,  Mismatches: 22, Indels: 3
        0.84            0.14        0.02

Matches are distributed among these distances:
 169   32  0.25
 170   57  0.44
 171   41  0.32

ACGTcount: A:0.36, C:0.10, G:0.13, T:0.39


Consensus pattern (160 bp):   
TGAAGGAATGAGTGACTATAAATAGACTTTTATTCTCAATTAATAACTTTTTGCACGTTTCTCAA
GACAAACATTTAATTATAGTCTAGTTTTAACAAAAAATGTAAAAAAGTTCAACTTAAAATCAATT
ATGAGATTATAAAACTATTTAAAGTGGTTT

Found at i:2395 original size:112 final size:103

Alignment explanation


    Indices: 2185--2395  Score: 208
    Period size: 112  Copynumber: 2.0  Consensus size: 103

       2175 GGCTTTTGAA

                                       *      *     *                        
       2185 GGAATGAGTGACTATAAATAGACTTTTTTTCTCAGTGAATGGCTTTTTTTTACATGTTTCCCGAG
          1 GGAATGAGTGACTATAAATAGACTTTTCTTCTCAATGAATAGC-TTTTTTTACATGTTTCCCGAG

             **                         *          
       2250 GTGGACATTCAATTATAGTATGTTTTAATAAAAAATGTT
         65 GCAGACATTCAATTATAGTATGTTTTAACAAAAAATGTT

                                                            *           *    
       2289 NNNNNNNNNNGGAATGAGTGACTATAAATAGACTTTTCTTCTCAATGACTAGC-TTTTTTGCATG
          1 ----------GGAATGAGTGACTATAAATAGACTTTTCTTCTCAATGAATAGCTTTTTTTACATG

                *             *      *  *              
       2353 TTTCTCGAGGCAGACATTTAATTATTGTCTGTTTTAACAAAAA
         56 TTTCCCGAGGCAGACATTCAATTATAGTATGTTTTAACAAAAA

       2396 TTTCAACTTA


Statistics
Matches: 85,  Mismatches: 12, Indels: 2
        0.86            0.12        0.02

Matches are distributed among these distances:
 112   46  0.54
 114   39  0.46

ACGTcount: A:0.28, C:0.12, G:0.17, T:0.38


Consensus pattern (103 bp):   
GGAATGAGTGACTATAAATAGACTTTTCTTCTCAATGAATAGCTTTTTTTACATGTTTCCCGAGG
CAGACATTCAATTATAGTATGTTTTAACAAAAAATGTT
Done.