Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018399907.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3140.0, 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: 5170
ACGTcount: A:0.23, C:0.08, G:0.07, T:0.21

Warning! 2149 characters in sequence are not A, C, G, or T


Found at i:3044 original size:171 final size:167

Alignment explanation


    Indices: 2634--3155  Score: 476
    Period size: 171  Copynumber: 3.1  Consensus size: 167

       2624 NNNNNATGGA

                                             *                               
       2634 TGACTATAAATGGACTTTTTTAGTCAATGAATGTCTTTTTTT-ACGTTTTCCAAGGTAGACATTC
          1 TGACTATAAATGGACTTTTTT-GTCAATGAATGACTTTTTTTCACGTTTT-CAAGGTAGACATTC

                    *                                    *                   
       2698 AATTATAAGTTGTTTTAACAAAAAATGTAAAAATATTCAACTTAATATCAATTATGCA-ATTATA
         64 AATTATAATTTGTTTTAACAAAAAATGTAAAAA-ATTCAACTTAAAATCAATTATG-AGATTATA

            *                *      *            * * 
       2762 CAACCATTTAAAGTAAGTAATAAGGCCTTTAAAGGAATATG
        127 AAACCATTTAAAGTAAGCAATAAGACCTTTAAAGGAACAGG

             *          *         *    *                  *********          
       2803 TTACTATAAATGAACTTTTTTTATCAAAGAATGACTTTTTCTTCANNNNNNNNNNGGTAGACATT
          1 TGACTATAAATGGAC-TTTTTTGTCAATGAATGACTTTTT-TTCA-CGTTTTCAAGGTAGACATT

                   *                    *         *               *          
       2868 CAATTATGATTTGTTTTAACAAAAAATGCAAAACAATTTAACTTAAAATCAATTTTGAGATTATA
         63 CAATTATAATTTGTTTTAACAAAAAATGTAAAA-AATTCAACTTAAAATCAATTATGAGATTATA

                       *  *            *        *     
       2933 AAACCATTTAACGTGAGCAATACA-ACTTTTAAAGGCACAGG
        127 AAACCATTTAAAGTAAGCAATA-AGACCTTTAAAGGAACAGG

                                          *  *           *            *    * 
       2974 TGACTATAAATGGACTTTTCTTGTCAATGATTGCCTTTTCTTTCATGTTTCTCAAGGTCGACACT
          1 TGACTATAAATGGACTTTT-TTGTCAATGAATGACTTTT-TTTCACGTTT-TCAAGGTAGACATT

                      *         *                     *                  *   
       3039 CAATTATAATCTGTTTTAACTAAAAATGTAAAAAAATTCAACATAAAA-CTAATTATGAGAATAT
         63 CAATTATAATTTGTTTTAACAAAAAATGT-AAAAAATTCAACTTAAAATC-AATTATGAGATTAT

                **            *      * *   *      **  
       3103 AAAATTATTTAAAGTAAGTAATAAGGCTTTTGAAGGAATGGG
        126 AAAACCATTTAAAGTAAGCAATAAGACCTTTAAAGGAACAGG

                       
       3145 TGACTATAAAT
          1 TGACTATAAAT

       3156 NNNNNNNNNN


Statistics
Matches: 276,  Mismatches: 64, Indels: 24
        0.76            0.18        0.07

Matches are distributed among these distances:
 169   28  0.10
 170   15  0.05
 171  226  0.82
 172    7  0.03

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


Consensus pattern (167 bp):   
TGACTATAAATGGACTTTTTTGTCAATGAATGACTTTTTTTCACGTTTTCAAGGTAGACATTCAA
TTATAATTTGTTTTAACAAAAAATGTAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
CATTTAAAGTAAGCAATAAGACCTTTAAAGGAACAGG

Found at i:4911 original size:170 final size:160

Alignment explanation


    Indices: 4699--5021  Score: 294
    Period size: 170  Copynumber: 2.0  Consensus size: 160

       4689 NNNNNNACTA

                              *        *                 *        *    *     
       4699 TTTAAAATGAGTAACAAGGCTTTTGAAGGAATAGTTGACTATAAATAGACT-TTTTTGGTTAATA
          1 TTTAAAATGAGTAACAAGACTTTTGAAAGAATAGTTGACTATAAACAGACTATTCTT-GCTAATA

                *                       *   *             *                  
       4763 AATGCCTTTTTCTTCACGTTTGC-TAAGGCAAGCATTCAATTATAAGTTGTTCTAACAAAAAAT-
         65 AATGACTTTTTCTTCACGTTT-CTTAAGACAAACATTCAATTATAACTTGTTCTAACAAAAAATG

                          *                  
       4826 AAAAAAAATTCAAATTAAAATCAATTATGAGAT
        129 AAAAAAAATTC-AACTAAAATCAATTATGAGAT

                            *       * *                              *       
       4859 NNNNNNNNNNTTTAAAGTGAGTAATATGACTTTTGAAAGAATGAG-TGACTATAAACGGACTATT
          1 ----------TTTAAAATGAGTAACAAGACTTTTGAAAGAAT-AGTTGACTATAAACAGACTATT

                     *                        *   *   *                  *   
       4923 CTTGCTAATGAATGACTTTTTCTTCACGTTTCTTGAGATAAATATTCAATTATAACTTGTTTTAA
         55 CTTGCTAATAAATGACTTTTTCTTCACGTTTCTTAAGACAAACATTCAATTATAACTTGTTCTAA

             *       *     *                  
       4988 CCAAAAATGTAAAAAGATTCAACTAAAATCAATT
        120 CAAAAAATGAAAAAAAATTCAACTAAAATCAATT

       5022 TTCAAATTAT


Statistics
Matches: 127,  Mismatches: 22, Indels: 8
        0.81            0.14        0.05

Matches are distributed among these distances:
 169    1  0.01
 170  111  0.87
 171   15  0.12

ACGTcount: A:0.38, C:0.11, G:0.13, T:0.35


Consensus pattern (160 bp):   
TTTAAAATGAGTAACAAGACTTTTGAAAGAATAGTTGACTATAAACAGACTATTCTTGCTAATAA
ATGACTTTTTCTTCACGTTTCTTAAGACAAACATTCAATTATAACTTGTTCTAACAAAAAATGAA
AAAAAATTCAACTAAAATCAATTATGAGAT
Done.