Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018401158.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4310.0, 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: 5955
ACGTcount: A:0.21, C:0.06, G:0.07, T:0.19

Warning! 2786 characters in sequence are not A, C, G, or T


Found at i:3914 original size:171 final size:170

Alignment explanation


    Indices: 3737--4331  Score: 573
    Period size: 171  Copynumber: 3.5  Consensus size: 170

       3727 GAATGAGAGG

                                          *                    *             
       3737 CTATAAATAGACTTTT-TTCGCCAATGAATGCTTTTTTCTTCACATTTCTCAAGGTAAATATTCA
          1 CTATAAATAGACTTTTCTT-GCCAATGAATACTTTTTTCTTCACATTTCTCGAGGTAAATATTCA

                  *                                 *      *                 
       3801 ATTATACCCTGTTTTAACAAAAAATATAAAAATATTTAACGTAAAATTAATTACGAGATTATAAA
         65 ATTATAGCCTGTTTTAAC-AAAAATATAAAAATATTTAACCTAAAATCAATTACGAGATTATAAA

                                         **********   
       3866 ACCATTTGAAGTGAGTAATATGGCTTTTGNNNNNNNNNNTGA
        129 ACCATTTGAAGTGAGTAATATGGCTTTTGAAGGAAAGAGTGA

                    *           *                     *          **          
       3908 CTATAAATGGACTTTTCTTGTCAATGAATACTTTTTTCTTCATATTTCTCGAGACAAATATTCAA
          1 CTATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTCACATTTCTCGAGGTAAATATTCAA

                  *                         *   *                        * **
       3973 TTATAGTCTGTTTTAATCAAAAATATAAAAAAAATTCAACCTAAAATCAATTACGAGATTAGANN
         66 TTATAGCCTGTTTTAA-CAAAAATAT-AAAAATATTTAACCTAAAATCAATTACGAGATTATAAA

            ********   *        *              *   * *
       4038 NNNNNNNNAAGCGAGTAATAAGGCTTTTGAAGGAATGAGGGG
        129 ACCATTTGAAGTGAGTAATATGGCTTTTGAAGGAAAGAGTGA

              *                           *      *                     *     
       4080 CTGTAAATAGACTTTGT-TTGCCAATGAATGCTTTTTCCTTCACATTTCTCGAGGTAAACATTCA
          1 CTATAAATAGACTTT-TCTTGCCAATGAATACTTTTTTCTTCACATTTCTCGAGGTAAATATTCA

                      *********                     *                        
       4144 ATTATAGCCNNNNNNNNNNAAAAATATAAAAATATTTAACTTAAAATCAATTACGAGATTATAAA
         65 ATTATAGCC-TGTTTTAACAAAAATATAAAAATATTTAACCTAAAATCAATTACGAGATTATAAA

              *         *                        *    
       4209 ACGATTTGAAGTAAGTAATATGGCTTTTGAAGGAAAGGGTGA
        129 ACCATTTGAAGTGAGTAATATGGCTTTTGAAGGAAAGAGTGA

                *   *           *              *                             
       4251 CTATGAATGGACTTTTCTTGTCAATGAATACTTTTCTCTTCACATTTCTCGAGGTAAATATTCAA
          1 CTATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTCACATTTCTCGAGGTAAATATTCAA

                  *         
       4316 TTATAGTCTGTTTTAA
         66 TTATAGCCTGTTTTAA

       4332 NNNNNNNNNN


Statistics
Matches: 323,  Mismatches: 95, Indels: 13
        0.75            0.22        0.03

Matches are distributed among these distances:
 170    1  0.00
 171  198  0.61
 172  123  0.38
 173    1  0.00

ACGTcount: A:0.35, C:0.12, G:0.13, T:0.35


Consensus pattern (170 bp):   
CTATAAATAGACTTTTCTTGCCAATGAATACTTTTTTCTTCACATTTCTCGAGGTAAATATTCAA
TTATAGCCTGTTTTAACAAAAATATAAAAATATTTAACCTAAAATCAATTACGAGATTATAAAAC
CATTTGAAGTGAGTAATATGGCTTTTGAAGGAAAGAGTGA

Found at i:5265 original size:32 final size:34

Alignment explanation


    Indices: 5221--5312  Score: 134
    Period size: 34  Copynumber: 2.7  Consensus size: 34

       5211 AAAGCTTTTA

                                               
       5221 AAAAATTCAATTATGAGATTATAAAAAATT-AA-T
          1 AAAAATT-AATTATGAGATTATAAAAAATTCAACT

            *                                 
       5254 TAAAATTAATTATGAGATTATAAAAAATTCAACT
          1 AAAAATTAATTATGAGATTATAAAAAATTCAACT

                  *             *    
       5288 AAAAATCAATTATGAGATTAGAAAA
          1 AAAAATTAATTATGAGATTATAAAA

       5313 CCATTTAAAG


Statistics
Matches: 53,  Mismatches: 4, Indels: 3
        0.88            0.07        0.05

Matches are distributed among these distances:
  32   22  0.42
  33    8  0.15
  34   23  0.43

ACGTcount: A:0.57, C:0.04, G:0.08, T:0.32


Consensus pattern (34 bp):   
AAAAATTAATTATGAGATTATAAAAAATTCAACT

Found at i:5299 original size:34 final size:32

Alignment explanation


    Indices: 5221--5312  Score: 130
    Period size: 32  Copynumber: 2.8  Consensus size: 32

       5211 AAAGCTTTTA

                                             
       5221 AAAAATTCAATTATGAGATTATAAAAAATTAAT
          1 AAAAA-TCAATTATGAGATTATAAAAAATTAAT

            *     *                           
       5254 TAAAATTAATTATGAGATTATAAAAAATTCAACT
          1 AAAAATCAATTATGAGATTATAAAAAATT-AA-T

                                *    
       5288 AAAAATCAATTATGAGATTAGAAAA
          1 AAAAATCAATTATGAGATTATAAAA

       5313 CCATTTAAAG


Statistics
Matches: 52,  Mismatches: 5, Indels: 3
        0.87            0.08        0.05

Matches are distributed among these distances:
  32   23  0.44
  33    6  0.12
  34   23  0.44

ACGTcount: A:0.57, C:0.04, G:0.08, T:0.32


Consensus pattern (32 bp):   
AAAAATCAATTATGAGATTATAAAAAATTAAT
Done.