Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018402680.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5743.0, 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, 920

Length: 1534
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.30

Warning! 267 characters in sequence are not A, C, G, or T


Found at i:417 original size:170 final size:161

Alignment explanation


    Indices: 240--575  Score: 356
    Period size: 170  Copynumber: 2.0  Consensus size: 161

        230 NNNNNNNNNN

                              *    *                         *     *         
        240 AATTATGAGATTATAAAATAATTTAAAGCGAG-TAATAAGCCTTTTGAAGGAATGTGTGACTATA
          1 AATTATGAGATTATAAAACAATTAAAAGCG-GTTAATAAGCCTTTTGAAAGAATGAGTGACTATA

                              *                           *          *       
        304 AAT-AGACTCTTT-TTCTTAATGAATGAC-TTTTTTACATGTTTCTTGAGGTAAACATTCAATTA
         65 AATGAG-CT-TTTCTTCTCAATGAATGACTTTTTTTACATGTTTCTCGAGGTAAACAATCAATTA

              *          *     * *            
        366 CAGTCTATTTTAATAAAAAGTGTAAAAAAATTCA
        128 CAATCTATTTTAACAAAAAATATAAAAAAATTCA

                                         *                  *                
        400 ANNNNNNNNNNATTATGAGATTATAAAACCATTAAAAGCGGTTAATAATCCTTTTGAAAGAATGA
          1 A----------ATTATGAGATTATAAAACAATTAAAAGCGGTTAATAAGCCTTTTGAAAGAATGA

                                           *  *                         *    
        465 GTGACTATAAATGAGCTTTTCTTCTCAATGATTGGCTTTTTTTACATGTTTCTCGAGGTAGACAA
         56 GTGACTATAAATGAGCTTTTCTTCTCAATGAATGACTTTTTTTACATGTTTCTCGAGGTAAACAA

                         *    *                    * 
        530 TCAATTACAATCTGTTTTGACAAAAAATATAAAAAAATTAA
        121 TCAATTACAATCTATTTTAACAAAAAATATAAAAAAATTCA

                 
        571 AATTA
          1 AATTA

        576 AAATCAATTA


Statistics
Matches: 143,  Mismatches: 19, Indels: 27
        0.76            0.10        0.14

Matches are distributed among these distances:
 160    1  0.01
 161    4  0.03
 169    4  0.03
 170   72  0.50
 171   62  0.43

ACGTcount: A:0.38, C:0.10, G:0.13, T:0.35


Consensus pattern (161 bp):   
AATTATGAGATTATAAAACAATTAAAAGCGGTTAATAAGCCTTTTGAAAGAATGAGTGACTATAA
ATGAGCTTTTCTTCTCAATGAATGACTTTTTTTACATGTTTCTCGAGGTAAACAATCAATTACAA
TCTATTTTAACAAAAAATATAAAAAAATTCA

Found at i:597 original size:171 final size:171

Alignment explanation


    Indices: 240--669  Score: 451
    Period size: 171  Copynumber: 2.5  Consensus size: 171

        230 NNNNNNNNNN

                              **   *              *         *     *          
        240 AATTATGAGATTATAAAATAATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGTGTGACTATAA
          1 AATTATGAGATTATAAAACCATTAAAAGCGAGTAATAATCCTTTTGAAAGAATGAGTGACTATAA

                             *                          *          *         
        305 AT-AGACTCTTT-TTCTTAATGAATGACTTTTTTACATGTTTCTTGAGGTAAACATTCAATTACA
         66 ATGAGACT-TTTCTTCTCAATGAATGACTTTTTTACATGTTTCTCGAGGTAAACAATCAATTACA

            *          *     * *          *  *********
        368 GTCTATTTTAATAAAAAGTGTAAAAAAATTCAANNNNNNNNN
        130 ATCTATTTTAACAAAAAATATAAAAAAATTAAAATTAAAATC

            *                                                                
        410 NATTATGAGATTATAAAACCATTAAAAGCG-GTTAATAATCCTTTTGAAAGAATGAGTGACTATA
          1 AATTATGAGATTATAAAACCATTAAAAGCGAG-TAATAATCCTTTTGAAAGAATGAGTGACTATA

                                   *  *                         *            
        474 AATGAG-CTTTTCTTCTCAATGATTGGCTTTTTTTACATGTTTCTCGAGGTAGACAATCAATTAC
         65 AATGAGACTTTTCTTCTCAATGAATGAC-TTTTTTACATGTTTCTCGAGGTAAACAATCAATTAC

                 *    *                                
        538 AATCTGTTTTGACAAAAAATATAAAAAAATTAAAATTAAAATC
        129 AATCTATTTTAACAAAAAATATAAAAAAATTAAAATTAAAATC

                  *              *                    *             *      * 
        581 AATTATAAGATTATAAAACCGTTTAAAA-CGAGTAATAAGT-TTTTTGAAAGAATGGGTGACTCT
          1 AATTATGAGATTATAAAACC-ATTAAAAGCGAGTAATAA-TCCTTTTGAAAGAATGAGTGACTAT

                            *          
        644 AAATG-GACTTTTCTTATCAATGAATG
         64 AAATGAGACTTTTCTTCTCAATGAATG

        670 CTTGTNNNNN


Statistics
Matches: 215,  Mismatches: 37, Indels: 15
        0.81            0.14        0.06

Matches are distributed among these distances:
 169    4  0.02
 170   73  0.34
 171  130  0.60
 172    8  0.04

ACGTcount: A:0.39, C:0.10, G:0.14, T:0.35


Consensus pattern (171 bp):   
AATTATGAGATTATAAAACCATTAAAAGCGAGTAATAATCCTTTTGAAAGAATGAGTGACTATAA
ATGAGACTTTTCTTCTCAATGAATGACTTTTTTACATGTTTCTCGAGGTAAACAATCAATTACAA
TCTATTTTAACAAAAAATATAAAAAAATTAAAATTAAAATC
Done.