Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018401618.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4737.0, 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: 3710
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.25

Warning! 1187 characters in sequence are not A, C, G, or T


Found at i:355 original size:170 final size:161

Alignment explanation


    Indices: 1--642  Score: 355
    Period size: 170  Copynumber: 3.8  Consensus size: 161

                                                                *  *         
          1 AAAGCAAGTAATAAGGCTTTTGAAGGAATGGGTGACTAT-AATGGACTTTTTTTTGTCAATGAAT
          1 AAAGCAAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGAC-TTTTCTTCTCAATGAAT

                   * *  * *         *                 *                      
         65 GCCTTTTTTTCACGTTTCTTAAGGTAGACATTCAATTATAGTTTGTTTTAAGCAAAAATGTAAAA
         65 GCCTTTTCTACAAGCTTCTTAAGGCAGACATTCAATTATAGTCTGTTTTAAGCAAAAATGTAAAA

                 *              *  *                 
        130 AAATTTAACTTNNNNNNNNNNATGAGATTATAAAACTATTT
        130 AAATTCAACTT---------TATAAGATTATAAAACTATTT

                   *                  *                *                     
        171 AAAGCAACTAATAAGGCTTTTGAAGGGATGGGTGACTATAAATAGACTTTTCTTCTCAATGAATG
          1 AAAGCAAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATG

            *                            *  *                                
        236 GCTTTTCCTACAAGCTTC-TAAGGCAGACTTTTAATTATAGTCTGTTTTAA-CTAAAAATGTAAA
         66 CCTTTT-CTACAAGCTTCTTAAGGCAGACATTCAATTATAGTCTGTTTTAAGC-AAAAATGTAAA

                                *                      
        299 AAAATTCAACTNNNNNNNNNNTATAAGATTATAAAA-TCATTT
        129 AAAATTCAACT---------TTATAAGATTATAAAACT-ATTT

                **                  **    *    *               *   *         
        341 AAAGTGAGTAATAAGGCTTTTGAAAAAATGAGTGATTATAAATGGACTTTTTTTAGT-AATGAAT
          1 AAAGCAAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTT-CTCAATGAAT

                    * *  * *    **   *       *       * *                     
        405 GCCTTGTTTTTCATGTTTCTCGAGGTAGACATTTAATTATAATTTGTTTTAA-CAAATAATGTAA
         65 GCCTT-TTCTACAAGCTTCTTAAGGCAGACATTCAATTATAGTCTGTTTTAAGCAAA-AATGT-A

                    *                 *                  
        469 AAAAAATTGAACTTAAAATCAATTTTGAGATTATAAAA-TCATTT
        127 AAAAAATTCAACTT----T--A---TAAGATTATAAAACT-ATTT

              **********                                * *             *    
        513 AANNNNNNNNNNAAGGCTTTTGAAGGAATGGGTGACTATAAATGAATTTTTCTTCTCAATAAATG
          1 AAAGCAAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATG

              *    *       *    *    *                   *      *       *    
        578 ACTTTTTTTA-AATGTTTCTCAAGGTAGACATTCAATTATAGTCTATTTTAACCAAAAATATAAA
         66 -CCTTTTCTACAA-GCTTCTTAAGGCAGACATTCAATTATAGTCTGTTTTAAGCAAAAATGTAAA

             
        642 A
        129 A

        643 NNNNNNNNNN


Statistics
Matches: 370,  Mismatches: 71, Indels: 61
        0.74            0.14        0.12

Matches are distributed among these distances:
 167    1  0.00
 169    3  0.01
 170  189  0.51
 171   54  0.15
 172  116  0.31
 173    7  0.02

ACGTcount: A:0.36, C:0.10, G:0.14, T:0.36


Consensus pattern (161 bp):   
AAAGCAAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTCTCAATGAATG
CCTTTTCTACAAGCTTCTTAAGGCAGACATTCAATTATAGTCTGTTTTAAGCAAAAATGTAAAAA
AATTCAACTTTATAAGATTATAAAACTATTT

Found at i:1962 original size:170 final size:171

Alignment explanation


    Indices: 1559--2012  Score: 486
    Period size: 170  Copynumber: 2.6  Consensus size: 171

       1549 TCACGTTTTT

                         *              *  *               *   * *      *    
       1559 TAAGGTAAACTTTTAATTATAGTCTGTTATAACAAAAAATGTAAAAATATTCAGCTTAAAGTCAA
          1 TAAGGTAAACTTTCAATTATAGTCTGTTTTAGC-AAAAATGTAAAAAAATTTAACTTAAAATCAA

                             *                    *                          
       1624 TTATGAGATTATAAAACAATTTAAAGCGAGTAATAAGATTTTTGAAGGAAAGAATGACTATAAAT
         65 TTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGACTTTTGAAGGAAAGAATGACTATAAAT

                     *  *                   *  *      *
       1689 AGACTTTTTTTTGTCAATGAATGCCCATTTCTTCATGTTTCTT
        130 AGAC-TTTTCTTCTCAATGAATGCCCATTTCTACAAGTTTCTC

                   *                *             *   *                      
       1732 TAA-GTAGA-TGTTCAATTATAGTTTGTTTTAAGCAAATATGAAAAAAAATTTAACTTAAAATCA
          1 TAAGGTAAACT-TTCAATTATAGTCTGTTTT-AGCAAAAATGTAAAAAAATTTAACTTAAAATCA

              *                        *   *      *       *    * **  *       
       1795 ATCATGAGATTATAAAACTATTTAAAGTGAGCAATAAGGCTTTTGATGGAATGGGTGGCTATAAA
         64 ATTATGAGATTATAAAACTATTTAAAGCGAGTAATAAGACTTTTGAAGGAAAGAATGACTATAAA

             *                     * **                
       1860 TGGA-TTTTCTTCTCAATGAATGGCTTTTTCTACAAGTTTC-C
        129 TAGACTTTTCTTCTCAATGAATGCCCATTTCTACAAGTTTCTC

                 *                                         *      *          
       1901 TAAGGCAAACTTTCAATTATAGTCTGTTTTAGCTAAAAATGTAAAAACATTTAAATTAAAATCAA
          1 TAAGGTAAACTTTCAATTATAGTCTGTTTTAGC-AAAAATGTAAAAAAATTTAACTTAAAATCAA

                * * *                                       
       1966 TTATCATACTATAAAA-TCATTTAAAGCGAGTAATAAGACTTTTGAAG
         65 TTATGAGATTATAAAACT-ATTTAAAGCGAGTAATAAGACTTTTGAAG

       2013 AAANNNNNNN


Statistics
Matches: 229,  Mismatches: 46, Indels: 15
        0.79            0.16        0.05

Matches are distributed among these distances:
 169    7  0.03
 170  114  0.50
 171    2  0.01
 172  101  0.44
 173    5  0.02

ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36


Consensus pattern (171 bp):   
TAAGGTAAACTTTCAATTATAGTCTGTTTTAGCAAAAATGTAAAAAAATTTAACTTAAAATCAAT
TATGAGATTATAAAACTATTTAAAGCGAGTAATAAGACTTTTGAAGGAAAGAATGACTATAAATA
GACTTTTCTTCTCAATGAATGCCCATTTCTACAAGTTTCTC
Done.