Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018403149.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_816.0, 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: 4099
ACGTcount: A:0.26, C:0.11, G:0.10, T:0.28

Warning! 995 characters in sequence are not A, C, G, or T


Found at i:2843 original size:172 final size:161

Alignment explanation


    Indices: 2707--3025  Score: 255
    Period size: 172  Copynumber: 1.9  Consensus size: 161

       2697 NNNNNNNNNN

                                                  *      * *                 
       2707 ATCTCAAAATTGATTTTATGTTCAATTATTTTGACATTTTTGGTTGAGACAAACTATAATTGAAT
          1 ATCTCAAAATTGATTTTATGTTCAATT-TTTTGACATTATTGGTTAAAACAAACTATAATTGAAT

                            *                   *                    *   *   
       2772 GTCGACCTAGAGAAACGTGAAGAAAAAAGCATTTATTGACAAGAAAAGAGCATTTATGGTCTC-C
         65 GTCGACCTAGAGAAACATGAAGAAAAAAGCATTTATCGACAAGAAAAGAGCATTTATAGTCACTC

                                                     **
       2836 TATTCCTTCAAAAGCCTTATTACTCACTCTAAATGATTTTATT
        130 -ATTCCTTCAAAAGCCTTATTA--C-C-C------ATTTTAAA

                       *     *              * *   *  *         *          *  
       2879 ATCTCAAAATTAATTTTTTGTTCAATATTTTTTATATTTTTCGTTAAAACAGACTATAATTGGAT
          1 ATCTCAAAATTGATTTTATGTTCAAT-TTTTTGACATTATTGGTTAAAACAAACTATAATTGAAT

                   * *                  * *   *  *           **      *      *
       2944 GTAC-ACATTGAGAAACATGAAGAAAAAGGTATTCATTGACAAGAAAAGTCCATTTAGAGTCACC
         65 GT-CGACCTAGAGAAACATGAAGAAAAAAGCATTTATCGACAAGAAAAGAGCATTTATAGTCACT

                              
       3008 CATTCCTTCAAAAGCCTT
        129 CATTCCTTCAAAAGCCTT

       3026 NNNNNNNNNN


Statistics
Matches: 124,  Mismatches: 20, Indels: 6
        0.83            0.13        0.04

Matches are distributed among these distances:
 172  121  0.98
 173    3  0.02

ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36


Consensus pattern (161 bp):   
ATCTCAAAATTGATTTTATGTTCAATTTTTTGACATTATTGGTTAAAACAAACTATAATTGAATG
TCGACCTAGAGAAACATGAAGAAAAAAGCATTTATCGACAAGAAAAGAGCATTTATAGTCACTCA
TTCCTTCAAAAGCCTTATTACCCATTTTAAA

Found at i:3222 original size:171 final size:157

Alignment explanation


    Indices: 3044--3370  Score: 352
    Period size: 170  Copynumber: 2.0  Consensus size: 157

       3034 NNNTAAATAG

                                                                             
       3044 TTTTATAATCTCATAATTGATTTAAAGTTA-AATTTTTTTACATTTTTCATTAAAACAAACTATA
          1 TTTTATAATCTCATAATTGATTTAAAG-TAGAA-TTTTTTACATTTTTCATTAAAACAAACTATA

                   ***  *                                 *                  
       3108 ATTGAATTTTTATCTTGAAAAACATGTA-GAAAAACCTATTTATTTGGAAGAAAAGTCTATTTAT
         64 ATTGAATACCTACCTTGAAAAACATGTAGGAAAAACC-ATTTATTTAGAAGAAAAGTCTATTTAT

                     *  *  *              
       3172 AGTCTCTCATTCGTTTAAAAGCCTTATTAC
        128 AGTCTCTCAGTCCTTCAAAAGCCTTATTAC

                                                *               *            
       3202 TNNNNNNNNNNNNNTTTATAATCTCATAATTGATTTTAAGTAGAATTTTTTAGATTTTTCATTAA
          1 T-------------TTTATAATCTCATAATTGATTTAAAGTAGAATTTTTTACATTTTTCATTAA

                *                       ** *             *                   
       3267 AACAGACTATAATTGAATACCTACCTTGTGAGACATGTAGGAAAAGCCATTTATTTAGAAGAAAA
         53 AACAAACTATAATTGAATACCTACCTTGAAAAACATGTAGGAAAAACCATTTATTTAGAAGAAAA

                *                                  
       3332 GTCTGTTTATAGTCTCTCAGTCCTTCAAAAGCCTTATTA
        118 GTCTATTTATAGTCTCTCAGTCCTTCAAAAGCCTTATTA

       3371 GTCNNNNNNN


Statistics
Matches: 138,  Mismatches: 16, Indels: 18
        0.80            0.09        0.10

Matches are distributed among these distances:
 158    1  0.01
 170  103  0.75
 171   34  0.25

ACGTcount: A:0.35, C:0.12, G:0.10, T:0.39


Consensus pattern (157 bp):   
TTTTATAATCTCATAATTGATTTAAAGTAGAATTTTTTACATTTTTCATTAAAACAAACTATAAT
TGAATACCTACCTTGAAAAACATGTAGGAAAAACCATTTATTTAGAAGAAAAGTCTATTTATAGT
CTCTCAGTCCTTCAAAAGCCTTATTAC
Done.