Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018400232.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3441.0, 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: 2406
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.27

Warning! 649 characters in sequence are not A, C, G, or T


Found at i:1201 original size:171 final size:161

Alignment explanation


    Indices: 1024--1332  Score: 327
    Period size: 171  Copynumber: 1.9  Consensus size: 161

       1014 GTCGAAGCGT

                                     *           *             *             
       1024 GTAATAAGGCTTTTGAAGGAATAGGTGACTATAA-ATGGACATTTCTTGA-TAATGAATACTTTT
          1 GTAATAAGGCTTTTGAAGGAATAGGAGACTATAAGA-AGACATTTCTT-ACCAATGAATACTTTT

                    *                                     *                  
       1087 TTCTTCACGTTTC-TCAAGATAAAAATTTAATTATTAACTGTTTTAGTCAAAAATATAAAAAAAT
         64 TTCTTCACATTTCTTCAA-ATAAAAATTTAATTATTAACTGTTTTAATCAAAAATATAAAAAAAT

                                                        
       1151 TCAACTTAAAATCAATTANNNNNNNNNNAAACCATTTAAAGTGA
        128 TCAACTTAAAATCAATTA----------AAACCATTTAAAGTGA

                          *     * *    *            *                        
       1195 GTAATAAGGCTTTTTAAGGAGTGGGAGGCTATAAGAAGACTTTTCTTACCAATGAATACTTTTTT
          1 GTAATAAGGCTTTTGAAGGAATAGGAGACTATAAGAAGACATTTCTTACCAATGAATACTTTTTT

                 *       *     * *           ***                             
       1260 CTTCATATTTCTTGAAATAGACATTTAATTATTGTTTGTTTTAATCAAAAATATAAAAAAATTCA
         66 CTTCACATTTCTTCAAATAAAAATTTAATTATTAACTGTTTTAATCAAAAATATAAAAAAATTCA

                    
       1325 ACTTAAAA
        131 ACTTAAAA

       1333 NNNNNNNNNN


Statistics
Matches: 118,  Mismatches: 17, Indels: 6
        0.84            0.12        0.04

Matches are distributed among these distances:
 170    1  0.01
 171  113  0.96
 172    4  0.03

ACGTcount: A:0.39, C:0.10, G:0.12, T:0.36


Consensus pattern (161 bp):   
GTAATAAGGCTTTTGAAGGAATAGGAGACTATAAGAAGACATTTCTTACCAATGAATACTTTTTT
CTTCACATTTCTTCAAATAAAAATTTAATTATTAACTGTTTTAATCAAAAATATAAAAAAATTCA
ACTTAAAATCAATTAAAACCATTTAAAGTGA

Found at i:1410 original size:171 final size:161

Alignment explanation


    Indices: 1179--1487  Score: 286
    Period size: 171  Copynumber: 1.9  Consensus size: 161

       1169 NNNNNNNNNN

                                    *     *        *   *                     
       1179 AAACCATTTAAAGTGAGTAATAAGGCTTTTTAAGGAGTGGGAGGCTATAAGAAGACTTTTCTTAC
          1 AAACCATTTAAAGTGAGTAATAAGCCTTTTGAAGGAGTGAGAGCCTATAAGAAGACTTTTCTTAC

                *     **         *                     *      *              
       1244 CAATGAATACTTTTTTCTTCATATTTCTTGA-AAT-AGACATTTAATTATTGTTTGTTTTAATCA
         66 CAATAAATACCCTTTTCTTCACATTTCTT-ATAATCA-ACATTCAATTATAGTTTGTTTTAATCA

                                                       
       1307 AAAATATAAAAAAATTCAACTTAAAANNNNNNNNNNGATTATA
        129 AAAATATAAAAAAATTCAACTTAAAA----------GATTATA

                                                                 *           
       1350 AAACCATTTAAAGCT-AGTAATAAGCCTTTTGAAGGA-TCGAGAGCCTATATATAA-ACTTTTCT
          1 AAACCATTTAAAG-TGAGTAATAAGCCTTTTGAAGGAGT-GAGAGCCTATA-AGAAGACTTTTCT

             **        *             *        **                            *
       1412 TGTCAATAAATGCCCTTTTCTTCACGTTTCTTATGTTCAACATTCAATTATAGTTTGTTTTAATG
         63 TACCAATAAATACCCTTTTCTTCACATTTCTTATAATCAACATTCAATTATAGTTTGTTTTAATC

                       
       1477 AAAAATATAAA
        128 AAAAATATAAA

       1488 NNNNNNNNNN


Statistics
Matches: 115,  Mismatches: 18, Indels: 10
        0.80            0.13        0.07

Matches are distributed among these distances:
 170    2  0.02
 171  108  0.94
 172    5  0.04

ACGTcount: A:0.36, C:0.12, G:0.12, T:0.37


Consensus pattern (161 bp):   
AAACCATTTAAAGTGAGTAATAAGCCTTTTGAAGGAGTGAGAGCCTATAAGAAGACTTTTCTTAC
CAATAAATACCCTTTTCTTCACATTTCTTATAATCAACATTCAATTATAGTTTGTTTTAATCAAA
AATATAAAAAAATTCAACTTAAAAGATTATA
Done.