Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018399892.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3126.0, 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, 831

Length: 1385
ACGTcount: A:0.27, C:0.10, G:0.09, T:0.30

Warning! 341 characters in sequence are not A, C, G, or T


Found at i:749 original size:171 final size:171

Alignment explanation


    Indices: 444--789  Score: 362
    Period size: 171  Copynumber: 2.0  Consensus size: 171

        434 NNNNNNNNNN

                              *          *   *     **                     *  
        444 TAAATAGTTTTATAATCTTATAATTGATTTTAAGTTAAATGTTTTTACATTTTTCATTAAAATAG
          1 TAAATAGTTTTATAATCTCATAATTGATTCTAAATTAAACATTTTTACATTTTTCATTAAAACAG

                 *                *     **  *                             *  
        509 ACTATCATAGAATGCTCACCTTGGGAAATGTATAGAAAAAGTGATTCACTTGGAAGAAAAGTTCA
         66 ACTATAATAGAATGCTCACCTTAGGAAACATAGAGAAAAAGTGATTCACTTGGAAGAAAAGTCCA

                      * **                        *    
        574 TTTATTA-TCTCTTATTCCTTCAAAAGCCTTT-TTACTTGCTT
        131 TTTA-TAGTCACCCATTCCTTCAAAAG-CTTTGTTACTCGCTT

                 *        * *                   *                 *          
        615 TAAATGGTTTTATAGTGTCATAATTGATTCTAAATTGAACATTTTTACATTTTTGATTAAAACAG
          1 TAAATAGTTTTATAATCTCATAATTGATTCTAAATTAAACATTTTTACATTTTTCATTAAAACAG

                    *         *     *       *                                
        680 ACTATAATTGAATG-TCTGCCTTATGAAACATCGAGAAAAAG-GCATTCA-TTGGCAAG-AAAGA
         66 ACTATAATAGAATGCTC-ACCTTAGGAAACATAGAGAAAAAGTG-ATTCACTTGG-AAGAAAAG-

                                    *                    
        741 TCCATTTATAGTCACCCATTCCTTGAAAAGCTTTGTTACTCGCTT
        127 TCCATTTATAGTCACCCATTCCTTCAAAAGCTTTGTTACTCGCTT

                
        786 TAAA
          1 TAAA

        790 ANNNNNNNNN


Statistics
Matches: 143,  Mismatches: 26, Indels: 12
        0.79            0.14        0.07

Matches are distributed among these distances:
 170   17  0.12
 171  126  0.88

ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39


Consensus pattern (171 bp):   
TAAATAGTTTTATAATCTCATAATTGATTCTAAATTAAACATTTTTACATTTTTCATTAAAACAG
ACTATAATAGAATGCTCACCTTAGGAAACATAGAGAAAAAGTGATTCACTTGGAAGAAAAGTCCA
TTTATAGTCACCCATTCCTTCAAAAGCTTTGTTACTCGCTT

Found at i:1372 original size:172 final size:171

Alignment explanation


    Indices: 1016--1385  Score: 388
    Period size: 172  Copynumber: 2.2  Consensus size: 171

       1006 ATTACTCGTT

                        *                                  *                 
       1016 TTAAATAGTTTTGTAATCTCATAATTGATTTTAAGTTGAATGTTTTTGCAATTTTGGTTAAAACA
          1 TTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATGTTTTTACAATTTTGGTTAAAACA

                      *                                         **           
       1081 GATTATAATTTAATGTTTACCTCAAGAAACATGAAGATAAAAGCAATCATTGGCAAGAAAGGTCT
         66 GATTATAATTGAATGTTTACCTCAAGAAACATGAAGATAAAAGCAATCATTGAAAAGAAAGGTCT

              *                  *          *********
       1146 ATTTATAGTCACTCATTCCTTTAAAAGCCTTANNNNNNNNN
        131 ATCTATAGTCACTCATTCCTTCAAAAGCCTTAATTACTTAC

            *     *               *          *   *   *         *         *   
       1187 NTAAATGGTTTTATAATCTCATTATTGATTTTAGGTTTAATTTTTTTAACATTTTTGGTTATAAC
          1 TTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATGTTTTT-ACAATTTTGGTTAAAAC

                        *  *       **         *            *              *  
       1252 AGATTATAATTGCATTTTTACCTTGAGAAACATGTAGA-AAAAGGCATTCATTGAAAAGAAAAGT
         65 AGATTATAATTGAATGTTTACCTCAAGAAACATGAAGATAAAA-GCAATCATTGAAAAGAAAGGT

                                                         
       1316 -TCATCTATAGTCAC-CAATTCCTTCAAAAGCCTT-ATTACTTAC
        129 CT-ATCTATAGTCACTC-ATTCCTTCAAAAGCCTTAATTACTTAC

                                        
       1358 TTGAAATAGTTTTATAATCTCATAATTG
          1 TT-AAATAGTTTTATAATCTCATAATTG


Statistics
Matches: 160,  Mismatches: 34, Indels: 9
        0.79            0.17        0.04

Matches are distributed among these distances:
 171   47  0.29
 172  113  0.71

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


Consensus pattern (171 bp):   
TTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATGTTTTTACAATTTTGGTTAAAACA
GATTATAATTGAATGTTTACCTCAAGAAACATGAAGATAAAAGCAATCATTGAAAAGAAAGGTCT
ATCTATAGTCACTCATTCCTTCAAAAGCCTTAATTACTTAC
Done.