Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018397811.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1113.0, 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: 2802
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.30

Warning! 501 characters in sequence are not A, C, G, or T


Found at i:1521 original size:171 final size:171

Alignment explanation


    Indices: 1097--1524  Score: 501
    Period size: 171  Copynumber: 2.5  Consensus size: 171

       1087 NNNNNNNTGA

                               *                      *    *      *          
       1097 GTGACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTTTACGTTTCTCGAGATAGACAT
          1 GTGACTATAAATAGACTTTCCTTGCCAATGAATG-CTTTTTCCTTACATTTCTCAAGATAGACAT

                         *    *                                         *    
       1162 TCAATTATTATCTATTTTCATAAAAAAAGTAAAAACAATTGAACTAAAAATCAATTTTGATATTA
         65 TCAATTATTATCTGTTTTAATAAAAAAAGTAAAAACAATTGAACTAAAAATCAATTTTGAGATTA

                                                    * 
       1227 TAAAATCATTTAAAGCGAGTAATAAGGCTTTGAAAGGAATGG
        130 TAAAATCATTTAAAGCGAGTAATAAGGCTTTGAAAGGAATAG

               *               *              *           * *     *   *      
       1269 GTGGCTATAAATAGACTTTGCTT-CTCAATGAACAGCTTTTT-CTCCATATTTCCCAACATA-AC
          1 GTGACTATAAATAGACTTTCCTTGC-CAATGAA-TGCTTTTTCCT-TACATTTCTCAAGATAGA-

                *                       *  *             *    *     *        
       1331 CATTAAATTA-TAGTCTGTTTTAATGAAGAATA-TAAAAA-AATTTAACTTAAAATTAATTTTGA
         62 CATTCAATTATTA-TCTGTTTTAAT-AAAAAAAGTAAAAACAATTGAACTAAAAATCAATTTTGA

                       *             *                      
       1393 GATTATAAAATTATTTAAAGCGAGTTATAAGGCTTTTG-AAGGAATAG
        125 GATTATAAAATCATTTAAAGCGAGTAATAAGGC-TTTGAAAGGAATAG

                        *                                            *       
       1440 GTGACTATAAATGGACTTTCCTTGCCAATGAATGCATTTTTCCTTACATTTCTCAAGGTAGACAT
          1 GTGACTATAAATAGACTTTCCTTGCCAATGAATGC-TTTTTCCTTACATTTCTCAAGATAGACAT

                                
       1505 TCAATTATTATCTGTTTTAA
         65 TCAATTATTATCTGTTTTAA

       1525 CCAAAAATGT


Statistics
Matches: 212,  Mismatches: 32, Indels: 25
        0.79            0.12        0.09

Matches are distributed among these distances:
 170    2  0.01
 171  126  0.59
 172   78  0.37
 173    6  0.03

ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37


Consensus pattern (171 bp):   
GTGACTATAAATAGACTTTCCTTGCCAATGAATGCTTTTTCCTTACATTTCTCAAGATAGACATT
CAATTATTATCTGTTTTAATAAAAAAAGTAAAAACAATTGAACTAAAAATCAATTTTGAGATTAT
AAAATCATTTAAAGCGAGTAATAAGGCTTTGAAAGGAATAG

Found at i:2802 original size:171 final size:169

Alignment explanation


    Indices: 2117--2799  Score: 499
    Period size: 171  Copynumber: 4.0  Consensus size: 169

       2107 NNNNNCTCGT

                       *  *   *   *            *       *      *    * *       
       2117 TTTAAATGGTTTTATAATTTCATAATTGATTTTAGGGTTCAATGTTTTTACATTACTAGTTAAAA
          1 TTTAAATGGTTATACAATCTCAAAATTGATTTTA-AGTTCAATTTTTTTATATT-TTTGTT-AAA

              *             * ** *  **      * *  * *                        *
       2182 CATATTATAATTGAATATCAATCTCAAGAAACATAAATAGAAA-ATAGTTCATTAGCAAGAAAAT
         63 CAGATTATAATTGAATGTTTACCTTGAGAAACGTGAAGAAAAAGATA-TTCATTAGCAAGAAAAG

                         * ***   **              *     
       2246 TCCATTTATAGTCTCTTTTTCGCTCAAAAGCCTTATTGCTCAC
        127 TCCATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTCAC

            *          *  *     *   *            * *            *            
       2289 GTTAAATGGTTTTATAATCTTATAGA-TGATTTTAAGCTGAATTTTTTTATCTTTTTTGTTACAA
          1 TTTAAATGGTTATACAATCTCA-AAATTGATTTTAAGTTCAATTTTTTTAT-ATTTTTGTTA-AA

            *   **                          *  *         *  *              * 
       2353 TAGACAATAATTGAATGTTTACCTTGAGAAACATGGAGAAAAAGACATCCATTAGCAAGAAAACT
         63 CAGATTATAATTGAATGTTTACCTTGAGAAACGTGAAGAAAAAGATATTCATTAGCAAGAAAAGT

                   *      *                           
       2418 CCATTTAGAGTCACTCATTCTTTCAAAAGCCTTATTACTCAC
        128 CCATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTCAC

                  **********                                 *      *   *    
       2460 TTTAAANNNNNNNNNNATCTCAAAATTGATTTTAAGTTCAATTTTTTTACATTTATGGCTAAAAC
          1 TTTAAATGGTTATACAATCTCAAAATTGATTTTAAGTTCAATTTTTTTATATTT-TTG-TTAAAC

            *                *              *        *    *     *            
       2525 TGATTATAATTGAATGTCTACCTTGAGAAACGAGAAGAAAACGATAGTCATTGGCAAGAAAAGTC
         64 AGATTATAATTGAATGTTTACCTTGAGAAACGTGAAGAAAAAGATATTCATTAGCAAGAAAAGTC

                        **********                 * 
       2590 CATTTATAGTCANNNNNNNNNNCAAAAGCCTTATTACTCGC
        129 CATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTCAC

                             *                                               
       2631 TTTAAATGGTTATACAAGCTCAAAATTGATTTTAAGTTCAATTTTTTATATATTTTTGTTCAAAC
          1 TTTAAATGGTTATACAATCTCAAAATTGATTTTAAGTTCAATTTTTT-TATATTTTTGTT-AAAC

                     *                *                 *         *    *     
       2696 AGATTATAAATGAATGTTTACC-TGTTGAAACGTGAAGAAAAAGGTATTCATTAACAAGGAAAGT
         64 AGATTATAATTGAATGTTTACCTTG-AGAAACGTGAAGAAAAAGATATTCATTAGCAAGAAAAGT

                                                    
       2760 CCATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTC
        128 CCATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTC

       2800 GCT


Statistics
Matches: 384,  Mismatches: 117, Indels: 21
        0.74            0.22        0.04

Matches are distributed among these distances:
 170    9  0.02
 171  335  0.87
 172   39  0.10
 173    1  0.00

ACGTcount: A:0.35, C:0.14, G:0.12, T:0.36


Consensus pattern (169 bp):   
TTTAAATGGTTATACAATCTCAAAATTGATTTTAAGTTCAATTTTTTTATATTTTTGTTAAACAG
ATTATAATTGAATGTTTACCTTGAGAAACGTGAAGAAAAAGATATTCATTAGCAAGAAAAGTCCA
TTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTCAC
Done.