Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018402873.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5923.0, 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, 945

Length: 1576
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33


Found at i:293 original size:171 final size:170

Alignment explanation


    Indices: 4--706  Score: 588
    Period size: 169  Copynumber: 4.1  Consensus size: 170

          1 CAT

                               **   *                     *           *      
          4 TTATAGTCACTCAAGCCTTTAAAAACCTTATTACTCGCTTTAAATGGTTTTATAATCTCA-AGAT
          1 TTATAGTCACTCAAGCCTTCGAAAGCCTTATTACTCGCTTTAAATGATTTTATAATCTTATA-AT

            *       *   *                                    *          *    
         68 AGATTTTATGTTAAATATTTTTACATTTTTGGTTAAAACTGATA--ATATTTGAATGTCTACCTC
         65 TGATTTTAAGTTGAATATTTTTACATTTTTGGTTAAAA-T-ATATTATAATTGAATGTCTGCCTC

                                *          *            
        131 AGGAAACATGAAG-AAATAGTTATTCATTAGTAAGAAAAGTCTA
        128 AGGAAACATGAAGCAAATAGCTATTCATT-GAAAGAAAAGTCTA

                       *  *                     *  *                    *    
        174 TCTATAGTCACCCATGCCTTCGAAAGCCTTATTACTTGCATTAAATGATTTTATAATCTTGTAAT
          1 T-TATAGTCACTCAAGCCTTCGAAAGCCTTATTACTCGCTTTAAATGATTTTATAATCTTATAAT

                    *                     **                        *      * 
        239 TGATTTTATGTTGAATATTTTTACATTTTTTATTAAAATATATTATAATTGAATGTTTGCCT-TG
         65 TGATTTTAAGTTGAATATTTTTACATTTTTGGTTAAAATATATTATAATTGAATGTCTGCCTCAG

                    *   *       *         *        * * 
        303 AGAAACATAAAGTAAA-AGCCA-TCTATTGCAAGAAAAGACCA
        130 -GAAACATGAAGCAAATAGCTATTC-ATTGAAAGAAAAGTCTA

                        *    *        *                      *   *           
        344 TTAATAGTCACTTAAGCTTTCGAAAGGCTTATTACTCGCTTTAAATG--CTTACAATCTTATAAT
          1 TT-ATAGTCACTCAAGCCTTCGAAAGCCTTATTACTCGCTTTAAATGATTTTATAATCTTATAAT

                             *      *   **         *                 *    *  
        407 TG-TATTTAAGTTGAATTTTTTTATATTGGTGGTTAAAAAATATTATAATTGAATGTTTGCCCCA
         65 TGAT-TTTAAGTTGAATATTTTTACATTTTTGGTTAAAATATATTATAATTGAATGTCTGCCTCA

            *     *                *         *         
        471 AGAAACGTGAAGCAAATA-CTATCCATTGAAAAAAAAAGTCTA
        129 GGAAACATGAAGCAAATAGCTATTCATTG-AAAGAAAAGTCTA

                      *   *  *        **  **     *        *            *     
        513 TTTATAGTCAATCATGCGTTCGAAAGTATTGCTACTCACTTTAAATAATTTTATAATCTCATAAT
          1 -TTATAGTCACTCAAGCCTTCGAAAGCCTTATTACTCGCTTTAAATGATTTTATAATCTTATAAT

                                         *        * *      *              * *
        578 TGATTTTAAGTTG-A-ATTTTTACATTTTAGGTTAAAACAGATTATATTTGAATGTCTGCCTTAA
         65 TGATTTTAAGTTGAATATTTTTACATTTTTGGTTAAAATATATTATAATTGAATGTCTGCCTCAG

                **             *  *      *          * 
        641 GAAATGTGAAGCAAA-AGCCATCCATTGCTAAGAAAAGTCCA
        130 GAAACATGAAGCAAATAGCTATTCATTG-AAAGAAAAGTCTA

                             *       
        682 TTTATAGTCACTCAAGCATTCGAAA
          1 -TTATAGTCACTCAAGCCTTCGAAA

        707 TGTAACACCC


Statistics
Matches: 428,  Mismatches: 87, Indels: 37
        0.78            0.16        0.07

Matches are distributed among these distances:
 167    1  0.00
 168   83  0.19
 169  142  0.33
 170   57  0.13
 171  140  0.33
 172    5  0.01

ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38


Consensus pattern (170 bp):   
TTATAGTCACTCAAGCCTTCGAAAGCCTTATTACTCGCTTTAAATGATTTTATAATCTTATAATT
GATTTTAAGTTGAATATTTTTACATTTTTGGTTAAAATATATTATAATTGAATGTCTGCCTCAGG
AAACATGAAGCAAATAGCTATTCATTGAAAGAAAAGTCTA

Found at i:612 original size:169 final size:170

Alignment explanation


    Indices: 1--706  Score: 613
    Period size: 171  Copynumber: 4.2  Consensus size: 170

                               *  **   *                     *               
          1 CATTTATAGTCACTCAAGCCTTTAAAAACCTTATTACTCGCTTTAAATGGTTTTATAATCTCA-A
          1 CATTTATAGTCACTCAAGCATTCGAAAGCCTTATTACTCGCTTTAAATGATTTTATAATCTCATA

               *       *    *                         *    *   *          *  
         65 GATAGATTTTATGTTAAATATTTTTACATTTTTGGTT-AAAACTGATAATATTTGAATGTCTACC
         66 -ATTGATTTTAAGTT-GATATTTTTACATTTTTGGTTAAAAAAT-ATTATAATTGAATGTCTGCC

               *                  **  *                  
        129 TCAGGAAACATGAAG-AAATAGTTATTCATT-AGTAAGAAAAGTC
        128 TCAAGAAACATGAAGCAAA-AGCCATCCATTGA-TAAGAAAAGTC

            *  *         *  *  *                  *  *                   **  
        172 TATCTATAGTCACCCATGCCTTCGAAAGCCTTATTACTTGCATTAAATGATTTTATAATCTTGTA
          1 CATTTATAGTCACTCAAGCATTCGAAAGCCTTATTACTCGCTTTAAATGATTTTATAATCTCATA

                      *                     **      *                 *     *
        237 ATTGATTTTATGTTGAATATTTTTACATTTTTTATTAAAATATATTATAATTGAATGTTTGCCTT
         66 ATTGATTTTAAGTTG-ATATTTTTACATTTTTGGTTAAAAAATATTATAATTGAATGTCTGCCTC

            *        *   *          *     *        * 
        302 GAGAAACATAAAGTAAAAGCCATCTATTG-CAAGAAAAGAC
        130 AAGAAACATGAAGCAAAAGCCATCCATTGATAAGAAAAGTC

                *         *    *        *                      *   *     *   
        342 CATTAATAGTCACTTAAGCTTTCGAAAGGCTTATTACTCGCTTTAAATG--CTTACAATCTTATA
          1 CATTTATAGTCACTCAAGCATTCGAAAGCCTTATTACTCGCTTTAAATGATTTTATAATCTCATA

                               *      *   **                           *    *
        405 ATTG-TATTTAAGTTGAATTTTTTTATATTGGTGGTTAAAAAATATTATAATTGAATGTTTGCCC
         66 ATTGAT-TTTAAGTTG-ATATTTTTACATTTTTGGTTAAAAAATATTATAATTGAATGTCTGCCT

                    *             *         *  *       
        469 CAAGAAACGTGAAGCAAATA-CTATCCATTGAAAAAAAAAGTC
        129 CAAGAAACATGAAGCAAA-AGCCATCCATTGATAAGAAAAGTC

            *           *   *  *        **  **     *        *                
        511 TATTTATAGTCAATCATGCGTTCGAAAGTATTGCTACTCACTTTAAATAATTTTATAATCTCATA
          1 CATTTATAGTCACTCAAGCATTCGAAAGCCTTATTACTCGCTTTAAATGATTTTATAATCTCATA

                                          *        * *      *              * 
        576 ATTGATTTTAAGTTGA-ATTTTTACATTTTAGGTTAAAACAGATTATATTTGAATGTCTGCCTTA
         66 ATTGATTTTAAGTTGATATTTTTACATTTTTGGTTAAAAAATATTATAATTGAATGTCTGCCTCA

                 **                     *           
        640 AGAAATGTGAAGCAAAAGCCATCCATTGCTAAGAAAAGTC
        131 AGAAACATGAAGCAAAAGCCATCCATTGATAAGAAAAGTC

                                       
        680 CATTTATAGTCACTCAAGCATTCGAAA
          1 CATTTATAGTCACTCAAGCATTCGAAA

        707 TGTAACACCC


Statistics
Matches: 424,  Mismatches: 99, Indels: 26
        0.77            0.18        0.05

Matches are distributed among these distances:
 167    1  0.00
 168   86  0.20
 169  139  0.33
 170   49  0.12
 171  140  0.33
 172    9  0.02

ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38


Consensus pattern (170 bp):   
CATTTATAGTCACTCAAGCATTCGAAAGCCTTATTACTCGCTTTAAATGATTTTATAATCTCATA
ATTGATTTTAAGTTGATATTTTTACATTTTTGGTTAAAAAATATTATAATTGAATGTCTGCCTCA
AGAAACATGAAGCAAAAGCCATCCATTGATAAGAAAAGTC
Done.