Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018401783.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4894.0, 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: 1721
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.32

Warning! 189 characters in sequence are not A, C, G, or T


Found at i:410 original size:168 final size:168

Alignment explanation


    Indices: 1--411  Score: 411
    Period size: 168  Copynumber: 2.4  Consensus size: 168

                 *      *                     *                              
          1 TTAACTAAAAATGTAAAAAAATTCAACTTAAAATTAATTATTAGTTTATAAAACATTTAAAGCAA
          1 TTAACCAAAAATAT-AAAAAATTCAACTTAAAATCAATTATTAGTTTATAAAACATTTAAAGCAA

                               **     *                      * *      *      
         66 GTAATAAGGCTTTCGAAGGCTTGAGCGACTATAAATGGACTTTTCGTAGTAGTGGATGGCTTTTC
         65 GTAATAAGGCTTTCGAAGGAATGAGCAACTATAAATGGACTTTTCGTAGCAATGGATGCCTTTTC

                                     *   *         
        131 CTTCACGTTCTCAAAGGTAGACATTTAATTATAGCCTTT
        130 CTTCACGTTCTCAAAGGTAGACATTGAATAATAGCCTTT

                  *     *          *    *            *  *              * *  *
        170 TTAACCTAAAATGTAAGAAAATTTAACTAAAAATCAATTATGAGATTATAAAACCATTTCACGCG
          1 TTAACCAAAAATATAA-AAAATTCAACTTAAAATCAATTATTAGTTTATAAAA-CATTTAAAGCA

            *             *           *                     *                
        235 TGTAATAAGGCTTTTGAAGGAATGAGTAACTATAAAT-GACTTTTC-TTGCCAAT-GATTGCCTT
         64 AGTAATAAGGCTTTCGAAGGAATGAGCAACTATAAATGGACTTTTCGTAG-CAATGGA-TGCCTT

              *     *      **                     *     
        297 TTTC-TCATGTTTCTTGAA-GTAGACATTGAATAATAGTCTATT
        127 TTCCTTCACG-TTCTCAAAGGTAGACATTGAATAATAGCCT-TT

                                               * *                         * 
        339 TTAA-CAAAAACTATAAAAAATTCAACTTAAAATCGAGTATTAGTTTATAAAATCATTTAAAGTA
          1 TTAACCAAAAA-TATAAAAAATTCAACTTAAAATCAATTATTAGTTTATAAAA-CATTTAAAGCA

                     
        403 AGTAATAAG
         64 AGTAATAAG

        412 NNNNNNNNNN


Statistics
Matches: 194,  Mismatches: 41, Indels: 15
        0.78            0.16        0.06

Matches are distributed among these distances:
 168   78  0.40
 169   77  0.40
 170   39  0.20

ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35


Consensus pattern (168 bp):   
TTAACCAAAAATATAAAAAATTCAACTTAAAATCAATTATTAGTTTATAAAACATTTAAAGCAAG
TAATAAGGCTTTCGAAGGAATGAGCAACTATAAATGGACTTTTCGTAGCAATGGATGCCTTTTCC
TTCACGTTCTCAAAGGTAGACATTGAATAATAGCCTTT

Found at i:839 original size:170 final size:171

Alignment explanation


    Indices: 464--839  Score: 405
    Period size: 170  Copynumber: 2.2  Consensus size: 171

        454 TGGATGGCTT

                                               **    *  * * *                
        464 TAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAATTAATGGGTGACTGTAAATGAACTTTTCTT
          1 TAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATGAGTAAATATAAATGAACTTTTCTT

                        *       *       *                        *           
        529 GCCAATAAATTATTTTTTCTTCACATTTTTCAAGGTAAACATTCAATTATAATCTGTTTTAATCA
         66 GCCAATAAATTACTTTTTCTACACATTTCTCAAGGTAAACATTCAATTATAATATGTTTTAATCA

               *                *               *    
        594 AAACTACAAAACAATTCAATTTAAAATCAATGATGAGATTA
        131 AAAATACAAAACAATTCAATATAAAATCAATGATGACATTA

                   *       *     *     *                      *    *         
        635 TAAAACTTTTTAAAGAGAGTATTAAGGATTTTGAAGAAATGAG-AAATATGAATGGACTTTTCTT
          1 TAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATGAGTAAATATAAATGAACTTTTCTT

            **    *                  *           * *    *       *         * *
        699 TTCAATGAA-TAGCTTTTTCTACACGTTTCTCAAGGTCAGCATTTAATTATAGTATGTTTTAGTG
         66 GCCAATAAATTA-CTTTTTCTACACATTTCTCAAGGTAAACATTCAATTATAATATGTTTTAATC

                  **         **             *         
        763 AAAAATGTAAAACAATTTGATATAAAATCAATTATGACATTA
        130 AAAAATACAAAACAATTCAATATAAAATCAATGATGACATTA

                         *    *                
        805 TAAAACTATTTAAGGCGAATAATAAGGCTTTTGAA
          1 TAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAA

        840 AGNNNNNNNN


Statistics
Matches: 164,  Mismatches: 40, Indels: 3
        0.79            0.19        0.01

Matches are distributed among these distances:
 169    2  0.01
 170  126  0.77
 171   36  0.22

ACGTcount: A:0.39, C:0.10, G:0.13, T:0.37


Consensus pattern (171 bp):   
TAAAACTATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATGAGTAAATATAAATGAACTTTTCTT
GCCAATAAATTACTTTTTCTACACATTTCTCAAGGTAAACATTCAATTATAATATGTTTTAATCA
AAAATACAAAACAATTCAATATAAAATCAATGATGACATTA
Done.