Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018399364.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2630.0, 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: 3244
ACGTcount: A:0.24, C:0.07, G:0.09, T:0.22

Warning! 1203 characters in sequence are not A, C, G, or T


Found at i:842 original size:10 final size:10

Alignment explanation


    Indices: 827--852  Score: 52
    Period size: 10  Copynumber: 2.6  Consensus size: 10

        817 ATGAATGCTT

                      
        827 GTTTCTTTGC
          1 GTTTCTTTGC

                      
        837 GTTTCTTTGC
          1 GTTTCTTTGC

                  
        847 GTTTCT
          1 GTTTCT

        853 CAAGGTAGAC


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   16  1.00

ACGTcount: A:0.00, C:0.19, G:0.19, T:0.62


Consensus pattern (10 bp):   
GTTTCTTTGC

Found at i:1474 original size:171 final size:171

Alignment explanation


    Indices: 855--1489  Score: 461
    Period size: 171  Copynumber: 3.7  Consensus size: 171

        845 GCGTTTCTCA

                 *      *          *      ***                   *            
        855 AGGTAGACATTCAATTATAGTCTGTTTTAATTGAAAATCTAAAA-AATTTCAGCTTAAAATCAAT
          1 AGGTAAACATTCCATTATAGTCTATTTTAACAAAAAATCTAAAACAA-TTCAACTTAAAATCAAT

                           **                *  *        *       *  *********
        919 TATGAGATTATAAAATTATTTAAAGCGAGTAATGAGACTTTTGAAGGAATAGGAGANNNNNNNNN
         65 TATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAAGAATAGGTGACTATAAATA

            *                  **         **  *     **
        984 NACTTTTCTTGCCAATGAATACTTTTTTCTTTACGTTTCTCA
        130 GACTTTTCTTGCCAATGAAGGCTTTTTTCTGCACATTTCTGG

               *       **     **          **       *    *                    
       1026 AGGCAAACATTTAATTATTCTCTATTTTAATGAAAAAT-AAAAAAAATTCAACTTAAAATCAATT
          1 AGGTAAACATTCCATTATAGTCTATTTTAACAAAAAATCTAAAACAATTCAACTTAAAATCAATT

                *         **             **********             *          * 
       1090 ATGACATTATAAAATAATTTAAAGCGAGTNNNNNNNNNNTTGAAAGAATAGGAGACTATAAATGG
         66 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAAGAATAGGTGACTATAAATAG

                              *        * *         * 
       1155 ACTTTTCTTGCCAATGAATGCTTTTTTTTTCACATTTCTTG
        131 ACTTTTCTTGCCAATGAAGGCTTTTTTCTGCACATTTCTGG

                                        *                                    
       1196 AGGTAAACATTCCATTATAGTCTATTTTCACAAAAAATCTAAAACAATTCAACTTAAAATCAATT
          1 AGGTAAACATTCCATTATAGTCTATTTTAACAAAAAATCTAAAACAATTCAACTTAAAATCAATT

                                **********              *                    
       1261 ATGAGATTATAAAACCATTTNNNNNNNNNNATAAGCCTTTTGAAGGAATAGGTGACTATAAATAG
         66 ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAAGAATAGGTGACTATAAATAG

                                              *        
       1326 ACTTTTCTT-CTCAATGAAAGGC-TTTTTCTGCATATTTCTGG
        131 ACTTTTCTTGC-CAATG-AAGGCTTTTTTCTGCACATTTCTGG

                  *                        *       *     *      *        *   
       1367 AGGTAAGCA-TCCAATTATAGTCTATTTTAATAAAAAATGTAAAAGAATTCAGCTTAAAATTAAT
          1 AGGTAAACATTCC-ATTATAGTCTATTTTAACAAAAAATCTAAAACAATTCAACTTAAAATCAAT

                *           *                 * *             *        
       1431 TATGCGATTATAAAACTATTTAAAGCGAGTAATATGGCTTTTGAAAGAATGGGTGACTA
         65 TATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAAGAATAGGTGACTA

       1490 NNNNNNNNNN


Statistics
Matches: 358,  Mismatches: 101, Indels: 10
        0.76            0.22        0.02

Matches are distributed among these distances:
 170  132  0.37
 171  222  0.62
 172    4  0.01

ACGTcount: A:0.37, C:0.11, G:0.13, T:0.34


Consensus pattern (171 bp):   
AGGTAAACATTCCATTATAGTCTATTTTAACAAAAAATCTAAAACAATTCAACTTAAAATCAATT
ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAAGAATAGGTGACTATAAATAG
ACTTTTCTTGCCAATGAAGGCTTTTTTCTGCACATTTCTGG

Found at i:1959 original size:170 final size:171

Alignment explanation


    Indices: 1677--2015  Score: 441
    Period size: 170  Copynumber: 2.0  Consensus size: 171

       1667 NNNNNAAAGC

                                                      *      *               
       1677 GAGTAATGAGGCTTTTGAAAGAATACGAGACTATAAATGGACTTTTCTTGACAATAAATACCTTT
          1 GAGTAATGAGGCTTTTGAAAGAATACGAGACTATAAATGGACCTTTCTTCACAATAAATACCTTT

                **                 *  *  *    *                  **          
       1742 TTCTTTACATTTCTCGAGGTAAATATTCAGTTATTGTCTGTTTTAATGAAAAATCTAAATA-AAC
         66 TTCTGCACATTTCTCGAGGTAAACATCCAATTATAGTCTGTTTTAATGAAAAAAATAAA-AGAAC

                                                      
       1806 TCAACTT-AAATCAATTATGAGATTATAAAACCATGTAAAAA
        130 TCAACTTAAAATCAATTATGAGATTATAAAACCATGTAAAAA

                                     ** *                      *    *   **   
       1847 GAGTAATGAGGCTTTT-AAAGGAATTGGTGACTATAAATGGACCTTTCTTCTCAATGAATGGCTT
          1 GAGTAATGAGGCTTTTGAAA-GAATACGAGACTATAAATGGACCTTTCTTCACAATAAATACCTT

                                   *                                        *
       1911 TTTCTGCACATTTCTCGAGGTAAGCATCCAATTATAGTCTGTTTTAATGAAAAAAATAAAAGAAT
         65 TTTCTGCACATTTCTCGAGGTAAACATCCAATTATAGTCTGTTTTAATGAAAAAAATAAAAGAAC

               *        *                      *    
       1976 TCAGCTTAAAATTAATTATGAGATTATAAAACCATTTAAA
        130 TCAACTTAAAATCAATTATGAGATTATAAAACCATGTAAA

       2016 GCGAGNNNNN


Statistics
Matches: 144,  Mismatches: 22, Indels: 5
        0.84            0.13        0.03

Matches are distributed among these distances:
 169    4  0.03
 170  110  0.76
 171   30  0.21

ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35


Consensus pattern (171 bp):   
GAGTAATGAGGCTTTTGAAAGAATACGAGACTATAAATGGACCTTTCTTCACAATAAATACCTTT
TTCTGCACATTTCTCGAGGTAAACATCCAATTATAGTCTGTTTTAATGAAAAAAATAAAAGAACT
CAACTTAAAATCAATTATGAGATTATAAAACCATGTAAAAA
Done.