Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018398058.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1366.0, 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: 2134
ACGTcount: A:0.22, C:0.09, G:0.07, T:0.23

Warning! 830 characters in sequence are not A, C, G, or T


Found at i:319 original size:170 final size:170

Alignment explanation


    Indices: 1--361  Score: 431
    Period size: 170  Copynumber: 2.1  Consensus size: 170

                        *          *        *            *  **      **       
          1 AGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTAATTTTGTGTTGCATTTTTTTAC
          1 AGCCTTATTACTTGCTTTAAATGCTTTTATAAACTCATAATTAATATTAAGTTGCAAGTTTTTAC

              *  **      *      *         *    *  *    *             *       
         66 ATTTTGGTTAAAATAGACTATAATTAAATGTCTACGTTGAGAAGCATGAAGAAAAATGCATTAAT
         66 ATCTTCATTAAAACAGACTAAAATTAAATGCCTACCTTAAGAAACATGAAGAAAAATCCATTAAT

                 *     *                     *      
        131 TGGCAGGAAAAGTCTATTTATAGTCACCAATTCTTTCAAA
        131 TGGCAAGAAAAATCTATTTATAGTCACCAATTCCTTCAAA

                                                      *                      
        171 AGCCTTATTACTTGCTTTAAATGCTTTTATAAACTCATAATTGATATTAAGTTG-AAGTTTTTAC
          1 AGCCTTATTACTTGCTTTAAATGCTTTTATAAACTCATAATTAATATTAAGTTGCAAGTTTTTAC

                                      *       *                              
        235 TATCTTCATTAAAACAGACTAAAATTGAATGCCTGCCTTAAGAAACATGTAA-AAAAATCCATTT
         66 -ATCTTCATTAAAACAGACTAAAATTAAATGCCTACCTTAAGAAACATG-AAGAAAAATCCA-TT

             *                          *              
        299 ATTTGG-AAGAAAAATCTATTTATAGTCTCCAATTCCTTCAAA
        128 AATTGGCAAGAAAAATCTATTTATAGTCACCAATTCCTTCAAA

              *                  
        341 AGTCTTATTACTTGCTTTAAA
          1 AGCCTTATTACTTGCTTTAAA

        362 NNNNNNNNNN


Statistics
Matches: 161,  Mismatches: 27, Indels: 6
        0.83            0.14        0.03

Matches are distributed among these distances:
 169    8  0.05
 170  144  0.89
 171    9  0.06

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


Consensus pattern (170 bp):   
AGCCTTATTACTTGCTTTAAATGCTTTTATAAACTCATAATTAATATTAAGTTGCAAGTTTTTAC
ATCTTCATTAAAACAGACTAAAATTAAATGCCTACCTTAAGAAACATGAAGAAAAATCCATTAAT
TGGCAAGAAAAATCTATTTATAGTCACCAATTCCTTCAAA

Found at i:380 original size:170 final size:162

Alignment explanation


    Indices: 196--512  Score: 327
    Period size: 172  Copynumber: 1.9  Consensus size: 162

        186 TTTAAATGCT

                                         *                                   
        196 TTTATAAA-CTCATAATTGATATTAAGTTGAAGTTTTTACTA-TCTTCATTAAAACAGACTAAAA
          1 TTTA-AAATCTCATAATTGATATTAAGTTAAAGTTTTTAC-ACTCTTCATTAAAACAGACTAAAA

             *        *     *         *        *                             
        259 TTGAATGCCTGCC-T-TAAGAAACATGTAAAAAAATCCATTTATTTGGAAGAAAAATCTATTTAT
         64 TCGAATGCCTACCATCCAAGAAACATATAAAAAAACCCATTTATTTGGAAGAAAAATCTATTTAT

                                              
        322 AGTCTCCAATTCCTTCAAAAGTCTTATTACTTGC
        129 AGTCTCCAATTCCTTCAAAAGTCTTATTACTTGC

                                          *  *       *          *  *        *
        356 TTTAAANNNNNNNNNNATCTCATAATTGATTTTTAGTTAAATTTTTTACACTTTTTATTAAAACT
          1 TTTAAA----------ATCTCATAATTGATATTAAGTTAAAGTTTTTACACTCTTCATTAAAACA

                 *                   **     *   *                          * 
        421 GACTATAATCGAATGCCTACCATCCCGGAAACGTATCAAAAAACCCATTTATTTGGAAGAAAATT
         56 GACTAAAATCGAATGCCTACCATCCAAGAAACATATAAAAAAACCCATTTATTTGGAAGAAAAAT

                           *           
        486 CTATTTATAGTCTCCGATTCCTTCAAA
        121 CTATTTATAGTCTCCAATTCCTTCAAA

        513 GGCCTATTAC


Statistics
Matches: 124,  Mismatches: 19, Indels: 16
        0.78            0.12        0.10

Matches are distributed among these distances:
 159    2  0.02
 160    4  0.03
 169    2  0.02
 170   56  0.45
 171    1  0.01
 172   59  0.48

ACGTcount: A:0.36, C:0.16, G:0.09, T:0.36


Consensus pattern (162 bp):   
TTTAAAATCTCATAATTGATATTAAGTTAAAGTTTTTACACTCTTCATTAAAACAGACTAAAATC
GAATGCCTACCATCCAAGAAACATATAAAAAAACCCATTTATTTGGAAGAAAAATCTATTTATAG
TCTCCAATTCCTTCAAAAGTCTTATTACTTGC
Done.