Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018398122.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1425.0, 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: 1895
ACGTcount: A:0.22, C:0.07, G:0.08, T:0.21

Warning! 810 characters in sequence are not A, C, G, or T


Found at i:1301 original size:172 final size:171

Alignment explanation


    Indices: 998--1329  Score: 417
    Period size: 172  Copynumber: 1.9  Consensus size: 171

        988 NNNNNNNNNN

                                                      *     *                
        998 ATCAATTATGAGATTATAAAACTATTTAAATCGAGTAATAAGCCTTTTGAAGGATGGGGTGACTA
          1 ATCAATTATGAGATTATAAAACTATTTAAATCGAGTAATAAGACTTTTAAAGGATGGGGTGACTA

                         *  *   *                  **                  *     
       1063 TAAATGGACTTTTTTTCTCATTGAATGGCTTTTTTTGCATGTTTCTCGAGACAACCATTTAATTA
         66 TAAATGGACTTTTCTTATCAATGAATGGCTTTTTTTGCACATTTCTCGAGACAACCATTCAATTA

                *                  *                   
       1128 TAGTCTGTTTTAA-CTAAAAATATTAAAAAAAATCAACTTAAA
        131 TAGTATGTTTTAATC-AAAAAT-GTAAAAAAAATCAACTTAAA

                                   *                   *                     
       1170 ATCAATTATGAGATTATAAAACTGTTTAAATCGAGTAATAAGAGTTTTAAAGGAAT-GGGTGACT
          1 ATCAATTATGAGATTATAAAACTATTTAAATCGAGTAATAAGACTTTTAAAGG-ATGGGGTGACT

            *   *                                                            
       1234 CTAACTGGACTTTTCTTATCAATGAAT-GCTTGTTTCTT-CACATTTCT-G-GACGTAGA-CATT
         65 ATAAATGGACTTTTCTTATCAATGAATGGCTT-TTT-TTGCACATTTCTCGAGAC--A-ACCATT

                                                
       1294 CAATTATAGTATGTTTTAATCAAAAATGTAAAAAAA
        125 CAATTATAGTATGTTTTAATCAAAAATGTAAAAAAA

       1330 TNNNNNNNNN


Statistics
Matches: 139,  Mismatches: 14, Indels: 15
        0.83            0.08        0.09

Matches are distributed among these distances:
 170    3  0.02
 171   13  0.09
 172  117  0.84
 173    6  0.04

ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37


Consensus pattern (171 bp):   
ATCAATTATGAGATTATAAAACTATTTAAATCGAGTAATAAGACTTTTAAAGGATGGGGTGACTA
TAAATGGACTTTTCTTATCAATGAATGGCTTTTTTTGCACATTTCTCGAGACAACCATTCAATTA
TAGTATGTTTTAATCAAAAATGTAAAAAAAATCAACTTAAA

Found at i:1717 original size:171 final size:160

Alignment explanation


    Indices: 1540--1865  Score: 339
    Period size: 170  Copynumber: 2.0  Consensus size: 160

       1530 TTATAAAACT

                               *                           *                 
       1540 ATTTAAAGCAAGTAATAAGCCTTCTGAAGGAATGGGTGACGATAAATTGACTTTTCTTCTCAATC
          1 ATTTAAAGCAAGTAATAAGACTTCTGAAGGAATGGGTGACGATAAATAGACTTTTCTTCTCAATC

                 *     *               *  *   *        *       *             
       1605 AATTGCTTTTTTTGCACCTTTCTCAAGTTAGACATTCAATTATTGTCTGTTTTTAA-AAAAAATA
         66 AA-TGATTTTTCTGCACCTTTCTCAAGGTAAACAATCAATTATAGTCTG-TCTTAACAAAAAATA

                                                      
       1669 TAAAAAAATTCAACTTAAAATCAATNNNNNNNNNNTAAAATC
        129 TAAAAAAATTCAACTTAAAATCAAT----------TAAAATC

                     **            *          *     *              *        *
       1711 ATTTAAAGCGGGTAATAAGACTTTTGAAGGAATGTGTGACTATAAATAGACTTTTTTTCTCAATG
          1 ATTTAAAGCAAGTAATAAGACTTCTGAAGGAATGGGTGACGATAAATAGACTTTTCTTCTCAATC

                           **      *             *                           
       1776 AATGATTTTTCTGCATGTTTCTCGAGGTAAACAATCACTTATAGTCTGTCTTAACAAAAAATATA
         66 AATGATTTTTCTGCACCTTTCTCAAGGTAAACAATCAATTATAGTCTGTCTTAACAAAAAATATA

            *  *                     
       1841 CAATAATTCAACTTAAAATCAATTA
        131 AAAAAATTCAACTTAAAATCAATTA

       1866 CGAGATTATA


Statistics
Matches: 132,  Mismatches: 22, Indels: 13
        0.79            0.13        0.08

Matches are distributed among these distances:
 160    2  0.02
 169    5  0.04
 170   67  0.51
 171   58  0.44

ACGTcount: A:0.37, C:0.13, G:0.12, T:0.35


Consensus pattern (160 bp):   
ATTTAAAGCAAGTAATAAGACTTCTGAAGGAATGGGTGACGATAAATAGACTTTTCTTCTCAATC
AATGATTTTTCTGCACCTTTCTCAAGGTAAACAATCAATTATAGTCTGTCTTAACAAAAAATATA
AAAAAATTCAACTTAAAATCAATTAAAATC
Done.