Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018403241.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_911.0, 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: 12684
ACGTcount: A:0.21, C:0.07, G:0.08, T:0.22

Warning! 5349 characters in sequence are not A, C, G, or T


Found at i:3241 original size:172 final size:170

Alignment explanation


    Indices: 2872--3242  Score: 404
    Period size: 172  Copynumber: 2.2  Consensus size: 170

       2862 NNNNNNNNNN

                          *                                                  
       2872 ATTTAAAGCGAGTAGTAAGCCTTTTGAAGGAATGGATGACTATAAATGGACTTTACTTCTCAATG
          1 ATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGATGACTATAAATGGACTTTACTTCTCAATG

                                  * *   *       *       *   *       **     * 
       2937 AATGCCTTTTTTTACATGTTTCTCGAGATAAGTATTTAATTATACTCTGTTTTAACCGAAAATGT
         66 AATGCCTTTTTTTACA-GTTTCCCAAGACAAGTATTCAATTATAATCTATTTTAACAAAAAATAT

                          *                          
       3002 AAAAAAATTCAACTTAAAATCAATCATGAGATTATAAAACC
        130 AAAAAAATTCAACTAAAAATCAATCATGAGATTATAAAACC

                 ***********   *               *                  **         
       3043 ATTTANNNNNNNNNNNAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTCTCAATG
          1 ATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGATGACTATAAATGGACTTTACTTCTCAATG

                                          *  *                               
       3108 AATAAG-CTTTTTCTGTAC-GTTTCCCAAGGCAGGTATTCAATTATAATCTATTTTAACAAAAAA
         66 AAT--GCCTTTTT-T-TACAGTTTCCCAAGACAAGTATTCAATTATAATCTATTTTAACAAAAAA

                                       *            *  *
       3171 TATAAAAAAATTCAACTAAAAATCAATTATGAGATTATAAGACT
        127 TATAAAAAAATTCAACTAAAAATCAATCATGAGATTATAAAACC

                                        
       3215 ATTTAAAGCGAGTAATAAGCCTTTTGAA
          1 ATTTAAAGCGAGTAATAAGCCTTTTGAA

       3243 NNNNNNNNNN


Statistics
Matches: 154,  Mismatches: 42, Indels: 7
        0.76            0.21        0.03

Matches are distributed among these distances:
 171   53  0.34
 172   96  0.62
 173    2  0.01
 174    3  0.02

ACGTcount: A:0.37, C:0.12, G:0.14, T:0.34


Consensus pattern (170 bp):   
ATTTAAAGCGAGTAATAAGCCTTTTGAAGGAATGGATGACTATAAATGGACTTTACTTCTCAATG
AATGCCTTTTTTTACAGTTTCCCAAGACAAGTATTCAATTATAATCTATTTTAACAAAAAATATA
AAAAAATTCAACTAAAAATCAATCATGAGATTATAAAACC

Found at i:4281 original size:124 final size:121

Alignment explanation


    Indices: 4052--4289  Score: 273
    Period size: 124  Copynumber: 1.9  Consensus size: 121

       4042 NNNTTGAAGG

                                          *   *    *                 ** **   
       4052 AATTGGTGACTATAAATGGACTTTTCTTCTTAATGAATGGTTTTTTTGCACGTTTCTTGAGGTAA
          1 AATTGGTGACTATAAATGGACTTTTCTTCTCAATCAATGCTTTTTTTGCACGTTTCTCAAAATAA

                 *                          *          *             
       4117 GCATTTAATTATACTCTGTTTTAACCAGAAAAGTAAAAAAATTGAACTTTTCTTCTC
         66 GCATTCAATTATACTCTGTTTTAA-CAGAAAAATAAAAAAATTCAACTTTTCTTCTC

                                                    *           *            
       4174 AATTGGGTGACTATAAATGGACTTTTCTTCTCAATCAATCTCTTTTTTTGCATGTTTCTCAAAAT
          1 AATT-GGTGACTATAAATGGACTTTTCTTCTCAATCAAT-GCTTTTTTTGCACGTTTCTCAAAAT

                           **                      *             
       4239 AGAG-ATTCAATTATTGTCTGTTTTAA-AGAAAAATATGTAAAAATTCAACTT
         64 A-AGCATTCAATTATACTCTGTTTTAACAGAAAAATA--AAAAAATTCAACTT

       4290 AAAATCCATA


Statistics
Matches: 96,  Mismatches: 15, Indels: 8
        0.81            0.13        0.07

Matches are distributed among these distances:
 122   12  0.12
 123   32  0.33
 124   50  0.52
 125    2  0.02

ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42


Consensus pattern (121 bp):   
AATTGGTGACTATAAATGGACTTTTCTTCTCAATCAATGCTTTTTTTGCACGTTTCTCAAAATAA
GCATTCAATTATACTCTGTTTTAACAGAAAAATAAAAAAATTCAACTTTTCTTCTC
Done.