Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018402996.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_662.0, 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: 9763
ACGTcount: A:0.19, C:0.07, G:0.06, T:0.19

Warning! 4723 characters in sequence are not A, C, G, or T


Found at i:4507 original size:171 final size:170

Alignment explanation


    Indices: 4330--4639  Score: 383
    Period size: 170  Copynumber: 1.8  Consensus size: 170

       4320 ACATATTTTA

                     *     *      * *      *                      *  *       
       4330 TTAAAACAGGCTATAGTTAAATTTTTGCCTTTAA-AAACA-AGAAGAAAAAGGCGTTTACTAATA
          1 TTAAAACAGACTATAATTAAATGTCTGCC-TCAAGAAACATA-AAG-AAAAGGCATTCACTAATA

                            *         *                                      
       4393 AGAAAAGTCCATTTATCGTCACCCATTCCTTCAAAAGCCTTATCACTCGCTTT-AACTAGTTTTA
         63 AGAAAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTATCACTCGCTTTAAAC-AGTTTTA

                                                        
       4457 TAATCTCACAATTTATTTTAAGTTGAATTTTTTTACATTTTCGG
        127 TAATCTCACAATTTATTTTAAGTTGAATTTTTTTACATTTTCGG

                      *       *                              *      * *  *   
       4501 TTAAAACAGATTATAATTGAATGTCTGCCTCAAGAAACATAAAGAAAAGTCATTCATTGATTAGA
          1 TTAAAACAGACTATAATTAAATGTCTGCCTCAAGAAACATAAAGAAAAGGCATTCACTAATAAGA

                             *          *           *             *          
       4566 AAAGTCCATTTATAGTCGCCCATGCCTTTAAAAGCCTTATTACTCGCTTTAAACGGTTTTATAAT
         66 AAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTATCACTCGCTTTAAACAGTTTTATAAT

                *    
       4631 CTCATAATT
        131 CTCACAATT

       4640 GATTNNNNNN


Statistics
Matches: 116,  Mismatches: 20, Indels: 7
        0.81            0.14        0.05

Matches are distributed among these distances:
 170   81  0.70
 171   34  0.29
 172    1  0.01

ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36


Consensus pattern (170 bp):   
TTAAAACAGACTATAATTAAATGTCTGCCTCAAGAAACATAAAGAAAAGGCATTCACTAATAAGA
AAAGTCCATTTATAGTCACCCATGCCTTCAAAAGCCTTATCACTCGCTTTAAACAGTTTTATAAT
CTCACAATTTATTTTAAGTTGAATTTTTTTACATTTTCGG

Found at i:5459 original size:171 final size:161

Alignment explanation


    Indices: 5282--5595  Score: 346
    Period size: 171  Copynumber: 1.9  Consensus size: 161

       5272 TACTATCAAG

                              *  * *             *         *                 
       5282 AAAAGTCCATTTATCA-TTACTCTTTCCTTCAAAAACTTTATTACTCGCTTTAAA-TAGTTTTAT
          1 AAAAGTCCATTTAT-AGTCACCCATTCCTTCAAAAACCTTATTACTCACTTTAAACT-GTTTTAT

                                                                             
       5345 AATCTCGTAATTTAATTTAAGTTAAATTTTTTTACA-TTTTCAGTTAAAACAGATTATAATTGAA
         64 AATCTCGTAATTTAATTTAAGTTAAATTTTTTTACACTTTT-AGTTAAAACAGATTATAATTGAA

                     *                                  
       5409 TGTCTGCCTTAAGAAACANNNNNNNNNNGTCATTCATTGATTAA
        128 TGTCTGCCTCAAGAAACA----------GTCATTCATTGATTAA

                              *          **   *                              
       5453 AAAAGTCCATTTATAGTCGCCCATTCCTTTGAAAGCCTTATTACTCACTTTAAACTGTTTTATAA
          1 AAAAGTCCATTTATAGTCACCCATTCCTTCAAAAACCTTATTACTCACTTTAAACTGTTTTATAA

               *        *        *                           *   *           
       5518 TCTTGTAATTTATTTTAAGTTGAATTTTTTTACACTTTTAGTTAAAACATATTTTAATTGAATGT
         66 TCTCGTAATTTAATTTAAGTTAAATTTTTTTACACTTTTAGTTAAAACAGATTATAATTGAATGT

            *            
       5583 TTGCCTCAAGAAA
        131 CTGCCTCAAGAAA

       5596 TGTGAAGAAA


Statistics
Matches: 124,  Mismatches: 16, Indels: 6
        0.85            0.11        0.04

Matches are distributed among these distances:
 170    1  0.01
 171  118  0.95
 172    5  0.04

ACGTcount: A:0.32, C:0.14, G:0.09, T:0.42


Consensus pattern (161 bp):   
AAAAGTCCATTTATAGTCACCCATTCCTTCAAAAACCTTATTACTCACTTTAAACTGTTTTATAA
TCTCGTAATTTAATTTAAGTTAAATTTTTTTACACTTTTAGTTAAAACAGATTATAATTGAATGT
CTGCCTCAAGAAACAGTCATTCATTGATTAA
Done.