Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018400589.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3782.0, 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, 959

Length: 1599
ACGTcount: A:0.21, C:0.08, G:0.08, T:0.21

Warning! 680 characters in sequence are not A, C, G, or T


Found at i:1516 original size:170 final size:173

Alignment explanation


    Indices: 1174--1518  Score: 409
    Period size: 170  Copynumber: 2.0  Consensus size: 173

       1164 NNNNNNTATT

                               **      *          *      *          *        
       1174 AATGGACTTTTCTTGCCAATGAATACTTTTTTCCTTCATGTTTCTTGACGTTGGAATTCAATTAT
          1 AATGGACTTTTCTTGCCAAAAAATACTCTTTTCCTTCACGTTTCTCGACGTTGGAAATCAATTAT

               * *                     *        * **                         
       1239 AATCTTTTTTAACCAAAAATGTACAAAGAATTCAAATTTCAAACAAATTTGAGATTACAAAACCA
         66 AATATGTTTTAACCAAAAATGTACAAACAATTCAAACTAAAAACAAATTTGAGATTACAAAACCA

                   *     *             *       *       
       1304 TTTAAAGTGAGTATTAAGGCTTTTGAAGGAATGGGTGACTATA
        131 TTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGGGACTATA

                                                *                            
       1347 AATGGACTTTTCTTGCCAAAAAATAC-CTTTTCCTTTACGTTTCTCGA-GATT-GACAATCAATT
          1 AATGGACTTTTCTTGCCAAAAAATACTCTTTTCCTTCACGTTTCTCGACG-TTGGA-AATCAATT

                                           *                               * 
       1409 ATAATATGTTTTAACCAAAAATGTA-AAACACTTC-AACTAAAAATC-AATTATG-GCATTA-TA
         64 ATAATATGTTTTAACCAAAAATGTACAAACAATTCAAACTAAAAA-CAAATT-TGAG-ATTACAA

                                *                           
       1469 AACCATTTAAAGCGAGTAATGAGGCTTTTGAAAGAATGGGGGACTATA
        126 AACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGGGACTATA

              
       1517 AA
          1 AA

       1519 CGAATTTTTC


Statistics
Matches: 147,  Mismatches: 20, Indels: 13
        0.82            0.11        0.07

Matches are distributed among these distances:
 170   57  0.39
 171   17  0.12
 172   49  0.33
 173   24  0.16

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


Consensus pattern (173 bp):   
AATGGACTTTTCTTGCCAAAAAATACTCTTTTCCTTCACGTTTCTCGACGTTGGAAATCAATTAT
AATATGTTTTAACCAAAAATGTACAAACAATTCAAACTAAAAACAAATTTGAGATTACAAAACCA
TTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGGGACTATA

Found at i:1579 original size:170 final size:172

Alignment explanation


    Indices: 1229--1599  Score: 401
    Period size: 170  Copynumber: 2.2  Consensus size: 172

       1219 TGACGTTGGA

                           *                     *        * **               
       1229 ATTCAATTATAATCTTTTTTAACCAAAAATGTACAAAGAATTCAAATTTCAAACAAATTTGAGAT
          1 ATTCAATTATAATCTGTTTTAACCAAAAATGTACAAACAATTCAAACTAAAAACAAATTTGAGAT

                             *     *             *       *         * *       
       1294 TACAAAACCATTTAAAGTGAGTATTAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTC
         66 TACAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGGGACTATAAACGAACTTTTC

              *                    *  *            *  
       1359 TTGCCAAAAAATACCTTTTCCTTTACGTTTCTCGAGATTGAC
        131 TTACCAAAAAATACCTTTTCCTTCACATTTCTCGAGATTCAC

             *           *                         *                         
       1401 AATCAATTATAATATGTTTTAACCAAAAATGTA-AAACACTTC-AACTAAAAATC-AATTATG-G
          1 ATTCAATTATAATCTGTTTTAACCAAAAATGTACAAACAATTCAAACTAAAAA-CAAATT-TGAG

                  *                     *                                 *  
       1462 CATTA-TAAACCATTTAAAGCGAGTAATGAGGCTTTTGAAAGAATGGGGGACTATAAACGAATTT
         64 -ATTACAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGGGACTATAAACGAACTT

                    * ***  *      *            *   *    *
       1526 TTCTTACCCATGTATGCCTTTTTCTTCACATTTCTTGAGGTTCAT
        128 TTCTTACCAAAAAATACCTTTTCCTTCACATTTCTCGAGATTCAC

                                   *     
       1571 ATTCAATTATAATCTGTTTTAACAAAAAA
          1 ATTCAATTATAATCTGTTTTAACCAAAAA


Statistics
Matches: 163,  Mismatches: 33, Indels: 8
        0.80            0.16        0.04

Matches are distributed among these distances:
 170  119  0.73
 171   14  0.09
 172   30  0.18

ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35


Consensus pattern (172 bp):   
ATTCAATTATAATCTGTTTTAACCAAAAATGTACAAACAATTCAAACTAAAAACAAATTTGAGAT
TACAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAATGGGGGACTATAAACGAACTTTTC
TTACCAAAAAATACCTTTTCCTTCACATTTCTCGAGATTCAC
Done.