Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018402963.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_624.0, 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: 3091
ACGTcount: A:0.18, C:0.07, G:0.08, T:0.19

Warning! 1476 characters in sequence are not A, C, G, or T


Found at i:416 original size:172 final size:169

Alignment explanation


    Indices: 116--516  Score: 495
    Period size: 172  Copynumber: 2.3  Consensus size: 169

        106 TTTTGAGATT

                                  *      **      * *                         
        116 AAAGTAAGTAATAAGGCTTTTGGAGGAATAAGTGACTCTAAATGGACTTTTCTT-TCCAATGAAC
          1 AAAGT-AGTAATAAGGCTTTTGAAGGAATGGGTGACTATTAATGGACTTTTCTTGT-CAATGAAC

                 **         *                                  *             
        180 CTTTTTTTTCATCTTTTTTGAGGTTGACATTCAATTATAATATGTTTTAAATAAAAATGTACAAA
         64 CTTTTCCTTCATCTTTCTTGAGGTTGACATTCAATTATAATATGTTTTAAACAAAAATGTACAAA

                                                 *    
        245 GAATTCAAA-TTCGAATCAATTTTGAGATTATAAAACTATTA
        129 GAATTCAAATTTC-AATCAATTTTGAGATTATAAAACCATTA

                          *                     *                           *
        286 AAAGTATGTAATAAAGCTTTTGAAGGAATGGGTGACAATTAATGGACTTTTCTTGTCAATGACTG
          1 AAAGTA-GTAATAAGGCTTTTGAAGGAATGGGTGACTATTAATGGACTTTTCTTGTCAATGA--A

                         *        *   *               * *      *             
        351 CCTTTTCCTTCATGTTTCTTGATGTTTACATTCAATTATAATCTTTTTTAACCAAAAATGTACAA
         63 CCTTTTCCTTCATCTTTCTTGAGGTTGACATTCAATTATAATATGTTTTAAACAAAAATGTACAA

                  *                                  *
        416 AGAATTGAAATTTCAATCAATTTTGAGATTATAAAACCATTT
        128 AGAATTCAAATTTCAATCAATTTTGAGATTATAAAACCATTA

                      *                                                  
        458 AAAGTGAGTATTAAGGCTTTTGAAGGAATGGGT-AGCTA-TAACTGGACTTTTCTTGTCAA
          1 AAAGT-AGTAATAAGGCTTTTGAAGGAATGGGTGA-CTATTAA-TGGACTTTTCTTGTCAA

        517 CAAATACCTT


Statistics
Matches: 199,  Mismatches: 24, Indels: 14
        0.84            0.10        0.06

Matches are distributed among these distances:
 169    1  0.01
 170   51  0.26
 171    5  0.03
 172  138  0.69
 173    4  0.02

ACGTcount: A:0.35, C:0.11, G:0.15, T:0.38


Consensus pattern (169 bp):   
AAAGTAGTAATAAGGCTTTTGAAGGAATGGGTGACTATTAATGGACTTTTCTTGTCAATGAACCT
TTTCCTTCATCTTTCTTGAGGTTGACATTCAATTATAATATGTTTTAAACAAAAATGTACAAAGA
ATTCAAATTTCAATCAATTTTGAGATTATAAAACCATTA

Found at i:560 original size:172 final size:172

Alignment explanation


    Indices: 202--584  Score: 472
    Period size: 172  Copynumber: 2.2  Consensus size: 172

        192 CTTTTTTGAG

                               *                                             
        202 GTTGACATTCAATTATAATATGTTTTAA-ATAAAAATGTACAAAGAATTCAAATTCGAATCAATT
          1 GTTGACATTCAATTATAATCTGTTTTAACA-AAAAATGTACAAAGAATTCAAATTCGAATCAATT

                           *                                                 
        266 TTGAGATTATAAAACTATTAAAAGTATGTAATAAAGCTTTTGAAGGAATGGGTGACAATTAATGG
         65 TTGAGATTATAAAACCATTAAAAGTATGTAATAAAGCTTTTGAAGGAATGGGTGACAATTAATGG

                          ** * *            * *    *   
        331 ACTTTTCTTGTCAATGACTGCCTTTTCCTTCATGTTTCTTGAT
        130 ACTTTTCTTGTCAACAAATACCTTTTCCTTCACGCTTCTCGAT

               *                 *       *                  *                
        374 GTTTACATTCAATTATAATCTTTTTTAACCAAAAATGTACAAAGAATTGAAATTTC-AATCAATT
          1 GTTGACATTCAATTATAATCTGTTTTAACAAAAAATGTACAAAGAATTCAAA-TTCGAATCAATT

                               *           *   *                      *      
        438 TTGAGATTATAAAACCATTTAAAGTGA-GTATTAAGGCTTTTGAAGGAATGGGT-AGCTA-TAAC
         65 TTGAGATTATAAAACCATTAAAAGT-ATGTAATAAAGCTTTTGAAGGAATGGGTGA-CAATTAA-

                                         *   **           
        500 TGGACTTTTCTTGTCAACAAATACCTTTTTCTTTGCGCTTCTCGA-
        127 TGGACTTTTCTTGTCAACAAATACCTTTTCCTTCACGCTTCTCGAT

                    *         *                     
        545 GATTGACAATCAATTATAGTCTGTTTTAACAAAAAATGTA
          1 G-TTGACATTCAATTATAATCTGTTTTAACAAAAAATGTA

        585 AAAAACTNNN


Statistics
Matches: 180,  Mismatches: 25, Indels: 12
        0.83            0.12        0.06

Matches are distributed among these distances:
 171    5  0.03
 172  171  0.95
 173    4  0.02

ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38


Consensus pattern (172 bp):   
GTTGACATTCAATTATAATCTGTTTTAACAAAAAATGTACAAAGAATTCAAATTCGAATCAATTT
TGAGATTATAAAACCATTAAAAGTATGTAATAAAGCTTTTGAAGGAATGGGTGACAATTAATGGA
CTTTTCTTGTCAACAAATACCTTTTCCTTCACGCTTCTCGAT
Done.