Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018398428.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1729.0, 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, 915

Length: 1525
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.32

Warning! 275 characters in sequence are not A, C, G, or T


Found at i:315 original size:170 final size:161

Alignment explanation


    Indices: 4--402  Score: 315
    Period size: 170  Copynumber: 2.4  Consensus size: 161

          1 TAC

                 *     *         *      *                       *            
          4 AATCTCATAATTGATTTTAAGTTGAATTTTTTTACA-TTTTTATTAAAACAGGTTAT-ATTGAAT
          1 AATCTAATAATAGATTTTAAGCTGAATTGTTTTACATTTTTTATTAAAACAGATTATAATTGAAT

            * *  *                         *    *            *               
         67 GTTTACCTCGAGAAAAGTGAAGAAAAGATATTCATTTGCAACAAAAGTCTATTTATAATCACCCA
         66 ATCTATCTC--G---A--G-A-AAAAGATATCCATTAGCAACAAAAGTCCATTTATAATCACCCA

                  *                           *      
        132 TACATTTGAAAGCCTTATTACTCAG-TTTAAATATTTTTAT
        122 TACATTCGAAAGCCTTATTACT-AGTTTTAAATAGTTTTAT

                                             **                              
        172 AATCTAATAATAGATTTTAAGCTGAATT-TTTTTTATATTTTT-TTAAAACAGATTATAATTGAA
          1 AATCTAATAATAGATTTTAAGCTGAATTGTTTTACAT-TTTTTATTAAAACAGATTATAATTGAA

                                                       *               *     
        235 TATCTATCTCGNNNNNNNNNNAGAAAAAGATATCCATTAGCAAGAAAAGTCCATTTATAGTCACC
         65 TATCTATCTCG----------AGAAAAAGATATCCATTAGCAACAAAAGTCCATTTATAATCACC

             *                    *  *                 
        300 CTTA-ACTTCGAAAGCCTTATTGCTTGTTTTAAATAGTTTTAT
        120 CATACA-TTCGAAAGCCTTATTACTAGTTTTAAATAGTTTTAT

                 *   * *       * *                         * *           
        342 AATCTCATACTTGATTTTAGGTTGAATTGTTTTACATTTTTTATTAACATAGATTATAATT
          1 AATCTAATAATAGATTTTAAGCTGAATTGTTTTACATTTTTTATTAAAACAGATTATAATT

        403 AAATGACTAC


Statistics
Matches: 186,  Mismatches: 31, Indels: 25
        0.77            0.13        0.10

Matches are distributed among these distances:
 167    6  0.03
 168   38  0.20
 169   20  0.11
 170   97  0.52
 171   23  0.12
 172    1  0.01
 174    1  0.01

ACGTcount: A:0.35, C:0.11, G:0.10, T:0.41


Consensus pattern (161 bp):   
AATCTAATAATAGATTTTAAGCTGAATTGTTTTACATTTTTTATTAAAACAGATTATAATTGAAT
ATCTATCTCGAGAAAAAGATATCCATTAGCAACAAAAGTCCATTTATAATCACCCATACATTCGA
AAGCCTTATTACTAGTTTTAAATAGTTTTAT

Found at i:463 original size:171 final size:169

Alignment explanation


    Indices: 4--504  Score: 478
    Period size: 171  Copynumber: 3.0  Consensus size: 169

          1 TAC

                                                                *            
          4 AATCTCATAATTGATTTTAAGTTGAATTTTTTTACA-TTTTTATTAAAACAGGTTAT-ATTGAAT
          1 AATCTCATAATTGATTTTAAGTTGAA-TTTTTTACATTTTTTATTAAAACAGATTATAATTGAAT

             **                               *       *       *       *      
         67 GTTTACCTCGAGAAAAGTGAAG-AAAAGATATTCATTTGCAACAAAAGTCTATTTATAATCACCC
         65 GACTACCTCGAGAAAAGTGAAGAAAAAGATA-TCCTTTGCAAAAAAAGTCCATTTATAGTCACCC

                                               *      
        131 AT-ACATTTGAAAGCCTTATTACTCAGTTTAAATATTTTTAT
        129 ATAAC-TTTGAAAGCCTTATTACTCAGTTTAAATAGTTTTAT

                 *     *         *          **                               
        172 AATCTAATAATAGATTTTAAGCTGAATTTTTTTTATATTTTT-TTAAAACAGATTATAATTGAAT
          1 AATCTCATAATTGATTTTAAGTTGAATTTTTTACAT-TTTTTATTAAAACAGATTATAATTGAAT

                  *    **********                 *    *                     
        236 -ATCTATCTCGNNNNNNNNNNAGAAAAAGATATCCATTAGCAAGAAAAGTCCATTTATAGTCACC
         65 GA-CTACCTCGAGAAAAGTGAAGAAAAAGATATCC-TTTGCAAAAAAAGTCCATTTATAGTCACC

             *      *            *   *                 
        300 CTTAACTTCGAAAGCCTTATTGCT-TGTTTTAAATAGTTTTAT
        128 CATAACTTTGAAAGCCTTATTACTCAG-TTTAAATAGTTTTAT

                     *         *                           * *           *   
        342 AATCTCATACTTGATTTTAGGTTGAATTGTTTTACATTTTTTATTAACATAGATTATAATTAAAT
          1 AATCTCATAATTGATTTTAAGTTGAATT-TTTTACATTTTTTATTAAAACAGATTATAATTGAAT

                     *    **                       *                   * *   
        407 GACTACCTCAAGAAGCGTGAAGAAAAAGATATCCTTTGGTAAAAAAAGTCCATTTATAGCCTCCC
         65 GACTACCTCGAGAAAAGTGAAGAAAAAGATATCCTTT-GCAAAAAAAGTCCATTTATAGTCACCC

               *                              
        472 ATACCTTTGAAAGCCTTATTACTC-GCTTTAAAT
        129 ATAACTTTGAAAGCCTTATTACTCAG-TTTAAAT

        505 GGTNNNNNNN


Statistics
Matches: 259,  Mismatches: 61, Indels: 23
        0.76            0.18        0.07

Matches are distributed among these distances:
 167    7  0.03
 168   36  0.14
 169   23  0.09
 170   95  0.37
 171   97  0.37
 172    1  0.00

ACGTcount: A:0.35, C:0.13, G:0.11, T:0.39


Consensus pattern (169 bp):   
AATCTCATAATTGATTTTAAGTTGAATTTTTTACATTTTTTATTAAAACAGATTATAATTGAATG
ACTACCTCGAGAAAAGTGAAGAAAAAGATATCCTTTGCAAAAAAAGTCCATTTATAGTCACCCAT
AACTTTGAAAGCCTTATTACTCAGTTTAAATAGTTTTAT
Done.