Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018400436.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3633.0, 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, 923

Length: 1539
ACGTcount: A:0.16, C:0.05, G:0.06, T:0.17

Warning! 854 characters in sequence are not A, C, G, or T


Found at i:47 original size:21 final size:20

Alignment explanation


    Indices: 18--56  Score: 51
    Period size: 20  Copynumber: 1.9  Consensus size: 20

          8 GAATGGGTGA

                                 
         18 CTATAAATGGACTTTTTTTAT
          1 CTATAAAT-GACTTTTTTTAT

                *    *        
         39 CTATGAATGCCTTTTTTT
          1 CTATAAATGACTTTTTTT

         57 TCACGTTTCT


Statistics
Matches: 16,  Mismatches: 2, Indels: 1
        0.84            0.11        0.05

Matches are distributed among these distances:
  20    9  0.56
  21    7  0.44

ACGTcount: A:0.23, C:0.13, G:0.10, T:0.54


Consensus pattern (20 bp):   
CTATAAATGACTTTTTTTAT

Found at i:1404 original size:172 final size:171

Alignment explanation


    Indices: 1129--1535  Score: 500
    Period size: 170  Copynumber: 2.4  Consensus size: 171

       1119 TTATAGTCTG

                    *                  *         *    *   *              *   
       1129 TTTTAAT-GAAAAATGTAAAAAATTTCTACTTAAAATTAATTATGATATTATAAAACCATTCAAA
          1 TTTTAATCAAAAAATGTAAAAAA-TTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAA

              *     *          *  *   *                *       *             
       1193 GGGAGTAATAAGACTTTTGTAGGAATGGGTGACTATAAATAGATTTTTCTTGCCAATGAATGCTT
         65 GGCAGTAAAAAGACTTTTGAAGAAATAGGTGACTATAAATAGACTTTTCTTACCAATGAATG--T

                  *                               *       
       1258 TTTTTTGTTCACATTTCTCTG-GGTAGACATTCAATTATAGAT-TA
        128 TTTTTTCTTCACATTTCT-TGAGGTAGACATTCAATTACA-ATCTA

                           *       *                                      *  
       1302 TTTTAA-CAAAAAATATAAAAAAATCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAGAG
          1 TTTTAATCAAAAAATGTAAAAAATTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAG

            *          *                   *       *                         
       1366 TCAGTAAAAAGCCTTTTGAAGAAATAGGTGATTATAAATGGACTTTTCTTACCAATGAATGTTTT
         66 GCAGTAAAAAGACTTTTGAAGAAATAGGTGACTATAAATAGACTTTTCTTACCAATGAATGTTTT

                    **                              *
       1431 TTTCTTCATGTTTCTTGAGGTAGACATTCAATTACAATCTG
        131 TTTCTTCACATTTCTTGAGGTAGACATTCAATTACAATCTA

                                        *                                    
       1472 TTTTAATCAAAAAA-GTAAAAAATTCAATTTAAAATCAATTTTGAGATTATAAAACCATTTAAAG
          1 TTTTAATCAAAAAATGTAAAAAATTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAG

       1536 TGAG


Statistics
Matches: 201,  Mismatches: 29, Indels: 11
        0.83            0.12        0.05

Matches are distributed among these distances:
 169    4  0.02
 170   86  0.43
 171    7  0.03
 172   85  0.42
 173   19  0.09

ACGTcount: A:0.40, C:0.10, G:0.12, T:0.37


Consensus pattern (171 bp):   
TTTTAATCAAAAAATGTAAAAAATTCAACTTAAAATCAATTTTGAGATTATAAAACCATTTAAAG
GCAGTAAAAAGACTTTTGAAGAAATAGGTGACTATAAATAGACTTTTCTTACCAATGAATGTTTT
TTTCTTCACATTTCTTGAGGTAGACATTCAATTACAATCTA

Found at i:1508 original size:170 final size:172

Alignment explanation


    Indices: 1112--1535  Score: 509
    Period size: 172  Copynumber: 2.5  Consensus size: 172

       1102 NNNNNNNNNN

                *     *              *     *            *         *    *   * 
       1112 CATTAAATTATAG-TCTGTTTTAATGAAAAATGTAAAAAATTTCTACTTAAAATTAATTATGATA
          1 CATTCAATTACAGATCTGTTTTAATCAAAAAAGTAAAAAA-TTCAACTTAAAATCAATTTTGAGA

                         *     *     *          *  *   *                *    
       1176 TTATAAAACCATTCAAAGGGAGTAATAAGACTTTTGTAGGAATGGGTGACTATAAATAGATTTTT
         65 TTATAAAACCATTTAAAGGCAGTAAAAAGACTTTTGAAGAAATAGGTGACTATAAATAGACTTTT

               *                   *                    
       1241 CTTGCCAATGAATGCTTTTTTTTGTTCACATTTCTCTGGGTAGA
        130 CTTACCAATGAATGC-TTTTTTTCTTCACATTTCTCTGGGTAGA

                      *      *               *       *                       
       1285 CATTCAATTATAGAT-TATTTTAA-CAAAAAATATAAAAAAATCAACTTAAAATCAATTTTGAGA
          1 CATTCAATTACAGATCTGTTTTAATCAAAAAA-GTAAAAAATTCAACTTAAAATCAATTTTGAGA

                           *  *          *                   *       *       
       1348 TTATAAAACCATTTAGAGTCAGTAAAAAGCCTTTTGAAGAAATAGGTGATTATAAATGGACTTTT
         65 TTATAAAACCATTTAAAGGCAGTAAAAAGACTTTTGAAGAAATAGGTGACTATAAATAGACTTTT

                                       **               
       1413 CTTACCAATGAATG-TTTTTTTCTTCATGTTTCT-TGAGGTAGA
        130 CTTACCAATGAATGCTTTTTTTCTTCACATTTCTCTG-GGTAGA

                                                         *                   
       1455 CATTCAATTACA-ATCTGTTTTAATCAAAAAAGTAAAAAATTCAATTTAAAATCAATTTTGAGAT
          1 CATTCAATTACAGATCTGTTTTAATCAAAAAAGTAAAAAATTCAACTTAAAATCAATTTTGAGAT

                             
       1519 TATAAAACCATTTAAAG
         66 TATAAAACCATTTAAAG

       1536 TGAG


Statistics
Matches: 214,  Mismatches: 32, Indels: 13
        0.83            0.12        0.05

Matches are distributed among these distances:
 169    4  0.02
 170   86  0.40
 171    7  0.03
 172   90  0.42
 173   26  0.12
 174    1  0.00

ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38


Consensus pattern (172 bp):   
CATTCAATTACAGATCTGTTTTAATCAAAAAAGTAAAAAATTCAACTTAAAATCAATTTTGAGAT
TATAAAACCATTTAAAGGCAGTAAAAAGACTTTTGAAGAAATAGGTGACTATAAATAGACTTTTC
TTACCAATGAATGCTTTTTTTCTTCACATTTCTCTGGGTAGA
Done.