Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018402706.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5769.0, 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, 922

Length: 1537
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.33

Warning! 128 characters in sequence are not A, C, G, or T


Found at i:345 original size:172 final size:171

Alignment explanation


    Indices: 164--542  Score: 406
    Period size: 171  Copynumber: 2.2  Consensus size: 171

        154 NNNNNNNNNN

                      *      *        *            *                         
        164 TCACTTTAAACGGTTTTGTAATCTCAAAATTGATTTAAATTTGAATTCTTCTGT-CATTTTTAGT
          1 TCACTTTAAATGGTTTTATAATCTCATAATTGATTTAAAGTTGAATT-TT-TGTACATTTTTAGT

                 * *        *             *                                  
        228 TAAAATATACTAGAATTGAATGCCTACCTCGAGAAACATGAAAAAAAAAGCA-TTCATTGGCAAG
         64 TAAAACAGACTAGAATAGAATGCCTACCTCAAGAAACATG-AAAAAAAAGCACTTCATTGGCAAG

            *                                        *   
        292 GAAAGTCTATTTA-TAGTCAACCATACCTTCAAAAGCCTCATTAC
        128 AAAAGTCTATTTACT-GTCAACCATACCTTCAAAAGCCTCAATAC

              *          *  *                    *             *             
        336 TCGCTTTAAATGGCTTAATAATGCT-ATAATTGATTTTAAGTTGAATTTTTTTACATTTTTAGTT
          1 TCACTTTAAATGGTTTTATAAT-CTCATAATTGATTTAAAGTTGAATTTTTGTACATTTTTAGTT

                    *  **     *  **             *    *      *    *           
        400 AAAACAGATTATTATAGATTGTGTACCTCAAGAAACGTGAAGAAAAAGGACTTTATTGGCAAGAA
         65 AAAACAGACTAGAATAGAATGCCTACCTCAAGAAACATGAAAAAAAAGCACTTCATTGGCAAGAA

                             *    * *        *  *     
        465 AAGTCTATTTACTGTCACCCATTCTTTCAAAAGTCTTAATAC
        130 AAGTCTATTTACTGTCAACCATACCTTCAAAAGCCTCAATAC

                                 *              
        507 TCACTTTAAATGGTTTTATAACCTCATAATTGATTT
          1 TCACTTTAAATGGTTTTATAATCTCATAATTGATTT

        543 TAGATTGAAT


Statistics
Matches: 168,  Mismatches: 34, Indels: 11
        0.79            0.16        0.05

Matches are distributed among these distances:
 170   13  0.08
 171  116  0.69
 172   37  0.22
 173    2  0.01

ACGTcount: A:0.36, C:0.15, G:0.13, T:0.37


Consensus pattern (171 bp):   
TCACTTTAAATGGTTTTATAATCTCATAATTGATTTAAAGTTGAATTTTTGTACATTTTTAGTTA
AAACAGACTAGAATAGAATGCCTACCTCAAGAAACATGAAAAAAAAGCACTTCATTGGCAAGAAA
AGTCTATTTACTGTCAACCATACCTTCAAAAGCCTCAATAC

Found at i:1242 original size:18 final size:18

Alignment explanation


    Indices: 1216--1265  Score: 66
    Period size: 17  Copynumber: 2.8  Consensus size: 18

       1206 CTTATTGCTC

                *    *        
       1216 ACTTTAAATGGTTTTTTA
          1 ACTTCAAATTGTTTTTTA

                              
       1234 ACTTCAAATTG-TTTTTA
          1 ACTTCAAATTGTTTTTTA

             *             
       1251 AGTTCAAATTGTTTT
          1 ACTTCAAATTGTTTT

       1266 ACATTNNNNN


Statistics
Matches: 28,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  17   16  0.57
  18   12  0.43

ACGTcount: A:0.28, C:0.08, G:0.10, T:0.54


Consensus pattern (18 bp):   
ACTTCAAATTGTTTTTTA

Found at i:1266 original size:16 final size:17

Alignment explanation


    Indices: 1228--1265  Score: 67
    Period size: 17  Copynumber: 2.2  Consensus size: 17

       1218 TTTAAATGGT

                             
       1228 TTTTTAACTTCAAATTG
          1 TTTTTAACTTCAAATTG

                   *         
       1245 TTTTTAAGTTCAAATTG
          1 TTTTTAACTTCAAATTG

                
       1262 TTTT
          1 TTTT

       1266 ACATTNNNNN


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  17   20  1.00

ACGTcount: A:0.26, C:0.08, G:0.08, T:0.58


Consensus pattern (17 bp):   
TTTTTAACTTCAAATTG
Done.