Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018399050.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2325.0, 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: 5411
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.16

Warning! 3112 characters in sequence are not A, C, G, or T


Found at i:1939 original size:171 final size:167

Alignment explanation


    Indices: 1747--2223  Score: 490
    Period size: 171  Copynumber: 2.8  Consensus size: 167

       1737 NNNNNNNNNN

                 *      * *           *        *                  *          
       1747 TAAAATCATTTAAAACGAGTAATAAGGCTTTTGAAAGAATGAGAGATTATAAATAGACTTTTTTT
          1 TAAAACCATTTAGAGCGAGTAATAAGACTTTTGAAGGAATGAGAGATTATAAATTGACTTTTTTT

                                         * *                      *          
       1812 GCCAATGAATGCTTTGTTTGTCATGTTTCCCCAGATAGACATTGC-ATTATTATCTGTTTTAATC
         66 GCCAATGAATGCTTT-TTT-TC-TGTTTCTCAAGATAGACATT-CAATTATTATATGTTTTAATC

                                             *********
       1876 AAAAATATACAATAATTCAACTTAAAATCAATTNNNNNNNNN
        127 AAAAATATACAA-AATTCAACTTAAAATCAATTATTAGATTA

            *                                        *             **     *  
       1918 NAAAACCATTTAGAGCGAGTAATAAGACTTTTGAAGGAATGGGAGATTATAAATTCTCTTTTCTT
          1 TAAAACCATTTAGAGCGAGTAATAAGACTTTTGAAGGAATGAGAGATTATAAATTGACTTTTTTT

                      *                   *                                  
       1983 GCCAATGAATACTTTTTTCTTCTTGTTTCTTAAGATAGACATTCAATTATTATATGTTTTAATCA
         66 GCCAATGAATGC-TTTTT-TTC-TGTTTCTCAAGATAGACATTCAATTATTATATGTTTTAATCA

              *********     *                        
       2048 ANNNNNNNNNNAAATTTAACTTAAAATCAATTATTAGATTA
        128 A-AAATATACAAAATTCAACTTAAAATCAATTATTAGATTA

                              *                                     *        
       2089 TAAAACCATTTAGAGCGAATAATAAGACTTTTGAAGGAATGAGAGATTATAAATTGGCTTTTCTT
          1 TAAAACCATTTAGAGCGAGTAATAAGACTTTTGAAGGAATGAGAGATTATAAATTGACTTTT-TT

                                                                             
       2154 T-CCAATGAATGCCTTTTTCTTCTCGTTTCTCAAGATAGACATTCAATTATTATATGTTTTAATC
         65 TGCCAATGAATG-CTTTTT-TTCT-GTTTCTCAAGATAGACATTCAATTATTATATGTTTTAATC

                  
       2218 AAAAAT
        127 AAAAAT

       2224 GTAAAAANNN


Statistics
Matches: 251,  Mismatches: 48, Indels: 15
        0.80            0.15        0.05

Matches are distributed among these distances:
 170    2  0.01
 171  241  0.96
 172    8  0.03

ACGTcount: A:0.35, C:0.12, G:0.12, T:0.37


Consensus pattern (167 bp):   
TAAAACCATTTAGAGCGAGTAATAAGACTTTTGAAGGAATGAGAGATTATAAATTGACTTTTTTT
GCCAATGAATGCTTTTTTTCTGTTTCTCAAGATAGACATTCAATTATTATATGTTTTAATCAAAA
ATATACAAAATTCAACTTAAAATCAATTATTAGATTA

Found at i:5316 original size:49 final size:49

Alignment explanation


    Indices: 5258--5362  Score: 158
    Period size: 49  Copynumber: 2.1  Consensus size: 49

       5248 TTTATAATGT

                            *                     * *         
       5258 AATAATTGATTTTAAGTTG-ATTGTTTTTACATTTTTGGTTAAAACAGAC
          1 AATAATTGATTTTAAGCTGAATT-TTTTTACATTTTTGATCAAAACAGAC

                                                             
       5307 AATAATTGATTTTAAGCTGAATTTTTTTACATTTTTGATCAAAACAGAC
          1 AATAATTGATTTTAAGCTGAATTTTTTTACATTTTTGATCAAAACAGAC

             *     
       5356 AGTAATT
          1 AATAATT

       5363 AAATGTCTAT


Statistics
Matches: 51,  Mismatches: 4, Indels: 2
        0.89            0.07        0.04

Matches are distributed among these distances:
  49   48  0.94
  50    3  0.06

ACGTcount: A:0.35, C:0.08, G:0.12, T:0.45


Consensus pattern (49 bp):   
AATAATTGATTTTAAGCTGAATTTTTTTACATTTTTGATCAAAACAGAC
Done.