Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018400322.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3526.0, 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: 2312
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.33

Warning! 308 characters in sequence are not A, C, G, or T


Found at i:321 original size:170 final size:159

Alignment explanation


    Indices: 135--461  Score: 309
    Period size: 170  Copynumber: 2.0  Consensus size: 159

        125 NNNNNNNNNN

                                                  *    *  *           *      
        135 TTTTCTTGCTAATGAAT-GCCTTTTTTTCATA-TTTCTTAAGGTAAGCATTCAATTATTGTCCGC
          1 TTTTCTTGCTAATGAATAG-CTTTTTTT-ATACTTTCTCAAGGAAAACATTCAATTATAGTCCGC

                                                         *         *         
        198 TTTAACCAAAAATATAAAAAAATTTAACTCAAAATCAATTATGAGTTTATAAAACCATTTAAAGA
         64 TTTAA-CAAAAATATAAAAAAATTTAACTCAAAATCAATTATGAGATTATAAAACAATTTAAAGA

                     *      *  *                      
        263 AAGTAATAAGGCTTTTGAAGGAATGGGTGNNNNNNNNNNGAT
        128 AAGTAATAAAGCTTTTAAAAGAATGGGTG----------GAT

                                        *                                 * *
        305 TTTTCTT-CTCAATGAATAGCTTTTTTTGTACGTTTCTCAAGGAAAACATTCAATTATAGTCTGT
          1 TTTTCTTGCT-AATGAATAGCTTTTTTTATAC-TTTCTCAAGGAAAACATTCAATTATAGTCCGC

                  *     * *             *  *       *  *                    **
        369 TTTAACTAAAATTTTAAAAAATTTAACTTAAGATCAATTTTGGGATTATAAAACAATTTAAAGCG
         64 TTTAACAAAAATATAAAAAAATTTAACTCAAAATCAATTATGAGATTATAAAACAATTTAAAGAA

                                        
        434 AGTAATAAAGCTTTTAAAAGAATGGGTG
        129 AGTAATAAAGCTTTTAAAAGAATGGGTG

        462 AATATAAATG


Statistics
Matches: 132,  Mismatches: 21, Indels: 8
        0.82            0.13        0.05

Matches are distributed among these distances:
 169    4  0.03
 170   96  0.73
 171   32  0.24

ACGTcount: A:0.36, C:0.11, G:0.13, T:0.37


Consensus pattern (159 bp):   
TTTTCTTGCTAATGAATAGCTTTTTTTATACTTTCTCAAGGAAAACATTCAATTATAGTCCGCTT
TAACAAAAATATAAAAAAATTTAACTCAAAATCAATTATGAGATTATAAAACAATTTAAAGAAAG
TAATAAAGCTTTTAAAAGAATGGGTGGAT

Found at i:1463 original size:34 final size:34

Alignment explanation


    Indices: 1425--1529  Score: 192
    Period size: 34  Copynumber: 3.1  Consensus size: 34

       1415 ATGACTATAA

                                              
       1425 ATAGACTTTTCTTGCTAATGAATGCCTTTTTTTC
          1 ATAGACTTTTCTTGCTAATGAATGCCTTTTTTTC

                                               
       1459 ATAGACTTTTCTTGCTAATGAATGCCTTTTTTTTC
          1 ATAGACTTTTCTTGCTAATGAATGCC-TTTTTTTC

                         *                    
       1494 ATAGACTTTTCTTACTAATGAATGCCTTTTTTTC
          1 ATAGACTTTTCTTGCTAATGAATGCCTTTTTTTC

              
       1528 AT
          1 AT

       1530 GTTTCTCAAA


Statistics
Matches: 69,  Mismatches: 1, Indels: 2
        0.96            0.01        0.03

Matches are distributed among these distances:
  34   36  0.52
  35   33  0.48

ACGTcount: A:0.22, C:0.17, G:0.10, T:0.50


Consensus pattern (34 bp):   
ATAGACTTTTCTTGCTAATGAATGCCTTTTTTTC

Found at i:1497 original size:35 final size:35

Alignment explanation


    Indices: 1425--1526  Score: 188
    Period size: 35  Copynumber: 2.9  Consensus size: 35

       1415 ATGACTATAA

                                               
       1425 ATAGACTTTTCTTGCTAATGAATGCC-TTTTTTTC
          1 ATAGACTTTTCTTGCTAATGAATGCCTTTTTTTTC

                                               
       1459 ATAGACTTTTCTTGCTAATGAATGCCTTTTTTTTC
          1 ATAGACTTTTCTTGCTAATGAATGCCTTTTTTTTC

                         *                   
       1494 ATAGACTTTTCTTACTAATGAATGCCTTTTTTT
          1 ATAGACTTTTCTTGCTAATGAATGCCTTTTTTT

       1527 CATGTTTCTC


Statistics
Matches: 66,  Mismatches: 1, Indels: 1
        0.97            0.01        0.01

Matches are distributed among these distances:
  34   26  0.39
  35   40  0.61

ACGTcount: A:0.22, C:0.17, G:0.11, T:0.51


Consensus pattern (35 bp):   
ATAGACTTTTCTTGCTAATGAATGCCTTTTTTTTC
Done.