Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018397591.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1980.0, 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: 5701
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.36

Warning! 110 characters in sequence are not A, C, G, or T


Found at i:2444 original size:29 final size:28

Alignment explanation


    Indices: 2398--2540  Score: 171
    Period size: 29  Copynumber: 5.0  Consensus size: 28

       2388 TGGTAGCTTT

                                        
       2398 AACATGTTTGTCTTAATTTAGACAAGAA
          1 AACATGTTTGTCTTAATTTAGACAAGAA

                                         
       2426 AACATGTTTAGTCTTAATTTAGACAAGAA
          1 AACATGTTT-GTCTTAATTTAGACAAGAA

              *                     *      
       2455 AATATGTTT-TCCTTAATTTAAGATAAGAAA
          1 AACATGTTTGT-CTTAATTT-AGACAAG-AA

              *   *     *                
       2485 AATACTTTTTGTTTTAATTTAGACAAGAA
          1 AACA-TGTTTGTCTTAATTTAGACAAGAA

                 *       *             
       2514 AACATATTTGTCTAAATTTAGACAAGA
          1 AACATGTTTGTCTTAATTTAGACAAGA

       2541 TAAAATATTT


Statistics
Matches: 100,  Mismatches: 9, Indels: 12
        0.83            0.07        0.10

Matches are distributed among these distances:
  27    1  0.01
  28   37  0.37
  29   38  0.38
  30   12  0.12
  31   11  0.11
  32    1  0.01

ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38


Consensus pattern (28 bp):   
AACATGTTTGTCTTAATTTAGACAAGAA

Found at i:2505 original size:31 final size:29

Alignment explanation


    Indices: 2404--2572  Score: 159
    Period size: 28  Copynumber: 5.7  Consensus size: 29

       2394 CTTTAACATG

                                        * 
       2404 TTTGTCTTAATTTAGACAAGAAAACAT-GT
          1 TTTGTCTTAATTTAGACAAGAAAA-ATATT

              *                           
       2433 TTAGTCTTAATTTAGACAAG-AAAATATGT
          1 TTTGTCTTAATTTAGACAAGAAAAATAT-T

                *            *             
       2462 TTT-CCTTAATTTAAGATAAGAAAAATACTT
          1 TTTGTCTTAATTT-AGACAAGAAAAATA-TT

                 *                        
       2492 TTTGTTTTAATTTAGACAAGAAAACATA--
          1 TTTGTCTTAATTTAGACAAGAAAA-ATATT

                   *                       
       2520 TTTGTCTAAATTTAGACAAGATAAAATATTT
          1 TTTGTCTTAATTTAGACAAGA-AAAATA-TT

                 *       *        
       2551 TTTGTGTTAATTACAGACAAGA
          1 TTTGTCTTAATT-TAGACAAGA

       2573 GTTGCTTTAA


Statistics
Matches: 115,  Mismatches: 13, Indels: 21
        0.77            0.09        0.14

Matches are distributed among these distances:
  27    2  0.02
  28   33  0.29
  29   31  0.27
  30   20  0.17
  31   21  0.18
  32    8  0.07

ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39


Consensus pattern (29 bp):   
TTTGTCTTAATTTAGACAAGAAAAATATT

Found at i:2512 original size:59 final size:59

Alignment explanation


    Indices: 2398--2572  Score: 171
    Period size: 59  Copynumber: 3.0  Consensus size: 59

       2388 TGGTAGCTTT

                 *       *                      *   *  *                
       2398 AACATGTTTGTCTTAATTTAGACAAGA-AAACAT--GTTTAGTCTTAATTTAGACAAGAA
          1 AACATATTTGTCTAAATTTAGACAAGATAAA-ATACTTTTTGTGTTAATTTAGACAAGAA

              *  *        *         *                   *                
       2455 AATATGTTT-TCCTTAATTTAAGATAAGA-AAAATACTTTTTGTTTTAATTTAGACAAGAA
          1 AACATATTTGT-CTAAATTT-AGACAAGATAAAATACTTTTTGTGTTAATTTAGACAAGAA

                                              *               *        
       2514 AACATATTTGTCTAAATTTAGACAAGATAAAATATTTTTTGTGTTAATTACAGACAAGA
          1 AACATATTTGTCTAAATTTAGACAAGATAAAATACTTTTTGTGTTAATT-TAGACAAGA

       2573 GTTGCTTTAA


Statistics
Matches: 99,  Mismatches: 12, Indels: 11
        0.81            0.10        0.09

Matches are distributed among these distances:
  56    1  0.01
  57   18  0.18
  58   17  0.17
  59   54  0.55
  60    9  0.09

ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38


Consensus pattern (59 bp):   
AACATATTTGTCTAAATTTAGACAAGATAAAATACTTTTTGTGTTAATTTAGACAAGAA

Done.