Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018399037.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2313.0, 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: 2762
ACGTcount: A:0.22, C:0.07, G:0.12, T:0.22

Warning! 1035 characters in sequence are not A, C, G, or T


Found at i:1305 original size:30 final size:30

Alignment explanation


    Indices: 1271--1338  Score: 100
    Period size: 30  Copynumber: 2.3  Consensus size: 30

       1261 CTTGATTGAG

                                          
       1271 GATGAAGAAGATGACATGCAAAGAAATGAA
          1 GATGAAGAAGATGACATGCAAAGAAATGAA

                              *  *  *     
       1301 GATGAAGAAGATGACATGGAAGGAGATGAA
          1 GATGAAGAAGATGACATGCAAAGAAATGAA

            *       
       1331 AATGAAGA
          1 GATGAAGA

       1339 TGAAGAAGAA


Statistics
Matches: 34,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  30   34  1.00

ACGTcount: A:0.51, C:0.04, G:0.31, T:0.13


Consensus pattern (30 bp):   
GATGAAGAAGATGACATGCAAAGAAATGAA

Found at i:1314 original size:15 final size:14

Alignment explanation


    Indices: 1272--1329  Score: 55
    Period size: 15  Copynumber: 3.9  Consensus size: 14

       1262 TTGATTGAGG

                          
       1272 ATGAAGAAGATGAC
          1 ATGAAGAAGATGAC

                            *
       1286 ATGCAAAGAA-ATGAAG
          1 ATG--AAGAAGATG-AC

                          
       1302 ATGAAGAAGATGAC
          1 ATGAAGAAGATGAC

                   *      
       1316 ATGGAAGGAGATGA
          1 AT-GAAGAAGATGA

       1330 AAATGAAGAT


Statistics
Matches: 36,  Mismatches: 3, Indels: 9
        0.75            0.06        0.19

Matches are distributed among these distances:
  14   11  0.31
  15   16  0.44
  16    9  0.25

ACGTcount: A:0.50, C:0.05, G:0.31, T:0.14


Consensus pattern (14 bp):   
ATGAAGAAGATGAC

Found at i:1337 original size:15 final size:15

Alignment explanation


    Indices: 1272--1338  Score: 50
    Period size: 15  Copynumber: 4.5  Consensus size: 15

       1262 TTGATTGAGG

                          *
       1272 ATGAAGAAGATG-AC
          1 ATGAAGAAGATGAAA

                            *
       1286 ATGCAAAGAA-ATGAAG
          1 ATG--AAGAAGATGAAA

                          *
       1302 ATGAAGAAGATG-AC
          1 ATGAAGAAGATGAAA

                   *        
       1316 ATGGAAGGAGATGAAA
          1 AT-GAAGAAGATGAAA

                   
       1332 ATGAAGA
          1 ATGAAGA

       1339 TGAAGAAGAA


Statistics
Matches: 42,  Mismatches: 5, Indels: 11
        0.72            0.09        0.19

Matches are distributed among these distances:
  14   11  0.26
  15   19  0.45
  16   12  0.29

ACGTcount: A:0.52, C:0.04, G:0.30, T:0.13


Consensus pattern (15 bp):   
ATGAAGAAGATGAAA
Done.