Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018400853.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4022.0, 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: 5605
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.37


Found at i:1218 original size:29 final size:29

Alignment explanation


    Indices: 1186--1270  Score: 98
    Period size: 29  Copynumber: 2.9  Consensus size: 29

       1176 AATAAATAAG

                   *        *          * 
       1186 AGTTGTACGTGAACAGTTATAAGAGAAGA
          1 AGTTGTATGTGAACAGATATAAGAGAAAA

                            *  *         
       1215 AGTTGTATGTGAACAGGTAAAAGAGAAAA
          1 AGTTGTATGTGAACAGATATAAGAGAAAA

              *          *        *    
       1244 AGCTGTATGTGAATAGATATAATAGAA
          1 AGTTGTATGTGAACAGATATAAGAGAA

       1271 CAAGCTAAAA


Statistics
Matches: 47,  Mismatches: 9, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  29   47  1.00

ACGTcount: A:0.45, C:0.05, G:0.26, T:0.25


Consensus pattern (29 bp):   
AGTTGTATGTGAACAGATATAAGAGAAAA

Found at i:2206 original size:2 final size:2

Alignment explanation


    Indices: 2199--2227  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       2189 AGATAAGGCC

                                                       
       2199 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       2228 GTTCAAGCAA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:4440 original size:18 final size:18

Alignment explanation


    Indices: 4386--4440  Score: 56
    Period size: 18  Copynumber: 3.0  Consensus size: 18

       4376 TAAGTTCTTC

                            ** 
       4386 TTTTGTTTCTTCTTTTACA
          1 TTTTGTTTCTT-TTTTTTA

                *    *   *    
       4405 TTTTTTTTCATTTCTTTA
          1 TTTTGTTTCTTTTTTTTA

                              
       4423 TTTTGTTTCTTTTTTTTA
          1 TTTTGTTTCTTTTTTTTA

       4441 GAGAGAATCA


Statistics
Matches: 28,  Mismatches: 8, Indels: 1
        0.76            0.22        0.03

Matches are distributed among these distances:
  18   19  0.68
  19    9  0.32

ACGTcount: A:0.09, C:0.11, G:0.04, T:0.76


Consensus pattern (18 bp):   
TTTTGTTTCTTTTTTTTA

Found at i:5540 original size:11 final size:11

Alignment explanation


    Indices: 5524--5552  Score: 58
    Period size: 11  Copynumber: 2.6  Consensus size: 11

       5514 TATGACGAAT

                       
       5524 GAAATAGGACA
          1 GAAATAGGACA

                       
       5535 GAAATAGGACA
          1 GAAATAGGACA

                   
       5546 GAAATAG
          1 GAAATAG

       5553 TTATTATGAC


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   18  1.00

ACGTcount: A:0.55, C:0.07, G:0.28, T:0.10


Consensus pattern (11 bp):   
GAAATAGGACA
Done.