Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018402070.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5167.0, 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: 3528
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.31

Warning! 100 characters in sequence are not A, C, G, or T


Found at i:1046 original size:17 final size:18

Alignment explanation


    Indices: 1004--1053  Score: 50
    Period size: 18  Copynumber: 2.8  Consensus size: 18

        994 TGTAAATGTA

                              *
       1004 ATAAAAA-ATAAATACATG
          1 ATAAAAATATAAA-ACATC

               *              
       1022 ATACAAATATAAAA-ATC
          1 ATAAAAATATAAAACATC

                           
       1039 ATAAAAATGATAAAA
          1 ATAAAAAT-ATAAAA

       1054 TGATTAATTT


Statistics
Matches: 27,  Mismatches: 3, Indels: 4
        0.79            0.09        0.12

Matches are distributed among these distances:
  17    9  0.33
  18   13  0.48
  19    5  0.19

ACGTcount: A:0.68, C:0.06, G:0.04, T:0.22


Consensus pattern (18 bp):   
ATAAAAATATAAAACATC

Found at i:1465 original size:3 final size:3

Alignment explanation


    Indices: 1440--1481  Score: 50
    Period size: 3  Copynumber: 13.7  Consensus size: 3

       1430 AATAAGAAAA

                                                           *        
       1440 AAT AA- AAT AAT AAAT AAT GAAT AAT AAT AAT AAT AGT AAT AA
          1 AAT AAT AAT AAT -AAT AAT -AAT AAT AAT AAT AAT AAT AAT AA

       1482 ATGAATAAAC


Statistics
Matches: 34,  Mismatches: 2, Indels: 6
        0.81            0.05        0.14

Matches are distributed among these distances:
   2    2  0.06
   3   26  0.76
   4    6  0.18

ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29


Consensus pattern (3 bp):   
AAT

Found at i:1465 original size:22 final size:22

Alignment explanation


    Indices: 1421--1489  Score: 68
    Period size: 22  Copynumber: 3.0  Consensus size: 22

       1411 TAGAAAGCTA

                *              *   
       1421 AAAAAAATAAATAA-GAAAAAAT
          1 AAAATAATAAATAATG-AATAAT

                                  
       1443 AAAATAATAAATAATGAATAAT
          1 AAAATAATAAATAATGAATAAT

                                     
       1465 AATAATAATAGTAATAAATGAATAA
          1 AA-AATAATA--AAT-AATGAATAA

       1490 ACTAGGTAAT


Statistics
Matches: 40,  Mismatches: 2, Indels: 6
        0.83            0.04        0.12

Matches are distributed among these distances:
  22   20  0.50
  23    8  0.20
  25    3  0.08
  26    9  0.22

ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23


Consensus pattern (22 bp):   
AAAATAATAAATAATGAATAAT

Found at i:1488 original size:20 final size:20

Alignment explanation


    Indices: 1465--1502  Score: 51
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       1455 AATGAATAAT

                                 
       1465 AATAATAATA-GTAATAAATG
          1 AATAA-AATAGGTAATAAATG

                  *           
       1485 AATAAACTAGGTAATAAA
          1 AATAAAATAGGTAATAAA

       1503 CCACCTTAAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 2
        0.84            0.05        0.11

Matches are distributed among these distances:
  19    3  0.19
  20   13  0.81

ACGTcount: A:0.61, C:0.03, G:0.11, T:0.26


Consensus pattern (20 bp):   
AATAAAATAGGTAATAAATG
Done.