FASTA Generator
Simplified STR allele constructs for CE allele numbers, built on the GRCh38 reference. For educational purposes.
Whole CE allele numbers from 1 to 100 (a technical input limit of this tool). The GRCh38 reference is kept and only its variable repeat block in the ISFG minimum range gains or loses whole copies of its motif, so each construct has the length of that CE allele; the header names the motif and its copy number. Microvariants (for example 9.3) are not currently supported.
Flanking sequence is cut from the plus strand of this assembly.
Select a marker and click "Generate Sequence" to begin
Generates simplified STR allele constructs for user-defined CE allele numbers. Each one is the GRCh38 reference with a single repeat block changed; other repeat blocks, interruptions and microvariants are not varied or modeled. Outputs should not be interpreted as validated forensic allele sequences.
For each locus, the variable block is the longest uninterrupted run of a variable motif of its STRNaming structure inside the ISFG minimum range (STRidER FSSG v6-1; Gettings et al. 2024). Allele N gets as many copies of that motif as the reference has, plus N minus the reference CE allele: the reference allele rebuilds GRCh38 exactly, and every other allele differs from it by whole motifs. Microvariants are not currently supported.
Overview
Choose a locus, enter whole CE allele numbers as a list or a range, set the flank length and export the constructs in one of several standard formats.
The current set contains 22 loci: the 20 CODIS core loci plus Penta D and Penta E.
Features
- The 20 CODIS core loci plus Penta D and Penta E
- Variable repeat block located in the ISFG minimum range of each locus
- Reference sequence from GRCh38 slices (plus strand)
- Customizable flanking regions (0–200 bp per side)
- Export formats: Standard FASTA, Reference-style FASTA, Multi-FASTA and Tabular CSV
- Direct download and copy options
Use cases
- Educational and training purposes in forensic genomics
- Simple in silico inputs, for example to see how software handles alleles of different lengths