Sequence Alignment Tool

The alignment tool provides access to pre-compiled alignments for individual HLA genes and sequence features (e.g. specific exons and introns), or alignments of commonly sequenced regions (e.g. exons 2+3).

Align Beta

The IPD team are currently working on a new version of the alignment tool based on some of the recent developments utilised in the IPD-MHC and IPD-NHKIR projects. To try the new version of the tool please click the following link.

  1. Link to Beta Tool

Alignment Tool Classic

Please Note:

Numbering of the nucleotide positions in the genomic alignments depends on the length of the 5'UTR in the locus reference. If an alternative reference is used that differs through presence of insertions or deletions this numbering may not be accurate.

For more help regarding use of the sequence alignment tool please see our Alignment Help

Select the alignment options
Select locus
Select features
Choose reference sequence
Any specific sequences required
(separated by a new line or a comma):
Only show exact matches
(e.g. 02:10 will not match 02:100)
Display mismatches
Numbering format
Filter unsequenced alleles
Nomenclature Field:
Output format