LAST Web Service

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Enter your "reference" sequence(s):

>mySeq1
catgctagtctttactgtatcgtaaaaaa
acgtagtgctagatgctagctcggg
>mySeq2
atctgatgctagatcgtacgtaaa

Or upload a file:

Enter your "query" sequence(s):

>mySeqX
catgctagtctttaccgtatcgtaaaaaa
cgtagggctagatgctagctcggg
>mySeqY
atctgatgctagatcgtacgtaaa

Or upload a file:

Sequence type:
DNA
protein
guess

Query strand (ignored for proteins):
forward
reverse
both

Alignment type:
maximum score
γ-centroid

Mask lowercase for initial matches:
no
yes

Mask lowercase for extensions:
neither
gapless
gapless and gapped

dotplot width limit (pixels)
dotplot height limit (pixels)
dotplot font size
letters per line

Upload a subset seed:

spaced seed pattern
max multiplicity for initial matches
min length for initial matches
step-size along reference sequences
step-size along query sequences
supress nearby repeats in exact matches
"temperature" (1/λ)
γ

Upload a score matrix:

r: match score (DNA:1, protein:blosum62)
q: mismatch cost (DNA:1, protein:blosum62)
a: gap existence cost (DNA:7, protein:11)
b: gap extension cost (DNA:1, protein:2)
c: unaligned pair cost (100000)
x: max gapped score drop (max[y, a+b×20])
y: max gapless score drop (temperature×10)
d: min gapless alignment score (e×3/5)
e: min gapped alignment score (DNA:30, protein:100)

LAST: sequence alignment coloured by reliability