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:

Alignment type:
maximum score
γ-centroid
LAMA

Sequence type:
DNA
protein
guess

Query strand (ignored for proteins):
forward
reverse
both

Lowercase:
simple repeats using tantan
preserve original case

Mask lowercase for initial matches:
no
yes

Mask lowercase for extensions:
never
gapless
gapless and gapped but not final
always

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

Upload a subset seed:

spaced seed pattern
max multiplicity for initial matches
minimum length for initial matches
maximum length for initial matches (∞)
max gapless alignments per query position (m)
step-size along reference sequences
use "minimum" positions in sliding windows of W consecutive positions
step-size along query sequences
suppress 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)
A: insertion existence cost (a)
B: insertion extension cost (b)
c: unaligned pair cost (∞)
x: max preliminary gapped score drop (z)
y: max gapless score drop (temperature×10)
z: max final gapped score drop (e-1)
d: min gapless alignment score (t×ln[1000×refSize/n])
e: min gapped alignment score

D: query letters per random alignment
E: max expected alignments per square giga