Matrix PAM30 PAM70 BLOSUM80 BLOSUM62 BLOSUM45

Gap costs Open:9 Ext:2 Open:8 Ext:2 Open:7 Ext:2 Open:12 Ext:1 Open:11 Ext:1 Open:10 Ext:1

Expect threshold 00.1 0.1 1 10 100 1000 10000 30000

Short queries Automatically adjust parameters for short input sequences

Filter Low complexity regions

Word size 2 3

ktup:1   (more sensitive)
 2   (faster)

Matrix: BLOSUM50 BLOSUM62 BLOSUM80 PAM120 PAM250 MDM10 MDM20 MDM40

Gap open: -23 -22 -18 -17 -16 -14 -12 -10 -8 -7 -6 -2 -0

Gap extend: 0 -1 -2 -3 -4 -6 -8

Expectation upper value 1e-600 1e-300 1e-600 1e-50 1e-10 1e-5 0.001 0.1 1.0 2.0 5.0 10.0 20.0 50

Expectation lower value default 1e-600 1e-300 1e-600 1e-50 1e-10 1e-5 0.001 0.1 1.0 2.0 5.0 10.0 20.0 50

Filter none seg xnu seg+xnu

Statistical model Regress MLE Altshul-Gish Regress/shuf. MLE/shuf.

Matrix: BLOSUM50 BLOSUM62 BLOSUM80 PAM120 PAM250 MDM10 MDM20 MDM40

Gap open: -23 -22 -18 -17 -16 -14 -12 -10 -8 -7 -6 -2 -0

Gap extend: 0 -1 -2 -3 -4 -6 -8

Expectation upper value 1e-600 1e-300 1e-600 1e-50 1e-10 1e-5 0.001 0.1 1.0 2.0 5.0 10.0 20.0 50

Expectation lower value default 1e-600 1e-300 1e-600 1e-50 1e-10 1e-5 0.001 0.1 1.0 2.0 5.0 10.0 20.0 50

Filter none seg xnu seg+xnu

Statistical model Regress MLE Altshul-Gish Regress/shuf. MLE/shuf.

Max target sequences 10 50 100 250 500

Exclude Allergome Molecules

Matrix PAM30 PAM70 BLOSUM80 BLOSUM62 BLOSUM45

Gap costs Open:9 Ext:2 Open:8 Ext:2 Open:7 Ext:2 Open:12 Ext:1 Open:11 Ext:1 Open:10 Ext:1

Expect threshold 00.1 0.1 1 10 100 1000 10000 30000

Short queries Automatically adjust parameters for short input sequences

Filter Low complexity regions

Word size 2 3

ktup:1   (more sensitive)
 2   (faster)

Matrix: BLOSUM50 BLOSUM62 BLOSUM80 PAM120 PAM250 MDM10 MDM20 MDM40

Gap open: -23 -22 -18 -17 -16 -14 -12 -10 -8 -7 -6 -2 -0

Gap extend: 0 -1 -2 -3 -4 -6 -8

Expectation upper value 1e-600 1e-300 1e-600 1e-50 1e-10 1e-5 0.001 0.1 1.0 2.0 5.0 10.0 20.0 50

Expectation lower value default 1e-600 1e-300 1e-600 1e-50 1e-10 1e-5 0.001 0.1 1.0 2.0 5.0 10.0 20.0 50

Filter none seg xnu seg+xnu

Statistical model Regress MLE Altshul-Gish Regress/shuf. MLE/shuf.

Matrix: BLOSUM50 BLOSUM62 BLOSUM80 PAM120 PAM250 MDM10 MDM20 MDM40

Gap open: -23 -22 -18 -17 -16 -14 -12 -10 -8 -7 -6 -2 -0

Gap extend: 0 -1 -2 -3 -4 -6 -8

Expectation upper value 1e-600 1e-300 1e-600 1e-50 1e-10 1e-5 0.001 0.1 1.0 2.0 5.0 10.0 20.0 50

Expectation lower value default 1e-600 1e-300 1e-600 1e-50 1e-10 1e-5 0.001 0.1 1.0 2.0 5.0 10.0 20.0 50

Filter none seg xnu seg+xnu

Statistical model Regress MLE Altshul-Gish Regress/shuf. MLE/shuf.

Max target sequences 10 50 100 250 500

Exclude Allergome Molecules