I don't think so. There is qseq and sseq, which report the aligned parts of the sequences only.

qseqid means Query Seq-id

qgi means Query GI

qacc means Query accesion

qaccver means Query accesion.version

qlen means Query sequence length

sseqid means Subject Seq-id

sallseqid means All subject Seq-id(s), separated by a ';'

sgi means Subject GI

sallgi means All subject GIs

sacc means Subject accession

saccver means Subject accession.version

sallacc means All subject accessions

slen means Subject sequence length

qstart means Start of alignment in query

qend means End of alignment in query

sstart means Start of alignment in subject

send means End of alignment in subject

qseq means Aligned part of query sequence

sseq means Aligned part of subject sequence

evalue means Expect value

bitscore means Bit score

score means Raw score

length means Alignment length

pident means Percentage of identical matches

nident means Number of identical matches

mismatch means Number of mismatches

positive means Number of positive-scoring matches

gapopen means Number of gap openings

gaps means Total number of gaps

ppos means Percentage of positive-scoring matches

frames means Query and subject frames separated by a '/'

qframe means Query frame

sframe means Subject frame

btop means Blast traceback operations (BTOP)

staxids means unique Subject Taxonomy ID(s), separated by a ';'

(in numerical order)

sscinames means unique Subject Scientific Name(s), separated by a ';'

scomnames means unique Subject Common Name(s), separated by a ';'

sblastnames means unique Subject Blast Name(s), separated by a ';'

(in alphabetical order)

sskingdoms means unique Subject Super Kingdom(s), separated by a ';'

(in alphabetical order)

stitle means Subject Title

salltitles means All Subject Title(s), separated by a ''

sstrand means Subject Strand

qcovs means Query Coverage Per Subject

qcovhsp means Query Coverage Per HSP

Thank you so much . sseq served the purpose. :)

Hi,

I'm interested in this question. I tried to get the ' sskingdoms' value for each subject sequence, but blast program always gave me 'N/A' as an answer. Could you tell me how to solve this problem?

Best,

Ruibo