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Try:
awk 'BEGIN { FS=OFS="\t" } NR==FNR { seq=$1; sub(/^[^\t]*\t*[^\t]*\t/,""); if(NR==1)hdr=$0; hold[seq]=$0; next } FNR==1 { print $0, hdr; next } ($1 in hold) { print $0, hold[$1]; next } { print }' fileB fileA >fileC
awk 'BEGIN { FS=OFS="\t" } NR==FNR { seq=$1; sub(/^[^\t]*\t*/,""); if(NR==1)hdr=$0; hold[seq]=$0; next } FNR==1 { print $0, hdr; next } ($1 in hold) { print $0, hold[$1]; next } { print }' fileB fileA >fileC
awk 'BEGIN { FS=OFS="\t" } NR==FNR { seq=$1; sub(/[^\t]*\t/,""); if(NR==1)hdr=$0; hold[seq]=$0; next } FNR==1 { print $0, hdr; next } ($1 in hold) { print $0, hold[$1]; next } { print }' fileB fileA >fileC
awk 'BEGIN { FS=OFS="\t" } NR==FNR { seq=$1; sub(/^[^\t]*\t*/,""); if(NR==1)hdr=$0; hold[seq]=$0; next } FNR==1 { print $0, hdr; next } ($1 in hold) { print $0, hold[$1]; next } { print }' fileB fileA
awk 'BEGIN { FS=OFS="\t" } NR==FNR { seq=$1; sub(/^[^\t]*\t*/,""); if(NR==1)hdr=$0; hold[seq]=$0; next } FNR==1 { print $0, hdrhdr; next } ($1 in hold) { print $0, hold[$1]hold[$1]; next } { print }' fileB fileA
awk 'BEGIN { FS=OFS="\t" } NR==FNR { seq=$1; sub(/^[^\t]*\t*/,""); if(NR==1)hdr=$0; hold[seq]=$0; next } FNR==1 { print $0, hdr } ($1 in hold) { print $0, hold[$1] }' fileB fileA
