If you want to extract Sbjct: lines, and print them out, the following should work fine:

#!/usr/bin/perl -w
use strict;

while (<>) {
    print if /^Sbjct:\s*\d+\D+\d+$/;
}
[download]

Sbjct: 38348818 AGGCATAAACCACATCCAGCCACCTCCTTCTGATCAGCAGCAAAGCTGACGTTT
+TGATCT 38348759
Sbjct: 38348758 CCATCTGTCTGATTCTTGTGTCTACTTCTCAGTTTACAACTCCAGTGGGAAAGA
+AAGAGC 38348699
Sbjct: 38348698 TTTATTTACAGACCCATAAAAATCCCATCAGTGTCGTCCCCTGCTGAGAGGCCA
+TGTGAG 38348639
Sbjct: 94217254 CAAGAAACTATATAGGTATACACTTACGACTTCACAAAACCTATACTTAATATA
+GTAAAT 94217195
Sbjct: 94217194 CTAAGTAAACATGTATTACTCAAAGTAATATATTTAGAATTATGTATTAGTATA
+AGATCA 94217135
Sbjct: 94217134 GAATTGAATTTAAGTTGTTGGTGACATCTGCATCATTTCATAGGATTAGAACTT
+ACTCAA 94217075
Sbjct: 94217074 AATAATGTAAATCTTTAAAAATATAAATTAGAATGACAAGTGGGAATCATAAAT
+TAAACG 94217015
[download]

Hope that helps,
Luke