I don't use Perl anymore, but here's something I wrote in Python. It's a 10-minute effort, but seems to work fine. Put your target sequences in a text file, one target sequence per line. Call the program like this:

python fasta_target_extractor target_seqs.txt my_genome.fasta

For each match it will print the header of the matching FASTA contig, and the target sequence match plus up to 7 bases from each side of the matched target sequence.

#!/usr/bin/python
from sys import argv

#run the application like this:
#python fasta_target_extractor.py target_seqs.txt fasta_file.fasta

#The target_seqs list holds the 6-mers you're querying on
target_seqs = []
with open(argv[1]) as tsf:
    for read in tsf:
        target_seqs.append(read.strip())

current_header = ''

with open(argv[2]) as faf:
    for read in faf:
        if read.startswith('>'):
            current_header = read.strip()
            continue
        for ts in target_seqs:
            ts_index = read.find(ts)
            if ts_index != -1:
                r = read.strip()
                start = 0 if ts_index - 7 < 0 else ts_index - 7
                end = len(r) - 1 if ts_index + len(ts) + 7 >= len(r) else ts_index + len(ts) + 7
                print current_header
                print r[start:end]

I don't have an exact solution, but you can extract the sequences with BBDuk like this:

bbduk.sh in=data.fasta out=filtered.fasta k=6 mm=f rcomp=f literal=AAAAAA,AAATTT,CCCGGG

It's also possible to change the matching parts of the sequences to lowercase, which may be helpful, with the flag "kmask=lc". You can mask an additional 7 bases around each matching kmer with the flag "trimpad=7".

Since you have enable the 'strict' syntax mode via 'use strict', you have to declare every variable such as:

$seq="ATGC" is wrong, it should be my $seq="ATGC"

So in your script, change $seq = $_; to my $seq = $_;. That will eliminate the errors