to extract the sequence of interest

spacer.sh

## OPTION 1
# convert the gzipped fastq file to a single line sequence files
zcat input.fastq.gz | sed -n '2~4p' > single_line_sequences.txt
# you are aksing it to print 2nd line followed every 4th line after that.
perl -ne 'while ($_ =~ m/GTGTTCCCCGCGCCAGCGGGGATAAACC([ATCG]{32})/g) {print $1."\t"} {print "\n"}' single_line_sequences.txt
# here, you are printing the 32 bases after the matching string using perl and using tab as delimiter. 
# the input is the above file you created in the first step.
# this will generate the output for the first part.

## OPTION 2
# if you prefer only bash then:
grep -one "GTGTTCCCCGCGCCAGCGGGGATAAACC.\{32\}" single_line_sequences.txt | \
sed 's/:GTGTTCCCCGCGCCAGCGGGGATAAACC/\t/g' |  \
awk -F"\t" '{a[$1]=a[$1]"\t"$2;} END{for (x in a) print x "\t" substr(a[x],2);}'

# does exactly as before, but it is little slower
# first step uses grep to "o"nly print the matches, with line "n"umbers using r"e"gular expressions. The matching part is crispr
# followed by 32 letters
# Next step removes the crispr sequence and pritns only the line numbers and spacers
# awk (complicated) will merge all the lines with same numbers using tab as delimiters


#example:
$ cat test.txt
CCGTAATTAATAATAGGTTATGTTTAGAGTGTTCCCCGCGCCAGCGGGGATAAACCGGCAAAAACCGGGCAATCGCAA
CCGTAATTAATAATAGGTTATGTTTAGAGTGTTCCCCGCGCCAGCGGGGATAAACCGATAATGCTGTATGATAAAAAAATGCTGGATAGGTGTTCCCCGCGCCAGCGGGGATAAACCGGCAAAAACCGGGCAATCGCAA
CCGTAATTAATAATAGGTTATGTTTAGAGTGTTCCCCGCGCCAGCGGGGATAAACCGGTTTTGCGCCATTCGATGGTGTCCGGGATCTCGTGTTCCCCGCGCCAGCGGGGATAAACCGGACAAGTTTTGGTGACTGCGCTCCTCCAAGCCGTGTTCCCCGCGCCAGCGGGGATAAACCGGCAAAAACCGGGCAATCGCAA


# OPTION 1
$ time perl -ne 'while ($_ =~ m/GTGTTCCCCGCGCCAGCGGGGATAAACC([ATCG]{32})/g) {print $1."\t"} {print "\n"}' test.txt

GATAATGCTGTATGATAAAAAAATGCTGGATA
GGTTTTGCGCCATTCGATGGTGTCCGGGATCT        GGACAAGTTTTGGTGACTGCGCTCCTCCAAGC

real    0m0.023s
user    0m0.005s
sys     0m0.004s

#OPTION 2

$ time grep -one "GTGTTCCCCGCGCCAGCGGGGATAAACC.\{32\}" test.txt | sed 's/:GTGTTCCCCGCGCCAGCGGGGATAAACC/\t/g' |  awk -F"\t" '{a[$1]=a[$1]"\t"$2;} END{for (x in a) print x "\t" substr(a[x],2);}'
2       GATAATGCTGTATGATAAAAAAATGCTGGATA
3       GGTTTTGCGCCATTCGATGGTGTCCGGGATCT        GGACAAGTTTTGGTGACTGCGCTCCTCCAAGC

real    0m0.033s
user    0m0.011s
sys     0m0.018s