How did you align the sequences? Be sure to use a global aligner such as EMBOSS-Needle which performs end-to-end alignments rather than something like BLAST which is not meant to capture longer deletions and favours local alignments as long as it returns a good alignment score.

Example:

Say the top was the WT sequence and the bottom was the sequence after deletion:

GTAGCGTACTGACGACGTATCTTATCGACGCGCGCGCGCGCGCGTAGCATCTCTTCGACGTACGACATCTACGCTACGACACATCACACTAC
GTAGCGTACTGACGACGTATCTTATCGACGCGCGCGCGCGCGCGTAGCATCTCT                            ATCACACTAC

EMBOSS-Needle gets it correctly:

ref                1 GTAGCGTACTGACGACGTATCTTATCGACGCGCGCGCGCGCGCGTAGCAT     50
                     ||||||||||||||||||||||||||||||||||||||||||||||||||
sanger             1 GTAGCGTACTGACGACGTATCTTATCGACGCGCGCGCGCGCGCGTAGCAT     50

ref               51 CTCTTCGACGTACGACATCTACGCTACGACACATCACACTAC     92
                     ||||                            ||||||||||
sanger            51 CTCT----------------------------ATCACACTAC     64

Whereas BLAST:

Query  1   GTAGCGTACTGACGACGTATCTTATCGAcgcgcgcgcgcgcgcgTAGCATCTCT  54
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  1   GTAGCGTACTGACGACGTATCTTATCGACGCGCGCGCGCGCGCGTAGCATCTCT  54

The alignment score of this alignment is simply higher than of the full-length sequence with all the deletions which create penalty scores. Hence, BLAST is not suitable here.