tblastn not providing full alignment even on exact-matching sequences

Question

I am using tblastn to search a polypeptide seq against transcripts. One of those transcripts contains the residues for that exact polypeptide once translated, yet BLAST only gets 88% of it rather than it being full length.

Here's the peptide:

>Syntaxin
MTKDRLAALKAAQSDDDDNDDVAVTVDSSGFMEEFFEQVDEIREMIDKIASNVDEVKKKHSAILSAPQTDD
KMKEELEELMSEIKKNANKVRAKLKVIEQNIEQEEHTNKSSADLRIRKTQHATLSRKFVEVMNDYNACQID
YRERCKGRIKRQLAITGKTTTNEELEDMIESGNPAIFTQGIIMETQQANETLADIEARHNDIMKLETSIRD
LHDMFMDMAMLVESQGEMIDRIEYNVEQAVDYIETAKMDTKKAVKYQSKARRKKIMILVCLAILIIILVGV
IGGTLG

And the transcript.

Here's the first-frame translation of the transcript which contains the exact polypeptide above:

frame +1

> - 669
PATRNITIVSIYDYH*NNDLKCVFTE*MEILNRIWILLNSHSP*AQRLHAI**MTKDRLAALKAAQSDDDD
NDDVAVTVDSSGFMEEFFEQVDEIREMIDKIASNVDEVKKKHSAILSAPQTDDKMKEELEELMSEIKKNAN
KVRAKLKVIEQNIEQEEHTNKSSADLRIRKTQHATLSRKFVEVMNDYNACQIDYRERCKGRIKRQLAITGK
TTTNEELEDMIESGNPAIFTQGIIMETQQANETLADIEARHNDIMKLETSIRDLHDMFMDMAMLVESQGEM
IDRIEYNVEQAVDYIETAKMDTKKAVKYQSKARRKKIMILVCLAILIIILVGVIGGTLG***PSSLPLVYS
LIQLFYAACTTAASNIWTHHNRNSYYYNSNSNSNSNCYSNYFSNYYSNRKHYYYYHYYYYYYYYYYYYYYY
YYYYYYDYYYYYYYYYYYYYYYYYCYYYYYYYYYHFHYYYHHYYYHYYYYHYYYHYHHHHHYHYHYHYHHH
HHYHYHYHYHYHYYYYYYYYYYYYYYYYYYYYYYCYYYYYYTFSLVISLYGSSEM*MRLLVLSLYTFYGLF
YPLQQKGSFFF*SLQQTGTGFYNFFSYCQLHNLSIPSPSYFF*EWVFSFLKKHLIEFFCFLILLKFVLSFS
PIISLIISVCRKKISRIFYTIYLKMS**NHYLLF

Yet when I do a local tblastn (using the modern blast+) or use NCBI's pairwise blast tool it doesn't return a full-length match.

Why does it leave off the last 12% of the sequence match?

Here's the alignment:

Answer 1

That's because by default, blast masks low complexity regions. With the online blast2seqs tool, you can disable this by clicking on the "Algorithm options" button:

And then deselect the "Low complexity regions" filter:

This will let you align the entire sequence as expected:

Alignment statistics for match #1
Score   Expect  Method  Identities  Positives   Gaps
Frame
588 bits(1516)  0.0 Compositional matrix adjust.    290/290(100%)   290/290(100%)   0/290(0%)
+1
Query  1     MTKDRLAALKAAQSDDDDNDDVAVTVDSSGFMEEFFEQVDEIREMIDKIASNVDEVKKKH  60
             MTKDRLAALKAAQSDDDDNDDVAVTVDSSGFMEEFFEQVDEIREMIDKIASNVDEVKKKH
Sbjct  154   MTKDRLAALKAAQSDDDDNDDVAVTVDSSGFMEEFFEQVDEIREMIDKIASNVDEVKKKH  333

Query  61    SAILSAPQTDDKMKEELEELMSEIKKNANKVRAKLKVIEQNIEQEEHTNKSSADLRIRKT  120
             SAILSAPQTDDKMKEELEELMSEIKKNANKVRAKLKVIEQNIEQEEHTNKSSADLRIRKT
Sbjct  334   SAILSAPQTDDKMKEELEELMSEIKKNANKVRAKLKVIEQNIEQEEHTNKSSADLRIRKT  513

Query  121   QHATLSRKFVEVMNDYNACQIDYRERCKGRIKRQLAITGKTTTNEELEDMIESGNPAIFT  180
             QHATLSRKFVEVMNDYNACQIDYRERCKGRIKRQLAITGKTTTNEELEDMIESGNPAIFT
Sbjct  514   QHATLSRKFVEVMNDYNACQIDYRERCKGRIKRQLAITGKTTTNEELEDMIESGNPAIFT  693

Query  181   QGIIMETQQANETLADIEARHNDIMKLETSIRDLHDMFMDMAMLVESQGEMIDRIEYNVE  240
             QGIIMETQQANETLADIEARHNDIMKLETSIRDLHDMFMDMAMLVESQGEMIDRIEYNVE
Sbjct  694   QGIIMETQQANETLADIEARHNDIMKLETSIRDLHDMFMDMAMLVESQGEMIDRIEYNVE  873

Query  241   QAVDYIETAKMDTKKAVKYQSKARRKKIMILVCLAILIIILVGVIGGTLG  290
             QAVDYIETAKMDTKKAVKYQSKARRKKIMILVCLAILIIILVGVIGGTLG
Sbjct  874   QAVDYIETAKMDTKKAVKYQSKARRKKIMILVCLAILIIILVGVIGGTLG  1023

This is the part of your transcript sequence that was masked:

acgctaggctgaccctcctccctccctctagtctactccttaatacaattgttctacgccgcgtgcacc

I am guessing it is the repeated ccct nucleotides that resulted in the sequence being masked, but I am not sure.