Why blast with same query sequence shows two different query length?

Question

[sharmatina189059]

Dear all I am using blast to align my sequences bot with command line as well as graphically. I want to know that my query sequence which is mentioned below has a total length of 169aa. I am aligning it with two sequence mentioned below. While aligning the blast results shows two different length of query sequence. WHy? It is showing 160 length while aligning to 1st sequence with default parameters and with 2nd sequence the query length is 169. Can you please tell me why it is happening? Query protein ID WP_000009660.1

>seq1_160_length                                                
MKKLLMLLCLGVSSHSVWANTLVEMQTNLGNIEIELYDDKAPMSVNNFKGYIKSGFYKETIFHRVIPGFMAQGGGMTTNMQEKTTRAPIKNEAGNGIANTRGTLAMARTSNPDSATSQFFINVADNNFLNRSPGNPGYAVFGKVVKGMDVVDRIVQAPTSNYGMHQNVPKQPIKIVDKKSKILKNKLTI                                                       

>seq2_169_length                                            
MSFPQVELNTNKGRIVLELNTEKAPKTAANFLEYVRDGFYDGVIFHRVIDGFMIQGGGFDENFKEKATRDAIENEADNGLSNDVGTIAMARTQAPHSASAQFFINVKNNSFLNHTSKTAQGWGYAVFGKVIEGMDVVEAIKGVRTGNRGYHADVPLENVVIESAKIISE

[GenoMax]

It is possibly just showing the part that is aligned. Are you referring to pair-wise alignment results?

[sharmatina189059]

Yes. Can you please show me example. I really could not understand how they are calculating alignment length.

[GenoMax]

 seq1_160_length
Sequence ID: Query_14151Length: 189Number of Matches: 1
Range 1: 23 to 179Graphics
Next Match
Previous Match
Alignment statistics for match #1 Score Expect  Method  Identities  Positives   Gaps
164 bits(415)   6e-57   Compositional matrix adjust.    85/160(53%)     106/160(66%)    3/160(1%)

Query  6    VELNTNKGRIVLELNTEKAPKTAANFLEYVRDGFYDGVIFHRVIDGFMIQGGGFDENFKE  65
            VE+ TN G I +EL  +KAP +  NF  Y++ GFY   IFHRVI GFM QGGG   N +E
Sbjct  23   VEMQTNLGNIEIELYDDKAPMSVNNFKGYIKSGFYKETIFHRVIPGFMAQGGGMTTNMQE  82

Query  66   KATRDAIENEADNGLSNDVGTIAMARTQAPHSASAQFFINVKNNSFLNHTSKTAQGWGYA  125
            K TR  I+NEA NG++N  GT+AMART  P SA++QFFINV +N+FLN +       GYA
Sbjct  83   KTTRAPIKNEAGNGIANTRGTLAMARTSNPDSATSQFFINVADNNFLNRSPGNP---GYA  139

Query  126  VFGKVVEGMDVVEAIKGVRTGNRGYHADVPLENVVIESAK  165
            VFGKVV+GMDVV+ I    T N G H +VP + + I   K
Sbjct  140  VFGKVVKGMDVVDRIVQAPTSNYGMHQNVPKQPIKIVDKK  179


And

 seq2_169_length
Sequence ID: Query_42759Length: 169Number of Matches: 1
Range 1: 1 to 169Graphics
Next Match
Previous Match
Alignment statistics for match #1 Score Expect  Method  Identities  Positives   Gaps
347 bits(889)   2e-129  Compositional matrix adjust.    168/169(99%)    169/169(100%)   0/169(0%)

Query  1    MSFPQVELNTNKGRIVLELNTEKAPKTAANFLEYVRDGFYDGVIFHRVIDGFMIQGGGFD  60
            MSFPQVELNTNKGRIVLELNTEKAPKTAANFLEYVRDGFYDGVIFHRVIDGFMIQGGGFD
Sbjct  1    MSFPQVELNTNKGRIVLELNTEKAPKTAANFLEYVRDGFYDGVIFHRVIDGFMIQGGGFD  60

Query  61   ENFKEKATRDAIENEADNGLSNDVGTIAMARTQAPHSASAQFFINVKNNSFLNHTSKTAQ  120
            ENFKEKATRDAIENEADNGLSNDVGTIAMARTQAPHSASAQFFINVKNNSFLNHTSKTAQ
Sbjct  61   ENFKEKATRDAIENEADNGLSNDVGTIAMARTQAPHSASAQFFINVKNNSFLNHTSKTAQ  120

Query  121  GWGYAVFGKVVEGMDVVEAIKGVRTGNRGYHADVPLENVVIESAKIISE  169
            GWGYAVFGKV+EGMDVVEAIKGVRTGNRGYHADVPLENVVIESAKIISE
Sbjct  121  GWGYAVFGKVIEGMDVVEAIKGVRTGNRGYHADVPLENVVIESAKIISE  169