[BioC] difference results by needle program and pairwiseAlignment

[Wang Peter]

dear Herve：
Thank you for your help

my needle setting is default
>> # Matrix: EBLOSUM62
>> # Gap_penalty: 10.0
>> # Extend_penalty: 0.5
>
and the score is 6

how can i set the pairwiseAlignment
Gap_penalty: ?
Extend_penalty: ?