Problems about Bowtie

[ECHo]

Our bench experimental data come from Solexa, which would offer us two BP ends.
Now, I'd like to use Bowtie to align the two end BP-sequencing with H. sapiens chromosomes.
Then, I use the following operation command:
./bowtie -a -v 2 -p 16 chr21 -q -1 TestData/s_1_1_sequence.txt -2 TestData/s_1_2_sequence.txt

I had transformed the chr21 to ebwt, which would be my chromosome sequence target.
The two txt files are the BP end sequences.

What I want to know is :
1. There must be some BPs between two end sequences.
Could I know how many BPs between two end sequences in my commands?
2. If my current command couldn't do the alignment, how could I modify my command to get it? ( The middle sequences is 200 bp)


Thanks a lot!