Alignment of multiple sequences to one (fixed) reference

[uloeber]

Hi all,
I have a reference sequence, which is shorter than the sequences I want to align. The first sequence is my reference, so it should be more or less fixed. The other sequences are locally or in some cases globally similar. Because my reference sequence is shorter than the other sequences, I'm not able to map the other sequences on that. If I do multiple sequence alignment, there are gaps inserted in the reference, which shouldn't be there. If I do pairwise alignments I miss the graphical representation of all sequences to my reference, I can only investigate each sequence pair individually.
Is there an alignment toll, which provides multiple pairwise sequence alignments with a good visualization of the results? Or a multiple sequence alignments with one anchor sequence? I only found the seed option in mafft, but this only works for a seed alignment not a seed sequence. Am I right?
Thank you for every answer!

[mastal]

How long are your sequences?

If they are relatively short, you could use bowtie1, which doesn't do gapped alignment, but I think the longest sequence it will map to the reference is about 1000 bp.

[uloeber]

My reference is ~4500 bp long. The other sequences are from 400bp - 9000bp I'm also interested in the overlapping region next to the reference. The reference should not contain gaps, while the other sequences might contain gaps. Maybe it's problematic if they contain indels.