According to what you write above, you are using the -r switch to Bowtie.

This is what the Bowtie manual says about the -r option:

-r

The query input files (...) are Raw files: one sequence per line, without quality values or names. All quality values are assumed to be 40 on the Phred quality scale.

So each line is supposed to be just a sequence, no quality, no name. Your example sequence is a bit weirdly formatted, but for sure it includes the name of the read at the beginning, so you can't use -r.

Another issue that could give this kind of result is if you use the wrong quality score scale. For the "phred+64" quality scale that Illumina data sometimes uses, you have to add the --solexa-1.3-quals option.

In addition to what @Mikael has said...

It looks like your input is FASTQ format--except messed up. Can you paste 8 lines directly from the file into your question? From your input above, somehow it looks like the 4 lines are merged into a single line.

Did bowtie give an error when you tried to run it? It should have been able to at least attempt to align 25% of the rows in your FASTQ file.

Maybe you'll also need to trim the tag from the left end of the read. You can do this with the --trim5 flag and specify the number of bases to skip in each read--likely 6 or so.

EDIT:

your data is not in FASTQ format. Save this into a file named tofq.py

import sys
for line in open(sys.argv[1]):
    header, seq, qual = line.rstrip().rsplit(":", 2)
    print "@%s\n%s\n+\n%s" % (header, seq, qual)

then run it as:

python tofq.py yourfile.not.fastq > output.fastq

where yourfile.not.fastq is the name of the file where you got the reads above. Then run output.fastq through bowtie.