I did an alignment with tophat, supplying the GFF file for gene annotations, and the chromosomes fasta (in bowtie2 index format). I converted the output accepted_hits.bam to SAM. In the SAM header, it is listing all the chromosomes, and the reads are mapped to the chromosmes, like this:

266GRCF1GCCAAT:1:1101:8591:43171        0 NC_000076.6   38894021        50      49M     *       0       0       GGCGGGGGGAGGGTATCATGGACTTTTGGGATAGCATTTGAAATATAAA      @@@DDDDDB6BBB+8>CDDCCCCCCCCCBB?ACCCCECCCCCCACCCDE AS:i:0 XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:49 YT:Z:UU NH:i:1
266GRCF1GCCAAT:1:2211:7290:90876        0 NC_000076.6   38894073        50      49M     *       0       0       AGAAAATATGTTAAAAATGTTTTGGAAAAAAGAAAAAAAGAAAATTGCC      CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJIJJJJJJJJJJJ AS:i:0 XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:49 YT:Z:UU NH:i:1
266GRCF1GCCAAT:1:2202:7215:55833        0 NC_000076.6   38894074        50      49M     *       0       0       GAAAATATGTTAAAAATGTTTTGGAAAAAAGAAAAAAAGAAAATTGCCA      @CCFFFFFHHHHHJJJJIGIJJJIJJIIIIGIIIIGGEGHJIJIEGHII AS:i:0 XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:49 YT:Z:UU NH:i:1

Where are the read alignments that map to two exons separated by an intron? How do I extract this information from the Tophat output?