I realized that I don't know what happens when illumina sequencing chemistry reaches the end of a fragment. Does the reaction stop for that fragment, or are bases added in some way? The reason I ask is because I have fragments ranging from 120-160bp in length and yet on 150 cycles I will always get 150bp long reads. And some of my reads will end in terminal repeats like this:

CGTCTTCTGCTTGAAAAAAAAAAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
"CGTCTTCTGCTTG" matches the end of an Illumina adapter sequence.  After you run off the end of an adapter, it's common to get poly-A, and sometimes eventually poly-G.  So, no, your adapters have NOT been trimmed - you are sequencing into them, and then off the end into no signal.

You can (and should) trim your adapters, as described in [this post][1].

Also, to clarify, the Illumina sequencing machine has no idea how long your fragments are.  You tell it to run for 150 cycles, so it gives you 150 cycles of data for every read, regardless of the actual length of the molecule.


  [1]: http://seqanswers.com/forums/showthread.php?t=42776