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I am wondering if I am wasting my time applying for some positions that are technically listed as a Jr associate with 1-3 years experience. I am currently a 3l but have worked in-house for two years during the school year and thus have some relavent transactional experience. Anyone with any stories? Successes? Failures?

Don't know, but I worked for a law clerk for <1 year and applied for a job asking for 1-4 years experience and got it. It sounds like you have about as much experience as I did.