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Neither dizziness or kidney pain are typical side effects to doxycycline. It certainly is possible that someone may have unique symptoms from the doxycycline or any drug, but it is rare for symptoms to occur that are not typically seen. However, if the symptoms resolve with stopping the drug, then that would be suspicious that the doxycycline did cause the symptoms.
Yes, 13 of 14 pills would likely have eradicated chlamydia if it was present. There are no studies to look at the likelihood of success with 13 pills, but it is unlikely that missnig one pill would make a significant difference.
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These symptoms are not typical for hepatitis. If the partner is actively infected with hepatitis B, then it is easily transmitted by unprotected sex, while condoms are good at reducing the risk of transmission.