"Studies have found the vaccine to be almost 100% effective in preventing diseases caused by the four HPV types covered by the vaccine� including precancers of the cervix, vulva and vagina, and genital warts....Because the vaccine does not protect against all types of HPV, it will not prevent all cases of cervical cancer or genital warts. About 30% of cervical cancers will not be prevented by the vaccine, so it will be important for women to continue getting screened for cervical cancer (regular Pap tests). Also, the vaccine does not prevent about 10% of genital warts�nor will it prevent other sexually transmitted infections (STIs)."
http://www.cdc.gov/std/HPV/STDFact-HPV-vac
cine.htm
"In women, genital warts can grow on the vulva, the walls of the vagina, the area between the external genitals and the anus, and the cervix. In men, they may occur on the tip or shaft of the penis, the scrotum or the anus....."
mayoclinic.com/health/genital-warts/DS0008
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"In addition to the external genitalia (i.e., penis, vulva, scrotum, perineum, and perianal skin), genital warts can occur on the uterine cervix and in the vagina, urethra, anus, and mouth."
cdc.gov/std/treatment/2006/genital-warts.h
tm
From what I have read, it sounds like anal warts are not uncommon, especially for men. Treatment seems to be the same for the warts if they are on the anus. You could try talking to someone else at the clinic who knows more about it though.
Definitely let your partner know what is going on.
"HPV can spread through skin-to-skin contact with any infected part of the body � but using a condom every time you have sex can significantly reduce your risk of contracting HPV....If warts are visible on your genital area or your partner's, avoid sexual contact until the warts are treated. If you've developed genital warts for the first time, inform your sexual partner so that he or she can be screened for infection and, if necessary, receive treatment."
mayoclinic.com/health/genital-warts/DS0008
7/DSECTION=9
