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If you had LMP od 6/18 then if your periods were normal then your expected date should be around 7/16-7/18.So the bleeding in between you had and even the brown discharge may be a part of menses or may be due to hormonal
imbalance.Irregularity in periods is mainly due to hormonal imbalance and even in case of cyst
.Presently you are having temperature of 99.1 so better visit a Gynaecologist for examination and treatment.To rule out cyst you can get a ultrasound
done and if that is not showing a cyst then you will be treated by the Gynaec for mild infection if you have and also give you medicine to regulate the periods.