What Causes Pain During Urination With Blood In Urine?

Hi, I have recently had the feeling of a tired penis when urinating, then last night progresed to pain when urinating. Only had 1 sexual partner for last 4 year s I do not questions her faithfulness. Have a history of kidney stones, had kidney type pain a couple weeks ago, didn t think much of it until this started going on. I went to Er last night they wouldn t run any tests just took urine said that was negative for a uti but they were going to send it off for cultures for stds and treated me for stds and sent me on my way. I know it s not stds. I m able to look at urinalysis online from hospital. They stated that there was blood in my urine. I also seen where mucus was present as well as bacteria, I m wondering what s going on I know it s not an std.