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When it comes to bigger holes that cannot be mended with a single seam, your best bet is to look into getting a patch-- an extra piece of fabric you can integrate into your jeans to cover the hole. You can find patches at a local arts and crafts or clothing specialty outlet. Buy a patch that matches the colour of your jeans as closely as possible. You'll want to get a patch that's slightly bigger than the hole you're covering; that way, you'll have some extra room to make errors.   While denim patches are the safest bet if you're looking to really repair your jeans, you can take the damage as an opportunity to stylize your jeans with brightly coloured or flannel patches.  Adding a patch that will clearly stand out from the rest of the clothing will give it a down-to-earth flair. While denim (or 'masked' alterations) are best sewn in on the inside of the jeans, patching different fabrics to the outside of your jeans will make them more prominent and eye-catching.   If you're feeling thrifty, you can harvest your own patches from jeans you don't use anymore. If you have a bigger hole that will require a patch, you should still cut off the frayed edges. Even if it sounds like you are consciously losing material, the frayed edges won't be any help in mending it, so it's best to get rid of them, leaving a clean hole. Take some scissors and cut excess threads around the hole. By the end, there shouldn't be any threads significantly sticking out. With patches in particular, it's recommended you turn your jeans inside out while you're patching them. That way, the most visible seams won't be externally visible. It'll also give you a bit of extra room to make sewing mistakes. It's typically better to sew a denim patch in from the inside. This will make the patch look less evident, as well as cover up the most visible stitch lines. Once you've got your jeans turned inside out, take a sewing needle and thread and sew the patch. Try to keep your sewing as close as possible; you want to integrate the fabric into your jeans as closely as closely as possible. Ironing your jeans following a patch is significantly more important than ironing a small tear. This will help even out and seal the patch.

Summary:
Get a patch that suits the style of your jeans and size of the hole. Cut frayed edges. Turn your pants inside out. Sew the patch with close-knit seams. Iron your patch out.