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Run another Malwarebytes full scan to see if it comes up clean this time.
Then run WDO or another of the free bootable anti-virus scans, after burning the downloaded ISO to CD using Windows Image Burner.
Once scans come up clean, proceed with the other Repair steps, starting with SFC /SCANNOW Run in Command Prompt at Boot to see if damaged System Files will repair enough to boot. Then you may need to also repair the boot using the methods given in Troubleshooting Windows 7 Failure to Start