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Lionel MMFlag for United States of America

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Malware or Security Breach on Hosted Website

I am using site5.com to host a joomla website and then a simple HTML website. This site has said that one of my sites with a  script may be compromised (only site that has any scripts is the joomla site). This site is version 2.5.28 -- I can't update it because when I do it screws up my site. So the question is how can I check these sites and/or the files and folders to see if indeed they are infected, or have been breached? I have downloaded all the files with filezilla to my local drive and scanned then with AVG and found nothing. So what is the best way to make sure there are no malicious scripts on my websites or that any of the scripts have been hijacked? They said that someone is using a valid username and password to send junk email but can't tell me how to remedy the situation and that it is my responsibility to get it fixed and so I need some help please--thank you.
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btan

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btan

Sure that is always the case regardless if the malware is found or not, as long as website suspected compromise, it need to be clean up and refurnished. Below is list of resources for info
A short overview:

http://sitecheck.sucuri.net/
You can use Sucuri's SiteCheck to quickly spot if they detect any malware, see if you're blacklisted and, the most useful part in this case is to check whether or not you have any outdated plugin or CMS running - as well as a list of links.

http://aw-snap.info/file-viewer/
Use Redleg's file viewer to easily see if any malicious iframes have been injected - you can even choose which Referrer and User Agent should be used (some malware requires you to visit the site via a specific Referrer or User Agent).

http://www.rexswain.com/httpview.html
Useful additional tool to Redleg's file viewer. Allows you to only fetch headers of a website, or fetch both header and content.

http://jsunpack.jeek.org/
Excellent tool in case any malicious Javascript (iframe) is injected into any of your web server files. Less intuitive, but provides a great overview.

http://urlquery.net/
Excellent tool and more graphical as opposed to JSunpack - especially useful is to see if any IDS was triggered as well as JavaScript and HTTP Transactions.

https://www.virustotal.com/
As usual, VirusTotal is a great resource as well - it can pinpoint which Antivirus (if any) is triggering an alert related to your website.
http://bartblaze.blogspot.sg/2015/03/c99shell-not-dead.html
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Already explained in my last comment