How can I tell where I was penalised?
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It seems for sometime now I have not been showing up the top for my keywords when I use to be ranking #1 and #2 for my main keywords, however now, I don't show up anywhere - this has been for almost a year now, can anyone tell me how I can find out (apart from google web masters tools) where I was penalised?
Thanks
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Can you pinpoint the date your site started to slip? then check that against: http://moz.com/google-algorithm-change that might help identify if you were hit by panda/penguin etc
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This recent in-depth case study that was published on Moz is a great place to start -- seriously, it's amazing!

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Definitely a good idea to check what pages you set up, when you put them together and compare that to the release of known updates to determine whether there is a correlation. If that isn't possible or is very labor intensive, you might do some research into the strategies and tactics you employed a year ago and make sure that they have not become punishable tactics in 2015 - sounds obvious but you never know.
You might also consider a website audit to see if that might illuminate a previously unknown problem.
Best of luck and feel free to ask follow-up questions if you have any.
Rob
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I personally would start by using the Panguin tool which gives an overlay of your Google Analytics - make sure you set your date back enough to cover the time prior to when you got hit in order to see if you have been hurt by any of the updates. I have been using this tool for several years and would definitely recommend it - I have done in several other Moz Q&As previously.
Samuel Scott's response mentions the post by Alan Bleweiss and he mentions this tool in it.
Depending on what your analysis uncovers you may find this an interesting read - http://moz.com/blog/ultimate-guide-to-google-penalty-removal
Hope this helps!