I was checking my own rankings (as you do) recently and I noted that this site was nowhere to be seen in the top 10 for a certain key phrase which I usually ranked around 3rd for on google.co.uk. The site was now ranking around position 36 for this phrase. This appeared to be what is known in SEO circles as a "-30 penalty" (a Google ranking drop of 30 positions). I also saw that only around 1/4 of pages from the site were indexed by Google. Were 3/4 of the pages deindexed in around a week? I thought "Here we go..." .
What had caused this? The Google updates known as Penguin (the links to my site causing this problem)? The Google updates known as Panda (low quality or duplicate content on my site)? Something else?
I looked in Google Webmaster Tools. There was no manual Google Penguin "Unnatural Link" algorithm update penalty which is notified there by a notice of detected unnatural links listed there. I remembered that not all of Google actions on a site will be notfied via Webmaster Tools.
There was evidence of a crash & sustained drop in impressions and clicks via Google search around a week before I had noticed the problem. Due to the deindexation (alongside the ranking drop) I used my experience to make the assumption that the most likely cause was duplicate content as I knew that content from this site was also indexed by Google on the sites.google.com domain. I had set up this site 3.5 years earlier with the free GBBO scheme which used Google Sites (I had used sites.google.com before) and had previously seen the content from the seolondonsurrey.co.uk domain indexed also on sites.google.com . Which one had been indexed first?
I've worked on a site with the Unnatural Link Penalty (not as a result of my work - I was only engaged after the penalty was in place -which 2 other "SEO experts" were not able to identify). This penalty from Google has now been lifted. Based on this experience I was quite sure that there were no issues with my inbound links. So it was (in my expert analysis) a Panda issue.
So I went to Webmaster Tools and used the Remove URLs tool (https://support.google.com/webmasters/answer/59819?hl=en) to remove the sites.google.com duplicate content from the Google index.
Around 4 days later the site had climbed up to 22nd for this key phrase with 6 pages indexed. This suggested I was on the right path at least. The day after that, this site was back at 3rd with 3/4 pages indexed. As they say, "job was a good 'un"!
Lessons Learnt / Questions Remaining
1. Install Google Analytics as soon as you create a new site. This will help you diagnose these kind of issues and give you historical data not available via Webmaster Tools.
2. Google Webmaster Guidelines are the 'Bible / laws of the land' in terms of internet search in the UK. This is your first port of call to help you diagnose the cause of these kind of issues.
3. Was a site (that was indexed first I would presume) penalised here? Was it the fact that the clone content was on google.com that made Google "assume" this site was the clone rather than the cloned?
4. I now track the position of the site for this key phrase for free over time with a free account on semrush.com.
5. There are multiple problems with GBBO sites built with sites.google.com, but I am getting the money's worth for the cost.
6. Always make a list of the site settings / Webmaster Tools changes you make including the date. This can help you work out if something you changed caused an issue.
Free tools below to help you diagnose a ranking drop on Google: http://www.seolondonsurrey.co.uk/blog/thebestfreepenguinunnaturallinkpenaltydiagnosisrecoverytools