Question
QUESTION: Is there a modern electronic timer that has a pause between cycles so the indexer can cycle? (The indexer works grate)
ANSWER: Im not familiar with an indexer.  What is it?

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QUESTION: Indexer has six ports, one solonoid feeds the indexer IT INDEXES from one port to another with a Mechanical timer..

Answer
There are some irrigation controllers that offer a delay feature between cycles.  We use Rainmaster controllers, and they do, but they are also very expensive.  You would be more likely to find this feature in the commercial type controllers than the homeowner type.  You may want to start by looking at Rainbird and Irritrol.  If there is an irrigation specialty store in your area, they would be a good resource.