SynMap analysis of Alligator (x-axis) to Chicken (y-axis). Alligator contigs ordered and oriented according to their Syntenic Path to chicken chromosomes, and syntenic gene pairs are colored by their synonymous mutation rates. Note that nearly the entire chicken genome is covered by alligator contigs, but there are many alligator contigs that are not syntenically mapped to chicken. These probably contain few genes to extract a syntenic signal (minimum of three genes required by this analyis) or are made up of only non-genic (repetitive) sequences.
Links to data are in the "Links and Downloads" section of the results. Links of interest:
SynMap syntenic gene pairs: "Final syntenic gene-set output with GEvo links"
Information on parsing the file: [SynMap#Results]
Mapping of alligator contigs to chicken: "Syntenic Path Assembly mapping"
vs. 
