Indels Alignment. Alignment of a fragment of Rag1 based on A) Venkatesh and colleagues  and B) the alignment used in this work. Numbers on the alignment are according to . Red boxes indicate synapomorphic indels according to . The green box indicates the indel identified as synapomorphic by  occurring in a highly variable region and not recovered as synapomorphic according to our alignment. Sequences of A) are as in . Sequences in B) (see [Additional file 1] for species names) Human: M29474; Rabbit: M77666; Chicken: M58530; Sparrow: AF143738; Alligator: AF143724 AY125022; Gharial: AF143725; Testudines AY687922; Caecilian EF551566; Salamander AY583351; Frog 1: L19324; Frog 2: AY323762; Frog 3: AY323771; Frog 4: AY571659; Fugu: AY700363; Zebrafish: U71093; Trout: U15663; Mullet: AY308783; Bowfin: AY430199; Chondrostei: AY430198; Shark: U62645. Names and species used in the Figure have been choosing as in . We added to the alignment in B) only a few sequences which help to show the higher variability of certain indels regions compared to the A) alignment.