Mainline CSIs are those in which a conserved insert or deletion is shared by several major phyla, but absent from other phyla.
Figure 2 shows an example of 5aa CSI found in a conserved region that is commonly present in the species belonging to phyla X, Y and Z, but it is absent in other phyla (A, B and C). This signature indicates a specific relationship of taxa X, Y and Z and also A, B and C. Based upon the presence or absence of such an indel, in out-group species (viz. Archaea), it can be inferred whether the indel is an insert or a deletion, and which of these two groups A, B, C or X, Y, Z is ancestral.
Mainline CSIs have been used in the past to determine the phylogenetic relationship of a number of bacterial phyla. The large CSI of about 150-180 amino acids within a conserved region of Gyrase B (between amino acids 529-751), is commonly shared between various Pseudomonadota, Chlamydiota, Planctomycetota and Aquificota species. This CSI is absent in other ancestral bacterial phyla as well as Archaea. Similarly a large CSI of about 100 amino acids in RpoB homologs (between amino acids 919-1058) is present in various species belonging to Pseudomonadota, Bacteroidota, Chlorobiota, Chlamydiota, Planctomycetota, and Aquificota. This CSI is absent in other ancestral bacterial phyla as well as Archaea. In both cases one can infer that the groups lacking the CSI are ancestral.