Tcoffee, Muscle and GLprobs differences

Fig.1 Position 534

Here every program aligns two Leucines (207 and 519).

Fig.2 Position 580

Here every program aligns Serine(248) and Glutamine(558).

Fig.3 Position 678

Here Tcoffee aligns two Serines (250 and 656), Muscle - Serine(250) and Leucine.

Generally speaking, GLprobs has several extremely long indels, when Muscle and Tcoffee have shorter ones, but more of them. Taking into account the significant difference in length between the two aligned sequences, it would make sense to preserve only the most important (conservative) sites. GLprobs is the only one that has reasonable aligned blocks closer to the center of the sequence. At the same time, Muscle and Tcoffee have smaller blocks closer to both ends. It seems to me that the most probable alignment is GLprobs.