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The murders took place near a medical college in Prayagraj when the two were apparently handcuffed.
The Commission also revealed that three of the deceased were minors at the time of death.
Shah had in his speech on Sunday also mentioned about a "mysterious death related to the gold smuggling case", to which Vijayan said the matter will be probed if the Home Minister provided more details about such an incident.
Opposition leader Ramesh Chennithala has demanded a high-level inquiry into Velmurugan's killing.
Judge Sharma ruled the prosecution has failed to put forth any 'documentary and substantive evidence' to suggest or establish the alleged conspiracy.
Sohrabuddin Sheikh, a suspected gangster with terror links, was shot dead on November 26, 2005 while he was in custody of the Gujarat Police in an alleged fake encounter.
The soldiers killed five of the youths in a fake encounter, branding them as ULFA militants.