Single-shot time-of-flight spectra for Coulomb explosion of N2 and I2 molecules have been recorded at the Free Electron LASer in Hamburg (FLASH) and have been analysed using a partial covariance mapping technique. The partial covariance analysis unravels a detailed picture of all significant Coulomb explosion pathways, extending up to the N4+–N5+ channel for nitrogen and up to the I8+–I9+ channel for iodine. The observation of the latter channel is unexpected if only sequential ionization processes from the ground state ions are considered. The maximum kinetic energy release extracted from the covariance maps for each dissociation channel shows that Coulomb explosion of nitrogen molecules proceeds much faster than that of the iodine. The N2 ionization dynamics is modelled using classical trajectory simulations in good agreement with the outcome of the experiments. The results suggest that covariance mapping of the Coulomb explosion can be used to measure the intensity and pulse duration of free-electron lasers.