Context. The Interface Region Imaging Spectrograph (IRIS) with its high spatial and temporal resolution facilitates exceptional plasma diagnostics of solar chromospheric and coronal activity during magnetic reconnection.Aims. The aim of this work is to study the fine structure and dynamics of the plasma at a jet base forming a mini-flare between two emerging magnetic fluxes (EMFs) observed with IRIS and the Solar Dynamics Observatory instruments.Methods. We proceed to a spatio-temporal analysis of IRIS spectra observed in the spectral ranges of Mg II, C II, and Si IV ions. Doppler velocities from Mg II lines were computed using a cloud model technique.Results. Strong asymmetric Mg II and C II line profiles with extended blue wings observed at the reconnection site (jet base) are interpreted by the presence of two chromospheric temperature clouds: one explosive cloud with blueshifts at 290 km s−1 and one cloud with smaller Doppler shift (around 36 km s−1). Simultaneously at the same location (jet base), strong emission of several transition region lines (e.g. O IV and Si IV), emission of the Mg II triplet lines, and absorption of identified chromospheric lines in Si IV broad profiles have been observed and analysed.Conclusions. Such observations of IRIS line and continuum emissions allow us to propose a stratification model for the white light, mini-flare atmosphere with multiple layers of different temperatures along the line of sight in a reconnection current sheet. It is the first time that we could quantify the fast speed (possibly Alfvénic flows) of cool clouds ejected perpendicularly to the jet direction via the cloud model technique. We conjecture that the ejected clouds come from plasma which was trapped between the two EMFs before reconnection or be caused by chromospheric-temperature (cool) upflow material similar to a surge during reconnection.