Improved version of this other Gist (https://gist.github.com/glS512/3dd2cfcb1357b92f3703), after the suggestions of @vnp on codereview.SE (http://codereview.stackexchange.com/a/117095/61165)

findCoincidences_5byte_afterVNP.py

#!/usr/bin/python3
import struct
import os
import time

start_time = time.time()
# ============ CONSTANTS TO (OPTIONALLY) SET =============
WINDOW_SIZE = 100
INPUT_FILE_NAME = 'timetags5byte.bin'
# OUTPUT_FILE_NAME = 'output.txt'

# ======== CODE TO READ AND PARSE 5 BYTE BINARY FILE =========================
# process data in INPUT_FILE_NAME and print results in OUTPUT_FILE_NAME
with open(INPUT_FILE_NAME, 'rb') as input_file:
        # open(OUTPUT_FILE_NAME, 'w') as output_file:

    # number of bytes found in every file produced when writing the binary file
    initial_offset = 40
    # number of bytes occupied by each timetag
    timetag_size = 5

    # each timetag is stored in 5 bytes. The first 4 bytes contain the
    # timestamp, with the first byte being the least significant one, and last
    # byte the most significant one

    def print_channels(channels):
        print('found the fourfold coincidence ', end = '')
        for channel in channels:
            print('{0: >5}'.format(channel), end = '')
        print('')

    input_file.seek(initial_offset)

    output_channels = []
    timetag = input_file.read(timetag_size)
    timetagStruct = struct.Struct('LB')
    timestamp, channel = timetagStruct.unpack(timetag)
    # timestamp, channel = struct.unpack('LB', timetag)

    triggering_timestamp = timestamp
    channels = [channel]
    try:
        while True:
            timetag = input_file.read(timetag_size)
            timestamp, channel = timetagStruct.unpack(timetag)
            # timestamp, channel = struct.unpack('LB', timetag)
            if 0 < timestamp - triggering_timestamp < WINDOW_SIZE:
                channels.append(channel)
            else:
                if len(channels) == 4:
                    print_channels(channels)
                    output_channels.append(channels)
                channels = [channel]
                triggering_timestamp = timestamp
    except struct.error:
        pass

    if len(channels) == 4:
        print_channels(channels)
        output_channels.append(channels)

print('Finished in '+ str(time.time() - start_time))