README.md

1. Software packages requirements
   The python code is included in ipynb files. The code is independent from operating systems. The user should install python3. Relevant packages that are required include jupyter notebook, numpy, scipy and matplotlib.
   The authors have tested the code on MacOS, using python 3.8.5, jupyter core 4.6.3, jupyter notebook 6.1.3, scipy 1.5.2, numpy 1.19.1, and matplotlib 3.3.1.
   There is no requirement for other non-standard hardware.

2. Installation guide
   Users can use pip command to install the above mentioned python packages, for example,
   pip install jupyter
pip install scipy, etc.
   The installation typically won't last longer than half an hour.

3. Demo
   All the code in the notebook can be executed immediately. We provided demon runs with outputs in separate cells in ipynb files. Demon runs are labeled with hashtags # demo example.

4. Simple guide for usage
   To start the ipynb files, on linux/MacOS, users can work from command line terminal. First, navigate to the directory where the ipynb files are located. Then, on command line type "jupyter notebook" and select the relevant ipynb file.
   On Windows, users can also launch from the terminal.

5. Experimental data for 4-bit patterns and 3x3 patterns, together with the code for data processing, are located in the folder experiment_data.

6. We included the annotated plasmids sequences in the directory plasmids_sequences_annotations.

7. We added a pdf file to show the fluorescence histograms in the experiment_data folder.