1. A computer-based system for generating comparison output data indicating differences in annotations in electronic files, comprising: a memory storing instructions; and a processor configured to execute the instructions to: identify a first annotation in a first electronic file; create a first index for the first annotation, the first index including a plurality of words, pixels, rows, columns, or coordinates in the first electronic file; create a second index for a second electronic file different than the first electronic file, the second index including a plurality of words, pixels, rows, columns, or coordinates in the second electronic file; compare the first index with the second index to determine whether the second electronic file contains a matching annotation having words, pixels, rows, columns, or coordinates corresponding to the first annotation; generate, based on the comparison, a matrix that identifies matches between the words, pixels, rows, columns, or coordinates in the first index of the first annotation and the second index of a second annotation in the second electronic file; determine, based on the matrix of the comparison, whether the words, pixels, rows, columns, or coordinates in the first index of the first annotation are present in the second index of the second annotation; and create, based on the determination, comparison output data including information for displaying a redline version of characters in the first annotation to indicate changes between the first annotation and the second annotation, wherein the processor inserts into the comparison output data a first hidden character marking a beginning of the redline version and a second hidden character marking an end of the redline version.