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The output probably has backslashes like this: \r\n. These are end-of-line ("EOL") characters, roughly termed "carriage return" and "new line." They probably come from a PC file or document, since Unix uses only one EOL, the \n.
You should store them if they are meaningful in the context of the data and if your application needs them. Otherwise you can trim() them off. It is possible to remove them from the interior of a data string, but it's a little more involved, and it's less likely that you would want to make a change in the middle of a data string.
These EOL characters interact with real_escape_string() functions because they contain backslashes that have programmatic meaning (just like escaped apostrophes). The MySQLi engine strips backslashes automatically, with the understanding that it expects to receive escaped data, and store exact representations of the data.
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