Did Tom feel sorry that he didn't tell about Muff?
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Tom was filled with sorrow and guilt over his neglect in telling the truth about Doctor Robinson's murderer.
This was worse than a thousand whippings, and Tom's heart was sorer now than his body. He cried, he pleaded for forgiveness, promised to reform over and over again, and then received his dismissal, feeling that he had won but an imperfect forgiveness and established but a feeble confidence.
The Adventures of Tom Sawyer/ Chapter 10