Table 1 Recognition of 3′-ends and 3′-end stem-loops of L1 and Alu sequences.

Class 1	Class 2	AUC			Accuracy			Precision			Recall
Class 1	Class 2	50 bp	SL1	SL2	50 bp	SL1	SL2	50 bp	SL1	SL2	50 bp	SL1	SL2
L1 3′ UTR	shuffled	0.99	0.97	0.98	0.98	0.93	0.94	0.98	0.96	0.98	0.98	0.90	0.90
L1 3′ UTR	L1 5′ UTR	1.00	0.99	0.99	0.99	0.96	0.98	0.99	0.96	0.98	0.99	0.97	0.98
L1 5′ UTR + L1 3′ UTR	shuffled	0.99	0.98	0.98	0.97	0.93	0.94	0.97	0.96	0.99	0.96	0.90	0.89
Alu 3′-end	shuffled	0.99	0.99	0.99	0.99	0.97	0.98	0.99	0.98	0.99	0.99	0.96	0.97
Alu 3′-end	L1 3′ UTR	0.99	0.99	0.99	0.99	0.99	0.99	0.99	0.99	0.99	0.99	0.99	0.99
Alu 3′-end + L1 3′ UTR	shuffled	0.99	0.98	0.99	0.98	0.95	0.97	0.98	0.97	0.99	0.98	0.93	0.94

Note: 50 bp designates models for recognizing 50 bp 3′-ends, SL1 designates models for recognizing 3′-end stem-loops with sequence-based models, and SL2 designates models for recognizing 3′-end stem-loops with structure-based models.

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