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Definition of overlapping alignments. Two alignments are output by FOLDALIGN and PLAST-ncRNA. The FOLDALIGN alignment is located between positions S1 and E1 on Seq1 and between S2 and E2 on Seq2. The PLAST-ncRNA alignment is located between positions S3 and E3 on Seq1 and between S4 and E4 on Seq2. N1 is the overlapping region on Seq1 and N2 is the overlapping region on Seq2.
