miRNA: 3'- -GGAGGGGGCGACGUUUGUUUGAGGCC- -5'
miRNA: 3'- gGAGGGGGCGACguUUGUUugA---GGCC- -5'
miRNA: 3'- -GGAGGGGGCGACGUu----UGUUUGAgGCc -5'
miRNA: 3'- -GGAgGGGG-------------CGACGUUUGU----UUGAGGcc -5'
Results 1 - 4 of 4 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand | Start Position | R_P_ratio# |
P value
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| Predicted miRNA align pattern | |||||||
| 997 | 3' | -54.1 | NC_000903.1 | + | 2854 | 1.12 | 0.000096 |
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Target: 5'- cCCUCCCCCGCUGCAAACAAACUCCGGu -3' miRNA: 3'- -GGAGGGGGCGACGUUUGUUUGAGGCC- -5' |
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| 997 | 3' | -54.1 | NC_000903.1 | + | 4737 | 0.74 | 0.100724 |
|
Target: 5'- aCUCCCCUGCUGguGAUGGugUgcaUCGGg -3' miRNA: 3'- gGAGGGGGCGACguUUGUUugA---GGCC- -5' |
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| 997 | 3' | -54.1 | NC_000903.1 | + | 10865 | 0.72 | 0.137974 |
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Target: 5'- aCCUUCUCCGUUGCGucuguACAGGCUgCGu -3' miRNA: 3'- -GGAGGGGGCGACGUu----UGUUUGAgGCc -5' |
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| 997 | 3' | -54.1 | NC_000903.1 | + | 840 | 0.66 | 0.351309 |
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Target: 5'- cCCUgUCCCguugauucucauaGCUGCGAGCGcccuGGCUCCu- -3' miRNA: 3'- -GGAgGGGG-------------CGACGUUUGU----UUGAGGcc -5' |
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Note:
When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.
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