miRNA: 3'- cguuaCGACUu-----GCCCCAGUAGAa--CGu -5'
miRNA: 3'- -CGUUa----CGACuu--GCCCCa--GUAGAa--CGU- -5'
miRNA: 3'- -CGUuaCGACuuGCCCCAGUAga-ACGu -5'
miRNA: 3'- -CGUUACGACUUGCCCCAGUAGAACGU- -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 | |||||||
| 723 | 5' | -50.5 | AC_000019.1 | + | 6475 | 0.66 | 0.840489 |
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Target: 5'- ----aGCUGAugggagUGGGGUCAUCUaagGCc -3' miRNA: 3'- cguuaCGACUu-----GCCCCAGUAGAa--CGu -5' |
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| 723 | 5' | -50.5 | AC_000019.1 | + | 10726 | 0.66 | 0.840489 |
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Target: 5'- uGCGAgggggGCUGuuguUGGGGgcgCAUCUgucGCAg -3' miRNA: 3'- -CGUUa----CGACuu--GCCCCa--GUAGAa--CGU- -5' |
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| 723 | 5' | -50.5 | AC_000019.1 | + | 13151 | 0.69 | 0.653792 |
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Target: 5'- uGCAucGCUGucCGGGGUCAUgggUGCu -3' miRNA: 3'- -CGUuaCGACuuGCCCCAGUAga-ACGu -5' |
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| 723 | 5' | -50.5 | AC_000019.1 | + | 22171 | 1.12 | 0.00103 |
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Target: 5'- gGCAAUGCUGAACGGGGUCAUCUUGCAg -3' miRNA: 3'- -CGUUACGACUUGCCCCAGUAGAACGU- -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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