miRNA: 3'- -UCCCUGU-----------GGUGGGGc-CAUcAGCCAUc -5'
miRNA: 3'- -UCCCUGUGGUGGGGC-CaUCAG-CCauc -5'
miRNA: 3'- -UCCCUGUGGUGGg---GCCaUCAGCCauc -5'
miRNA: 3'- -UCCCUGUGGUGGGGCCAUCAGCCAUC- -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 | |||||||
| 22447 | 3' | -58.4 | NC_005062.1 | + | 5712 | 0.66 | 0.167136 |
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Target: 5'- aAGGGACGaaccaugcuguCCGCCCCucGUAcUCGGUGa -3' miRNA: 3'- -UCCCUGU-----------GGUGGGGc-CAUcAGCCAUc -5' |
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| 22447 | 3' | -58.4 | NC_005062.1 | + | 7218 | 0.7 | 0.084774 |
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Target: 5'- uAGGGAUACCACUCCGaG-AGUCaGGa-- -3' miRNA: 3'- -UCCCUGUGGUGGGGC-CaUCAG-CCauc -5' |
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| 22447 | 3' | -58.4 | NC_005062.1 | + | 4695 | 0.72 | 0.05979 |
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Target: 5'- uGGGGACACCGCCagguCGG-AGUUGGc-- -3' miRNA: 3'- -UCCCUGUGGUGGg---GCCaUCAGCCauc -5' |
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| 22447 | 3' | -58.4 | NC_005062.1 | + | 2778 | 1.09 | 4.8e-05 |
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Target: 5'- cAGGGACACCACCCCGGUAGUCGGUAGg -3' miRNA: 3'- -UCCCUGUGGUGGGGCCAUCAGCCAUC- -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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