miRNA: 3'- -UCCCGUC-----------UGGGUUGGUGCaGGUGacu -5'
miRNA: 3'- uCCCGUCUGGGUug-GUGCa---------GGUGacu -5'
miRNA: 3'- uCCCGucUGGGUUGGUgCAgGUGACU- -5'
miRNA: 3'- -UCCCGUCUGGGUUGGUGCAGGUGACU- -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 | |||||||
| 13613 | 5' | -57.3 | NC_003460.1 | + | 5567 | 0.67 | 0.091241 |
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Target: 5'- uGGGGCAGcgcggacagccACCUGGCCACGaUCACg-- -3' miRNA: 3'- -UCCCGUC-----------UGGGUUGGUGCaGGUGacu -5' |
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| 13613 | 5' | -57.3 | NC_003460.1 | + | 2267 | 0.68 | 0.074525 |
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Target: 5'- cGGGCAGGCCCGugaCGCGgugaagggugCCGCg-- -3' miRNA: 3'- uCCCGUCUGGGUug-GUGCa---------GGUGacu -5' |
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| 13613 | 5' | -57.3 | NC_003460.1 | + | 2283 | 0.69 | 0.051212 |
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Target: 5'- cGGGCcuGCCCGAUCAgGU-CGCUGAu -3' miRNA: 3'- uCCCGucUGGGUUGGUgCAgGUGACU- -5' |
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| 13613 | 5' | -57.3 | NC_003460.1 | + | 2130 | 1.08 | 2e-05 |
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Target: 5'- cAGGGCAGACCCAACCACGUCCACUGAu -3' miRNA: 3'- -UCCCGUCUGGGUUGGUGCAGGUGACU- -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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