miRNA: 3'- -GAUUCUc-CAAAuUUGGGg--UGGUUGGG- -5'
miRNA: 3'- gauuCUCCAAAUUUGGGG----UGGU---UGGG- -5'
miRNA: 3'- -GAUuCUCCaaauuUG-GGGUGGUUGGG- -5'
miRNA: 3'- -GAUUCUCCAAAUUUGGGGUGGUUGGG- -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 | |||||||
| 9551 | 3' | -47.5 | NC_002551.1 | + | 5186 | 0.67 | 0.560543 |
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Target: 5'- cCUGAGAcaGUUU-GGCCUgaaACCGACCCg -3' miRNA: 3'- -GAUUCUc-CAAAuUUGGGg--UGGUUGGG- -5' |
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| 9551 | 3' | -47.5 | NC_002551.1 | + | 104 | 0.7 | 0.389618 |
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Target: 5'- ---uGGGGUUUAAACCUCuuagGCCGaagGCCUg -3' miRNA: 3'- gauuCUCCAAAUUUGGGG----UGGU---UGGG- -5' |
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| 9551 | 3' | -47.5 | NC_002551.1 | + | 4190 | 0.72 | 0.281541 |
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Target: 5'- aCUAcGAGGagu--GCaCUCACCAACCCg -3' miRNA: 3'- -GAUuCUCCaaauuUG-GGGUGGUUGGG- -5' |
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| 9551 | 3' | -47.5 | NC_002551.1 | + | 77 | 1.15 | 0.000195 |
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Target: 5'- cCUAAGAGGUUUAAACCCCACCAACCCa -3' miRNA: 3'- -GAUUCUCCAAAUUUGGGGUGGUUGGG- -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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