miRNA: 3'- cucaAGCcGUCGUUGCACUUuCGCac -5'
miRNA: 3'- cucaAGCCGUCGUUgcaCUUUCGCAc -5'
miRNA: 3'- -CUCaaGCC-GUCGUU---------GCACU--UUCGCAC- -5'
miRNA: 3'- cucaAGCCGUCGUUGCaCUU--------UCGCAC- -5'
miRNA: 3'- -CUCAAGCCGUCGUUGCACUUUCGCAC- -5'
Results 1 - 5 of 5 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 | |||||||
| 27685 | 5' | -51.2 | NC_005882.1 | + | 30668 | 0.66 | 0.815586 |
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Target: 5'- ---gUCGaCGGCAACGUGAAcGCGa- -3' miRNA: 3'- cucaAGCcGUCGUUGCACUUuCGCac -5' |
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| 27685 | 5' | -51.2 | NC_005882.1 | + | 18300 | 0.66 | 0.784753 |
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Target: 5'- ---gUCGGCGGCAA---GAAGGCGUa -3' miRNA: 3'- cucaAGCCGUCGUUgcaCUUUCGCAc -5' |
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| 27685 | 5' | -51.2 | NC_005882.1 | + | 26948 | 0.67 | 0.763272 |
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Target: 5'- cGGGcgCGGcCGGCAAguucgcggcCGUGAucGGGCGUGc -3' miRNA: 3'- -CUCaaGCC-GUCGUU---------GCACU--UUCGCAC- -5' |
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| 27685 | 5' | -51.2 | NC_005882.1 | + | 10674 | 0.73 | 0.414243 |
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Target: 5'- ---gUCGGCAGCGGCG-GAGgcggcggcAGCGUGu -3' miRNA: 3'- cucaAGCCGUCGUUGCaCUU--------UCGCAC- -5' |
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| 27685 | 5' | -51.2 | NC_005882.1 | + | 27444 | 1.1 | 0.001192 |
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Target: 5'- cGAGUUCGGCAGCAACGUGAAAGCGUGg -3' miRNA: 3'- -CUCAAGCCGUCGUUGCACUUUCGCAC- -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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