miRNA: 3'- -UGU--UCGCUUGGUGc-CGGGUG------------ACGAAa -5'
miRNA: 3'- -UGUUCgCUUGGUGCCGG---------------GUGACgaaa -5'
miRNA: 3'- -UGUUCGCu-----UGGUGcCGGG-UGACGaaa -5'
miRNA: 3'- -UGUUCGCUUGGUGCCGGGUGACGAAA- -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 | |||||||
| 13586 | 3' | -55.4 | NC_003444.1 | + | 29286 | 0.67 | 0.47037 |
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Target: 5'- cACAacGGUGAACCACacGCCCACucugacguaacuUGCUUg -3' miRNA: 3'- -UGU--UCGCUUGGUGc-CGGGUG------------ACGAAa -5' |
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| 13586 | 3' | -55.4 | NC_003444.1 | + | 15265 | 0.67 | 0.453609 |
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Target: 5'- cGCAAGgGGGCCACGGCUgccagcggguauaugCGCUGg--- -3' miRNA: 3'- -UGUUCgCUUGGUGCCGG---------------GUGACgaaa -5' |
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| 13586 | 3' | -55.4 | NC_003444.1 | + | 28172 | 0.69 | 0.38063 |
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Target: 5'- uGCAGGCGugguguACCACuGCCCaACUGUa-- -3' miRNA: 3'- -UGUUCGCu-----UGGUGcCGGG-UGACGaaa -5' |
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| 13586 | 3' | -55.4 | NC_003444.1 | + | 34056 | 1.05 | 0.000789 |
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Target: 5'- cACAAGCGAACCACGGCCCACUGCUUUa -3' miRNA: 3'- -UGUUCGCUUGGUGCCGGGUGACGAAA- -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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