miRNA: 3'- aGGGGUu-----UUUAUUUGgCCg---UGCGGag -5'
miRNA: 3'- -AGGGgUUUUUA----UUUGGCCGUGCGGag -5'
miRNA: 3'- aGGGG--UUUUUa--UUUGGCCGUg-----CGGAG- -5'
miRNA: 3'- agGGGUUUUUaUUUGGCCGUGCGgag -5'
miRNA: 3'- -AGGGGUUUUUAUUUGGCCGUGCGGAG- -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 | |||||||
| 21803 | 3' | -50.4 | NC_004827.1 | + | 9916 | 0.66 | 0.861485 |
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Target: 5'- gCCCCAuacuuuAAGUAAGCgGGacugACGCCg- -3' miRNA: 3'- aGGGGUu-----UUUAUUUGgCCg---UGCGGag -5' |
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| 21803 | 3' | -50.4 | NC_004827.1 | + | 40225 | 0.66 | 0.861485 |
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Target: 5'- aUUUUgAAAAAUuaucAAACCGGCACGCUa- -3' miRNA: 3'- -AGGGgUUUUUA----UUUGGCCGUGCGGag -5' |
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| 21803 | 3' | -50.4 | NC_004827.1 | + | 3612 | 0.67 | 0.852659 |
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Target: 5'- aCCUUauGAAAGgcgGAACCGGCAagcauaGCUUCa -3' miRNA: 3'- aGGGG--UUUUUa--UUUGGCCGUg-----CGGAG- -5' |
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| 21803 | 3' | -50.4 | NC_004827.1 | + | 5689 | 0.67 | 0.824662 |
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Target: 5'- -aUCCAGAAAcAAACUGGCGCGUa-- -3' miRNA: 3'- agGGGUUUUUaUUUGGCCGUGCGgag -5' |
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| 21803 | 3' | -50.4 | NC_004827.1 | + | 40335 | 1.12 | 0.001375 |
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Target: 5'- gUCCCCAAAAAUAAACCGGCACGCCUCa -3' miRNA: 3'- -AGGGGUUUUUAUUUGGCCGUGCGGAG- -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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