miRNA: 3'- -UGGuuCGGCUUUAGGCcgAGC-AGGAA- -5'
miRNA: 3'- -UGGuuCGGCUuu-AGGCCGAGCAGgaa -5'
miRNA: 3'- -UGGU-------------UCGGCUU----UAGGCCGaGCAGGaa -5'
miRNA: 3'- -UGGUUCGGCUUUAGGCCGAGCAGGAA- -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 | |||||||
| 12095 | 5' | -55.3 | NC_003309.1 | + | 5698 | 0.66 | 0.687819 |
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Target: 5'- gACUuuGCCGAGAUCCGuuUCGaUCUUUu -3' miRNA: 3'- -UGGuuCGGCUUUAGGCcgAGC-AGGAA- -5' |
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| 12095 | 5' | -55.3 | NC_003309.1 | + | 39847 | 0.69 | 0.500824 |
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Target: 5'- gGCCcuGCUGAuccUCUGGCUCGUCg-- -3' miRNA: 3'- -UGGuuCGGCUuu-AGGCCGAGCAGgaa -5' |
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| 12095 | 5' | -55.3 | NC_003309.1 | + | 25374 | 0.73 | 0.291468 |
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Target: 5'- aGCCGucggcgucggucuGGCCGGAuauuGUCCGGC-CGUCCg- -3' miRNA: 3'- -UGGU-------------UCGGCUU----UAGGCCGaGCAGGaa -5' |
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| 12095 | 5' | -55.3 | NC_003309.1 | + | 221 | 1.06 | 0.001418 |
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Target: 5'- gACCAAGCCGAAAUCCGGCUCGUCCUUa -3' miRNA: 3'- -UGGUUCGGCUUUAGGCCGAGCAGGAA- -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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