miRNA: 3'- aguUUCUUC--GUGGGAGUUU-UGGUUCc -5'
miRNA: 3'- aGUUUCuUCg---UGGGAGUU------------UUGGUUCC- -5'
miRNA: 3'- aguuuCuuCGugGGAGUUUUGgUUCC- -5'
miRNA: 3'- -AGUUUCUUCGUGGGAGUUUUGGUUCC- -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 | |||||||
| 32410 | 5' | -46 | NC_007069.1 | + | 11393 | 0.67 | 0.791314 |
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Target: 5'- --uGAGAAGgaUAUCCUCAAGuACCAAGa -3' miRNA: 3'- aguUUCUUC--GUGGGAGUUU-UGGUUCc -5' |
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| 32410 | 5' | -46 | NC_007069.1 | + | 40 | 0.71 | 0.549861 |
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Target: 5'- aCAAAGcAGaaaaACCCUCAGgggaggccgccgGACCGGGGu -3' miRNA: 3'- aGUUUCuUCg---UGGGAGUU------------UUGGUUCC- -5' |
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| 32410 | 5' | -46 | NC_007069.1 | + | 4373 | 0.71 | 0.549861 |
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Target: 5'- ----uGggGCugCCUCGAAAC-AAGGu -3' miRNA: 3'- aguuuCuuCGugGGAGUUUUGgUUCC- -5' |
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| 32410 | 5' | -46 | NC_007069.1 | + | 3259 | 1.13 | 0.000939 |
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Target: 5'- cUCAAAGAAGCACCCUCAAAACCAAGGu -3' miRNA: 3'- -AGUUUCUUCGUGGGAGUUUUGGUUCC- -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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