miRNA: 3'- uaGUGUAGUUCG------------CCGAACua-----GACGUA- -5'
miRNA: 3'- -UAGUGU----AGUUCGC--CGAACUAGACGua -5'
miRNA: 3'- -UAGUGUAG-----UUCGCCGAacUAGACGua -5'
miRNA: 3'- -UAGUGUAGUUCGCCGAACUAGACGUA- -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 | |||||||
| 32278 | 5' | -51.2 | NC_007023.1 | + | 62738 | 0.66 | 0.989155 |
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Target: 5'- -aCGCAUCAAGCcuguauaauaacGGCUUGcuguuuaCUGCAUa -3' miRNA: 3'- uaGUGUAGUUCG------------CCGAACua-----GACGUA- -5' |
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| 32278 | 5' | -51.2 | NC_007023.1 | + | 162476 | 0.66 | 0.987639 |
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Target: 5'- gAUCACAccguUCAGGUGuuGUUUGAUCUGUu- -3' miRNA: 3'- -UAGUGU----AGUUCGC--CGAACUAGACGua -5' |
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| 32278 | 5' | -51.2 | NC_007023.1 | + | 110077 | 0.68 | 0.954457 |
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Target: 5'- cAUCGCGUCcuguaGAGCGGCU--AUCUGUg- -3' miRNA: 3'- -UAGUGUAG-----UUCGCCGAacUAGACGua -5' |
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| 32278 | 5' | -51.2 | NC_007023.1 | + | 109744 | 1.04 | 0.015118 |
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Target: 5'- gAUCACAUCAAGCGGCUUGAUCUGCAUc -3' miRNA: 3'- -UAGUGUAGUUCGCCGAACUAGACGUA- -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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