miRNA: 3'- -UAGGUa----AUGUAUUGucGUUGACUaug -5'
miRNA: 3'- uAGGUaAUGUAUu-GUCGUUGACUA--UG- -5'
miRNA: 3'- uaGGUAAUGUau----UGUCGU---------UGACUAUG- -5'
miRNA: 3'- -UAGGUA-------AUGUaUUGUCGUUGACua-UG- -5'
miRNA: 3'- -UAGGUAAUGUAUUGUCGUUGACUAUG- -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 | |||||||
| 4321 | 5' | -43.2 | NC_001720.1 | + | 5564 | 0.66 | 0.998847 |
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Target: 5'- gGUCCGgagugUACAUGACc-CAGCUGAa-- -3' miRNA: 3'- -UAGGUa----AUGUAUUGucGUUGACUaug -5' |
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| 4321 | 5' | -43.2 | NC_001720.1 | + | 35063 | 0.67 | 0.997274 |
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Target: 5'- uUCCG-UGCAUGcuCAGUAGCUGGUcaGCc -3' miRNA: 3'- uAGGUaAUGUAUu-GUCGUUGACUA--UG- -5' |
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| 4321 | 5' | -43.2 | NC_001720.1 | + | 1504 | 0.68 | 0.993137 |
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Target: 5'- -aCUGUUACAgagcguACAGCAgggccucuuGCUGGUGCu -3' miRNA: 3'- uaGGUAAUGUau----UGUCGU---------UGACUAUG- -5' |
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| 4321 | 5' | -43.2 | NC_001720.1 | + | 12958 | 0.69 | 0.982552 |
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Target: 5'- gAUCCGUaccucaaUACG-AGCAGCAGCUGucgGCc -3' miRNA: 3'- -UAGGUA-------AUGUaUUGUCGUUGACua-UG- -5' |
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| 4321 | 5' | -43.2 | NC_001720.1 | + | 2317 | 1.1 | 0.00984 |
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Target: 5'- uAUCCAUUACAUAACAGCAACUGAUACa -3' miRNA: 3'- -UAGGUAAUGUAUUGUCGUUGACUAUG- -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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