miRNA: 3'- -ACGUAGca-CUA-GUgUCUGGUCCGcug -5'
miRNA: 3'- aCGUAGCacuaGUGUCUGG-----------UCCGCUG- -5'
miRNA: 3'- aCG-UAGCacuagUGUCUGGUCCGCUG- -5'
miRNA: 3'- -ACGUAGCACUAGUGUCUGGUCCGCUG- -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 | |||||||
| 16685 | 5' | -53.9 | NC_004156.1 | + | 3743 | 0.66 | 0.984832 |
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Target: 5'- gUGCAUCuccGAUaCAgGGGCCAGGCu-- -3' miRNA: 3'- -ACGUAGca-CUA-GUgUCUGGUCCGcug -5' |
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| 16685 | 5' | -53.9 | NC_004156.1 | + | 83560 | 0.66 | 0.982994 |
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Target: 5'- gGCAUCGg---CGCAGAUUcuaacacuggaGGGCGAUg -3' miRNA: 3'- aCGUAGCacuaGUGUCUGG-----------UCCGCUG- -5' |
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| 16685 | 5' | -53.9 | NC_004156.1 | + | 136541 | 0.7 | 0.884197 |
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Target: 5'- aGCaAUCGg----ACAGACCGGGUGACg -3' miRNA: 3'- aCG-UAGCacuagUGUCUGGUCCGCUG- -5' |
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| 16685 | 5' | -53.9 | NC_004156.1 | + | 139928 | 1.09 | 0.006432 |
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Target: 5'- gUGCAUCGUGAUCACAGACCAGGCGACc -3' miRNA: 3'- -ACGUAGCACUAGUGUCUGGUCCGCUG- -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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