miRNA: 3'- -UCACuGGGCUgAGCUACcCUGa----GCUu -5'
miRNA: 3'- ucaCUGGGCUGaGCU----------ACCCUGa---GCUu -5'
miRNA: 3'- ucaCUGGG--CUGAGCUaCCC--UGAGCUu -5'
miRNA: 3'- -UCACUGGGCUGAGCUACCCUGAGCUU- -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 | |||||||
| 22058 | 5' | -55.9 | NC_004927.1 | + | 60783 | 0.66 | 0.774671 |
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Target: 5'- cGGUGuCCCGAgUCGAUGcGACgacugCGGc -3' miRNA: 3'- -UCACuGGGCUgAGCUACcCUGa----GCUu -5' |
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| 22058 | 5' | -55.9 | NC_004927.1 | + | 57550 | 0.66 | 0.744647 |
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Target: 5'- --cGGCCCGAC-CGAgcagaagaugUGGGACguagCGAc -3' miRNA: 3'- ucaCUGGGCUGaGCU----------ACCCUGa---GCUu -5' |
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| 22058 | 5' | -55.9 | NC_004927.1 | + | 61208 | 0.67 | 0.703144 |
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Target: 5'- --cGGCCCgcGACUCGGaGGGcuACUCGAc -3' miRNA: 3'- ucaCUGGG--CUGAGCUaCCC--UGAGCUu -5' |
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| 22058 | 5' | -55.9 | NC_004927.1 | + | 32345 | 1.06 | 0.002137 |
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Target: 5'- gAGUGACCCGACUCGAUGGGACUCGAAc -3' miRNA: 3'- -UCACUGGGCUGAGCUACCCUGAGCUU- -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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