miRNA: 3'- guuuuCGu---GAAUGUc----ACCGCUAGUGG- -5'
miRNA: 3'- -GUuuUCGUGaa-UGUCACCGc-------UAGUGG- -5'
miRNA: 3'- gUUUu--CGUGaAUGUCACCGc--UAGUGG- -5'
miRNA: 3'- -GUUUUCGUGAAUGUCACCGCUAGUGG- -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 | |||||||
| 13529 | 5' | -47.1 | NC_003436.1 | + | 4555 | 0.66 | 0.926967 |
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Target: 5'- ----uGCuuuuCUUGCAuguguUGGUGAUCGCCa -3' miRNA: 3'- guuuuCGu---GAAUGUc----ACCGCUAGUGG- -5' |
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| 13529 | 5' | -47.1 | NC_003436.1 | + | 17251 | 0.68 | 0.873888 |
|
Target: 5'- gUAuuAGCAUgagACGGUGGCaacaaaucAUCACCu -3' miRNA: 3'- -GUuuUCGUGaa-UGUCACCGc-------UAGUGG- -5' |
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| 13529 | 5' | -47.1 | NC_003436.1 | + | 14669 | 0.69 | 0.826521 |
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Target: 5'- uGAGuuuGCAUaUGCGGUGGUugcAUCACCa -3' miRNA: 3'- gUUUu--CGUGaAUGUCACCGc--UAGUGG- -5' |
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| 13529 | 5' | -47.1 | NC_003436.1 | + | 4627 | 1.15 | 0.001192 |
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Target: 5'- aCAAAAGCACUUACAGUGGCGAUCACCa -3' miRNA: 3'- -GUUUUCGUGAAUGUCACCGCUAGUGG- -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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