miRNA: 3'- -CGAGC-----UUGCCGa---ACG---UCACGUCGCUu -5'
miRNA: 3'- -CGAGCu-UGCCGaaCGUCa------CGUCGCUu -5'
miRNA: 3'- -CGAGCu----UGCCGAACGUCACGUcGCUU- -5'
miRNA: 3'- -CGAGC-UUGCCGaaCGucaCGUCGCUU- -5'
miRNA: 3'- -CGAGCUUGCCGAACGUCACGUCGCUU- -5'
Results 21 - 25 of 25 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 | |||||||
| 28001 | 3' | -54.7 | NC_005887.1 | + | 10989 | 0.72 | 0.276132 |
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Target: 5'- cGCUCGucgagGAUGGCguggUGCucgGGUGCGGCGGu -3' miRNA: 3'- -CGAGC-----UUGCCGa---ACG---UCACGUCGCUu -5' |
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| 28001 | 3' | -54.7 | NC_005887.1 | + | 14697 | 0.73 | 0.261863 |
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Target: 5'- gGCUCGucGCGGCggGCGGgccgggcGCGGCGAu -3' miRNA: 3'- -CGAGCu-UGCCGaaCGUCa------CGUCGCUu -5' |
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| 28001 | 3' | -54.7 | NC_005887.1 | + | 37452 | 0.73 | 0.248199 |
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Target: 5'- cGCUUGccugcGCGGUUUGCAGUGCGcCGGAu -3' miRNA: 3'- -CGAGCu----UGCCGAACGUCACGUcGCUU- -5' |
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| 28001 | 3' | -54.7 | NC_005887.1 | + | 11300 | 0.74 | 0.235131 |
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Target: 5'- uGCUCGcAGCGGCcgGCucgGCAGCGAGc -3' miRNA: 3'- -CGAGC-UUGCCGaaCGucaCGUCGCUU- -5' |
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| 28001 | 3' | -54.7 | NC_005887.1 | + | 40232 | 1.08 | 0.000743 |
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Target: 5'- aGCUCGAACGGCUUGCAGUGCAGCGAAu -3' miRNA: 3'- -CGAGCUUGCCGAACGUCACGUCGCUU- -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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