miRNA: 3'- ccCGGAAa--AGCGCUa--UCAGU------ACGUGa -5'
miRNA: 3'- -CC-CGga--AAAGCGCUaUCAGUACGUGa -5'
miRNA: 3'- cCCGGAAAAGCGCUAU-CAGUAcgUGA- -5'
miRNA: 3'- -CCCGGaaaAGCGCUa-----UCAGUACGUGa -5'
miRNA: 3'- -CCCGGAAAAGCGCUAUCAGUACGUGA- -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 | |||||||
| 4151 | 5' | -50.1 | NC_001664.1 | + | 11775 | 0.67 | 0.993252 |
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Target: 5'- -uGCCUUaucUCGCGAgcgAGUCGcauggaUGCACa -3' miRNA: 3'- ccCGGAAa--AGCGCUa--UCAGU------ACGUGa -5' |
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| 4151 | 5' | -50.1 | NC_001664.1 | + | 44510 | 0.67 | 0.993252 |
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Target: 5'- uGGcGCauugUUUCGUGAaAGUUAUGUACg -3' miRNA: 3'- -CC-CGga--AAAGCGCUaUCAGUACGUGa -5' |
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| 4151 | 5' | -50.1 | NC_001664.1 | + | 32553 | 0.67 | 0.991059 |
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Target: 5'- uGGCCUUUUUGUGAUAcGUUAUugACUa -3' miRNA: 3'- cCCGGAAAAGCGCUAU-CAGUAcgUGA- -5' |
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| 4151 | 5' | -50.1 | NC_001664.1 | + | 143496 | 0.68 | 0.98102 |
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Target: 5'- cGGGUCc--UUGUGAguuagcGGUCAUGCACg -3' miRNA: 3'- -CCCGGaaaAGCGCUa-----UCAGUACGUGa -5' |
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| 4151 | 5' | -50.1 | NC_001664.1 | + | 77818 | 1.1 | 0.00925 |
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Target: 5'- uGGGCCUUUUCGCGAUAGUCAUGCACUc -3' miRNA: 3'- -CCCGGAAAAGCGCUAUCAGUACGUGA- -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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