miRNA: 3'- agGGCUGCUACG---------CGUAGGa------GGCGGUa -5'
miRNA: 3'- -AGGGCUGCUACGCGUAGGAGGCGGUA- -5'
miRNA: 3'- aGGGCUGCuACG----CGUAGGaGGCGGua -5'
miRNA: 3'- -AGGGCUGC--UACGcGUaGGAgGCGGUa -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 |
| Predicted miRNA align pattern | |||||||
| 22396 | 5' | -59.1 | NC_005056.1 | + | 1696 | 0.68 | 0.246339 |
|
Target: 5'- -aCCGGCGGUGCcaguaccacGCAUCCggcgcugUCGCCAc -3' miRNA: 3'- agGGCUGCUACG---------CGUAGGa------GGCGGUa -5' |
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| 22396 | 5' | -59.1 | NC_005056.1 | + | 3147 | 1.05 | 0.000367 |
|
Target: 5'- uUCCCGACGAUGCGCAUCCUCCGCCAUc -3' miRNA: 3'- -AGGGCUGCUACGCGUAGGAGGCGGUA- -5' |
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| 22396 | 5' | -59.1 | NC_005056.1 | + | 5949 | 0.66 | 0.351677 |
|
Target: 5'- aCCUGACGcUGUaccgGCGUCCaCCGCCc- -3' miRNA: 3'- aGGGCUGCuACG----CGUAGGaGGCGGua -5' |
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| 22396 | 5' | -59.1 | NC_005056.1 | + | 8168 | 0.66 | 0.360316 |
|
Target: 5'- uUCCUGACGcaGUGC-CA-CCUgCGCCAg -3' miRNA: 3'- -AGGGCUGC--UACGcGUaGGAgGCGGUa -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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