miRNA: 3'- uuGUGAUgcCCACGCUCA-CAUGAc--CG- -5'
miRNA: 3'- uuGUGAugCCCaCGCUCa--------CAUGaCCG- -5'
miRNA: 3'- uugUGAUGCCCa---CGcuCACAUGACCg -5'
miRNA: 3'- -UUGUGAUGCCCACGCUCACAUGACCG- -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 | |||||||
| 9420 | 5' | -53.7 | NC_002531.1 | + | 95264 | 0.66 | 0.927937 |
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Target: 5'- -uCACUGaaGGUGCGAGUaGUGCUccaGCu -3' miRNA: 3'- uuGUGAUgcCCACGCUCA-CAUGAc--CG- -5' |
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| 9420 | 5' | -53.7 | NC_002531.1 | + | 38054 | 0.67 | 0.922358 |
|
Target: 5'- -cCACUugGGG-GCGAGcggugggaaGUGCgGGCc -3' miRNA: 3'- uuGUGAugCCCaCGCUCa--------CAUGaCCG- -5' |
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| 9420 | 5' | -53.7 | NC_002531.1 | + | 29185 | 0.7 | 0.752655 |
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Target: 5'- --aACUACGGGggaaGCuuGUGUACUGGa -3' miRNA: 3'- uugUGAUGCCCa---CGcuCACAUGACCg -5' |
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| 9420 | 5' | -53.7 | NC_002531.1 | + | 29307 | 1.1 | 0.002961 |
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Target: 5'- aAACACUACGGGUGCGAGUGUACUGGCa -3' miRNA: 3'- -UUGUGAUGCCCACGCUCACAUGACCG- -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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