miRNA: 3'- cgGCUGCCgu--CUAUGGAgUUGUAGGG- -5'
miRNA: 3'- -CG-GCUGCCG----------UCUAUGGaGUUGUa--GGG- -5'
miRNA: 3'- -CGGC---------------UGCCGUCUAUGGA---------GUugUAgGG- -5'
miRNA: 3'- -CGGCUGCCGUCUAUGGAGUUGUAGGG- -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 | |||||||
| 33657 | 5' | -52.7 | NC_011450.1 | + | 4498 | 0.66 | 0.307737 |
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Target: 5'- -aUGACGGacuuGGUGCCU-GGCAUCCUc -3' miRNA: 3'- cgGCUGCCgu--CUAUGGAgUUGUAGGG- -5' |
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| 33657 | 5' | -52.7 | NC_011450.1 | + | 3468 | 0.68 | 0.242831 |
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Target: 5'- gGCaCGAUGGUaaucugaccuGGGUGCC-CAACGgugCCCc -3' miRNA: 3'- -CG-GCUGCCG----------UCUAUGGaGUUGUa--GGG- -5' |
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| 33657 | 5' | -52.7 | NC_011450.1 | + | 2240 | 0.7 | 0.164041 |
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Target: 5'- uGCCGucggcaaccaguucaACGGCGGGUGCCUucugguggcCAugGUgCCa -3' miRNA: 3'- -CGGC---------------UGCCGUCUAUGGA---------GUugUAgGG- -5' |
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| 33657 | 5' | -52.7 | NC_011450.1 | + | 2257 | 1.15 | 0.000045 |
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Target: 5'- uGCCGACGGCAGAUACCUCAACAUCCCa -3' miRNA: 3'- -CGGCUGCCGUCUAUGGAGUUGUAGGG- -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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