miRNA: 3'- -UGGAGUAGuGGUG-C-CGC-GCGUUGGUg -5'
miRNA: 3'- -UGGAGUA-GUGGug-CCG-------------CgCGUUGGUG- -5'
miRNA: 3'- -UGGAGUa-GUGGUGCCGCgCGuuGGUG- -5'
miRNA: 3'- -UGGAGUAGUGGUGCCGCGCGUUGGUG- -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 | |||||||
| 4260 | 3' | -57.3 | NC_001710.1 | + | 7123 | 0.69 | 0.086299 |
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Target: 5'- aGCCUUAUUuCCACaGaGCGaCGCGACCAg -3' miRNA: 3'- -UGGAGUAGuGGUG-C-CGC-GCGUUGGUg -5' |
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| 4260 | 3' | -57.3 | NC_001710.1 | + | 6146 | 0.7 | 0.078012 |
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Target: 5'- uACCUCAUcCACCuuaGGCucccuguugaccaGgGCAACCACu -3' miRNA: 3'- -UGGAGUA-GUGGug-CCG-------------CgCGUUGGUG- -5' |
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| 4260 | 3' | -57.3 | NC_001710.1 | + | 2340 | 0.75 | 0.029946 |
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Target: 5'- gACCUCAccUGCCACGGCG-GCuuCCACa -3' miRNA: 3'- -UGGAGUa-GUGGUGCCGCgCGuuGGUG- -5' |
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| 4260 | 3' | -57.3 | NC_001710.1 | + | 3185 | 1.09 | 0.000036 |
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Target: 5'- aACCUCAUCACCACGGCGCGCAACCACg -3' miRNA: 3'- -UGGAGUAGUGGUGCCGCGCGUUGGUG- -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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