miRNA: 3'- gUUGaaCGCGACAagGUCA------UGGUGGU- -5'
miRNA: 3'- gUUGaACGC-GACAaGGUC-AUGGUGGU- -5'
miRNA: 3'- -GUUGAaCGCGAC----AAGGUCAUGGUGgu -5'
miRNA: 3'- -GUUGAACGCGACAAGGUCAUGGUGGU- -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 | |||||||
| 22476 | 5' | -51.5 | NC_005066.1 | + | 80036 | 0.66 | 0.988491 |
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Target: 5'- uGACc-GCGCUGUg-CAGUaaaugcGCCACCAu -3' miRNA: 3'- gUUGaaCGCGACAagGUCA------UGGUGGU- -5' |
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| 22476 | 5' | -51.5 | NC_005066.1 | + | 88942 | 0.66 | 0.985217 |
|
Target: 5'- aGGC-UGCGaCUGUcCCGGcUGCUACCGu -3' miRNA: 3'- gUUGaACGC-GACAaGGUC-AUGGUGGU- -5' |
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| 22476 | 5' | -51.5 | NC_005066.1 | + | 141237 | 0.69 | 0.944759 |
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Target: 5'- gUAGCUgGUGCUGcggcUUCCAGUGCUGCg- -3' miRNA: 3'- -GUUGAaCGCGAC----AAGGUCAUGGUGgu -5' |
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| 22476 | 5' | -51.5 | NC_005066.1 | + | 148011 | 1.1 | 0.006739 |
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Target: 5'- aCAACUUGCGCUGUUCCAGUACCACCAa -3' miRNA: 3'- -GUUGAACGCGACAAGGUCAUGGUGGU- -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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