miRNA: 3'- cUCGGCGAUa------------GGCUUGAUGgUGGcuu -5'
miRNA: 3'- cuCGGCGAUAGGcUUGAUGGUGgcuu -5'
miRNA: 3'- -CUCG--GCGAUAgGCUUGAUGGUG--GCUU- -5'
miRNA: 3'- cucGGCGAUAGGCUUGAU---GGUGGCUU- -5'
miRNA: 3'- -CUCGGCGAUAGGCUUGAUGGUGGCUU- -5'
Results 1 - 5 of 5 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 | |||||||
| 22526 | 3' | -54.6 | NC_005083.1 | + | 118992 | 0.66 | 0.968548 |
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Target: 5'- cAGCCGCUAcaucugcgccuagCCGAGCUACaGCCa-- -3' miRNA: 3'- cUCGGCGAUa------------GGCUUGAUGgUGGcuu -5' |
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| 22526 | 3' | -54.6 | NC_005083.1 | + | 87482 | 0.67 | 0.94841 |
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Target: 5'- -cGUCGCUAUCUaGACUACCACg--- -3' miRNA: 3'- cuCGGCGAUAGGcUUGAUGGUGgcuu -5' |
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| 22526 | 3' | -54.6 | NC_005083.1 | + | 10577 | 0.69 | 0.913202 |
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Target: 5'- uGAGCacCGCUGUgCGGGCUGCUACaaCGAAu -3' miRNA: 3'- -CUCG--GCGAUAgGCUUGAUGGUG--GCUU- -5' |
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| 22526 | 3' | -54.6 | NC_005083.1 | + | 177193 | 0.7 | 0.859201 |
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Target: 5'- --aUCGCUGUCUGAACUGaguUCGCCGAGc -3' miRNA: 3'- cucGGCGAUAGGCUUGAU---GGUGGCUU- -5' |
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| 22526 | 3' | -54.6 | NC_005083.1 | + | 56785 | 1.06 | 0.009282 |
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Target: 5'- uGAGCCGCUAUCCGAACUACCACCGAAu -3' miRNA: 3'- -CUCGGCGAUAGGCUUGAUGGUGGCUU- -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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