miRNA: 3'- -CCCACCugCCCU----C-CUG----------UCUCC--UGUCU- -5'
miRNA: 3'- -CC-CAC-----CUgCCCUCCUgUCUCCUGucu -5'
miRNA: 3'- cCCaCCugCCCU--CC--UGUCUCCuGUCU- -5'
miRNA: 3'- -CCC--ACCUgCC----CUCCU-GUCUCCUGuCU- -5'
Results 21 - 24 of 24 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 | |||||||
| 28345 | 5' | -57.8 | NC_005946.1 | + | 88134 | 0.67 | 0.720506 |
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Target: 5'- aGGGUGGugGGGAccaaGaGACccucugccguGGAGGuuGCGGGc -3' miRNA: 3'- -CCCACCugCCCU----C-CUG----------UCUCC--UGUCU- -5' |
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| 28345 | 5' | -57.8 | NC_005946.1 | + | 58212 | 0.67 | 0.720506 |
|
Target: 5'- uGGaGUGuuuguGAgGGGAGGAgAGAGGACc-- -3' miRNA: 3'- -CC-CAC-----CUgCCCUCCUgUCUCCUGucu -5' |
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| 28345 | 5' | -57.8 | NC_005946.1 | + | 13662 | 0.66 | 0.749936 |
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Target: 5'- aGGaGGugGGGAucGGcuGCGGAGGcCAGGa -3' miRNA: 3'- cCCaCCugCCCU--CC--UGUCUCCuGUCU- -5' |
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| 28345 | 5' | -57.8 | NC_005946.1 | + | 85253 | 0.66 | 0.75955 |
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Target: 5'- gGGGcuUGGAgGGagcuGGGGGcCAGGGGACuGAg -3' miRNA: 3'- -CCC--ACCUgCC----CUCCU-GUCUCCUGuCU- -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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