miRNA: 3'- -AAUAGUUUCGACucuGCUCUU----UUGGG- -5'
miRNA: 3'- aAUAGUuUCGACUCUg-----CUC---UUUUGGG- -5'
miRNA: 3'- aaUAGuuuCGaCUCUGCUCUuu---UGGG- -5'
miRNA: 3'- -AAUAGUUUCGACUCUGCUCUUUUGGG- -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 | |||||||
| 17434 | 5' | -45.2 | NC_004452.3 | + | 1420 | 0.67 | 0.362118 |
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Target: 5'- aUUGUCGAAGCUGu--UGGGGAugcaAAUCCa -3' miRNA: 3'- -AAUAGUUUCGACucuGCUCUU----UUGGG- -5' |
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| 17434 | 5' | -45.2 | NC_004452.3 | + | 3580 | 0.69 | 0.287704 |
|
Target: 5'- cUAUCAuAGCUGGGGgccccgGAGugcGAAACCCu -3' miRNA: 3'- aAUAGUuUCGACUCUg-----CUC---UUUUGGG- -5' |
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| 17434 | 5' | -45.2 | NC_004452.3 | + | 465 | 0.73 | 0.157358 |
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Target: 5'- -cGUCuuuGCcGAGACGAGAugguuACCCa -3' miRNA: 3'- aaUAGuuuCGaCUCUGCUCUuu---UGGG- -5' |
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| 17434 | 5' | -45.2 | NC_004452.3 | + | 2157 | 1.12 | 0.000128 |
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Target: 5'- cUUAUCAAAGCUGAGACGAGAAAACCCa -3' miRNA: 3'- -AAUAGUUUCGACUCUGCUCUUUUGGG- -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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