miRNA: 3'- gCCACUGgUAGU-----AUUCu--CCgGGAUGu -5'
miRNA: 3'- -GCCac--UGGUAGUau---UCUCCGGG--AUGU- -5'
miRNA: 3'- gCCaCUGGuaguauUCUCCGGGAUGU- -5'
miRNA: 3'- gCCACUGGUAgUAUUCU-----CCG-------GGAUGU- -5'
miRNA: 3'- gCCACuGGUAGUAU--UCUCCGGGaugu -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 | |||||||
| 30652 | 3' | -52.3 | NC_006549.1 | + | 80941 | 0.66 | 0.979071 |
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Target: 5'- aGGUGGCgGUCAguguuUGAGucuGGgCCUGCc -3' miRNA: 3'- gCCACUGgUAGU-----AUUCu--CCgGGAUGu -5' |
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| 30652 | 3' | -52.3 | NC_006549.1 | + | 36631 | 0.66 | 0.976643 |
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Target: 5'- cCGGcagaACCAUCAaaaccGGAGGCCCcgUACAu -3' miRNA: 3'- -GCCac--UGGUAGUau---UCUCCGGG--AUGU- -5' |
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| 30652 | 3' | -52.3 | NC_006549.1 | + | 101924 | 0.67 | 0.961346 |
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Target: 5'- uGGaGACCc-----GGGGGCCCUGCAg -3' miRNA: 3'- gCCaCUGGuaguauUCUCCGGGAUGU- -5' |
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| 30652 | 3' | -52.3 | NC_006549.1 | + | 66639 | 0.68 | 0.929462 |
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Target: 5'- uGGUGGCCAUgGUGGGAagcuuGGUgaaccauCCUACGg -3' miRNA: 3'- gCCACUGGUAgUAUUCU-----CCG-------GGAUGU- -5' |
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| 30652 | 3' | -52.3 | NC_006549.1 | + | 64417 | 0.78 | 0.477232 |
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Target: 5'- uGGUGuCCAUCAUGacGGAGGCCCc--- -3' miRNA: 3'- gCCACuGGUAGUAU--UCUCCGGGaugu -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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