miRNA: 3'- -GGUCUaUUUACCGauc---ACCguCGGUu -5'
miRNA: 3'- ggUCUa----UUUACCG-AUCACCGU--CGGUu -5'
miRNA: 3'- gGUCUAuUUACCGaUCA-----------CCGUCGGUU- -5'
miRNA: 3'- -GGUCUAUUUACCGAUCACCGUCGGUU- -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 | |||||||
| 22836 | 3' | -50.7 | NC_005135.1 | + | 88465 | 0.68 | 0.973566 |
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Target: 5'- gCCAGGcAAAUGGCggaaacUGGguGCCGu -3' miRNA: 3'- -GGUCUaUUUACCGauc---ACCguCGGUu -5' |
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| 22836 | 3' | -50.7 | NC_005135.1 | + | 138402 | 0.68 | 0.967511 |
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Target: 5'- -uGGAaugcgAAAUGGCaUGGUGGCAgaGCCAu -3' miRNA: 3'- ggUCUa----UUUACCG-AUCACCGU--CGGUu -5' |
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| 22836 | 3' | -50.7 | NC_005135.1 | + | 96626 | 0.69 | 0.948231 |
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Target: 5'- gCGGAU-AAUGGCcGGUaacagacuuauGGCGGCCAAc -3' miRNA: 3'- gGUCUAuUUACCGaUCA-----------CCGUCGGUU- -5' |
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| 22836 | 3' | -50.7 | NC_005135.1 | + | 72287 | 1.09 | 0.007821 |
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Target: 5'- aCCAGAUAAAUGGCUAGUGGCAGCCAAg -3' miRNA: 3'- -GGUCUAUUUACCGAUCACCGUCGGUU- -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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