miRNA: 3'- aAAGG--UUGCUCCg----GACCGCUGA--------UCUG- -5'
miRNA: 3'- aaAGGuUGCUCCGgACCGCuGA--UCUG- -5'
miRNA: 3'- aaaGGUUGCU-CC-GGACCGCu--GAUCUg -5'
miRNA: 3'- -AAAGGUUGCUCCGGACCGCUGAUCUG- -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 | |||||||
| 1188 | 3' | -54.9 | NC_001132.2 | + | 25372 | 0.67 | 0.869214 |
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Target: 5'- aUUCUgaGGCGAGGaggauCUGGCGGCUcucucacaAGGCg -3' miRNA: 3'- aAAGG--UUGCUCCg----GACCGCUGA--------UCUG- -5' |
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| 1188 | 3' | -54.9 | NC_001132.2 | + | 2419 | 0.68 | 0.861554 |
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Target: 5'- -gUCCcGCGGGGUaUGGCGuCUccGGACa -3' miRNA: 3'- aaAGGuUGCUCCGgACCGCuGA--UCUG- -5' |
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| 1188 | 3' | -54.9 | NC_001132.2 | + | 126945 | 0.69 | 0.802307 |
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Target: 5'- --aUCGACGAcGGaCCUGGCGuguCUAGAa -3' miRNA: 3'- aaaGGUUGCU-CC-GGACCGCu--GAUCUg -5' |
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| 1188 | 3' | -54.9 | NC_001132.2 | + | 156614 | 1.06 | 0.00481 |
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Target: 5'- gUUUCCAACGAGGCCUGGCGACUAGACc -3' miRNA: 3'- -AAAGGUUGCUCCGGACCGCUGAUCUG- -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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