miRNA: 3'- -AGgCUCCACCa-CUCG--UCGCagGUCCU- -5'
miRNA: 3'- agGCUCCACCACUCGu-------------CGCaGGu---CCU- -5'
miRNA: 3'- aGGCUCCA-CCACUCGuCGCaGGU-CCU- -5'
miRNA: 3'- -AGGCUCCACCACUCGUCGCAGGUCCU- -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 | |||||||
| 364 | 5' | -58.9 | AC_000011.1 | + | 23522 | 0.66 | 0.397092 |
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Target: 5'- gUCgGAGGUGGcgGGGCugGGCGg-CGGGGc -3' miRNA: 3'- -AGgCUCCACCa-CUCG--UCGCagGUCCU- -5' |
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| 364 | 5' | -58.9 | AC_000011.1 | + | 26824 | 0.68 | 0.292581 |
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Target: 5'- -aCGAGGUGGUGAGCucuucgcugggucuGCGaCCugacGGAg -3' miRNA: 3'- agGCUCCACCACUCGu-------------CGCaGGu---CCU- -5' |
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| 364 | 5' | -58.9 | AC_000011.1 | + | 20939 | 0.77 | 0.072994 |
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Target: 5'- gCCGAGGUcGGUGAGC-GCGcCCAuGGAc -3' miRNA: 3'- aGGCUCCA-CCACUCGuCGCaGGU-CCU- -5' |
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| 364 | 5' | -58.9 | AC_000011.1 | + | 15080 | 1.09 | 0.000247 |
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Target: 5'- gUCCGAGGUGGUGAGCAGCGUCCAGGAg -3' miRNA: 3'- -AGGCUCCACCACUCGUCGCAGGUCCU- -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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