miRNA: 3'- -CGAGAUGCG-----GCAa-GGCGGUC-GCAGCc -5'
miRNA: 3'- -CGAGaUGC---GGCA--AGGCGGUCGC---AGCc -5'
miRNA: 3'- cGAGAUGCGgCaAGGCG---GUCGC---AGCC- -5'
miRNA: 3'- -CGAGAUGCGGCAAGGCGGUCGCAGCC- -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 | |||||||
| 32002 | 5' | -57 | NC_006949.1 | + | 45301 | 0.66 | 0.621007 |
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Target: 5'- uGCUUUGCGCgaugaUGUcgCCGCUGGuCGUCGu -3' miRNA: 3'- -CGAGAUGCG-----GCAa-GGCGGUC-GCAGCc -5' |
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| 32002 | 5' | -57 | NC_006949.1 | + | 22704 | 0.67 | 0.577796 |
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Target: 5'- uGCUCaACGguuCCGUggUUCGCCAGCGcguUCGa -3' miRNA: 3'- -CGAGaUGC---GGCA--AGGCGGUCGC---AGCc -5' |
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| 32002 | 5' | -57 | NC_006949.1 | + | 28473 | 0.68 | 0.463862 |
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Target: 5'- aCUCUGCGCgGgUCCGCguuCGGUGuuaUCGGg -3' miRNA: 3'- cGAGAUGCGgCaAGGCG---GUCGC---AGCC- -5' |
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| 32002 | 5' | -57 | NC_006949.1 | + | 28513 | 1.12 | 0.000427 |
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Target: 5'- aGCUCUACGCCGUUCCGCCAGCGUCGGu -3' miRNA: 3'- -CGAGAUGCGGCAAGGCGGUCGCAGCC- -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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