miRNA: 3'- -GUGG---UGACACCA--UGaAGGGUCUcugc -5'
miRNA: 3'- -GUGG-UGACACcaUGAAGGGUCuCUGc -5'
miRNA: 3'- gUGGUGacaCC----AUGAAGGGUCuCUGC- -5'
miRNA: 3'- gUGG--UGaCACCAUGAa-------GGGUCUCUGC- -5'
miRNA: 3'- -GUGGUGACACCAUGAAGGGUCUCUGC- -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 | |||||||
| 654 | 5' | -53.2 | AC_000017.1 | + | 30110 | 0.66 | 0.713909 |
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Target: 5'- aCACCuuaACUGUGGUuuGC-UCCCAGAc--- -3' miRNA: 3'- -GUGG---UGACACCA--UGaAGGGUCUcugc -5' |
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| 654 | 5' | -53.2 | AC_000017.1 | + | 25630 | 0.66 | 0.679953 |
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Target: 5'- cCACCuGCUGUGc-GCUUCCUAGcGACu -3' miRNA: 3'- -GUGG-UGACACcaUGAAGGGUCuCUGc -5' |
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| 654 | 5' | -53.2 | AC_000017.1 | + | 26202 | 0.67 | 0.634036 |
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Target: 5'- aGCCGCg--GGcccuUGCUUCCCAG-GAUGg -3' miRNA: 3'- gUGGUGacaCC----AUGAAGGGUCuCUGC- -5' |
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| 654 | 5' | -53.2 | AC_000017.1 | + | 4292 | 0.72 | 0.350642 |
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Target: 5'- aGCUcuGCaGUGGUGCUaccuccacCCCAGAGACGg -3' miRNA: 3'- gUGG--UGaCACCAUGAa-------GGGUCUCUGC- -5' |
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| 654 | 5' | -53.2 | AC_000017.1 | + | 27454 | 1.08 | 0.001093 |
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Target: 5'- cCACCACUGUGGUACUUCCCAGAGACGc -3' miRNA: 3'- -GUGGUGACACCAUGAAGGGUCUCUGC- -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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