miRNA: 3'- -UAUCGCUuCG-GUCUuaaCAUCCUCgg -5'
miRNA: 3'- -UAUCG--CUUCGGUCuuAAcA--------UCCUCGG- -5'
miRNA: 3'- -UAUCGCUUCGG---UC------------UUAAC-----AUCCUCGG- -5'
miRNA: 3'- -UAUCGCUUCGGUCUUAACAUCCUCGG- -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 | |||||||
| 33261 | 3' | -50 | NC_007603.1 | + | 43644 | 0.66 | 0.895837 |
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Target: 5'- aAUAGCGAcGCgCAGGg--GUGGGAGg- -3' miRNA: 3'- -UAUCGCUuCG-GUCUuaaCAUCCUCgg -5' |
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| 33261 | 3' | -50 | NC_007603.1 | + | 39853 | 0.67 | 0.836076 |
|
Target: 5'- uAUGGCcuGAGGCCGGggUUuUagccuccaGGGAGUCg -3' miRNA: 3'- -UAUCG--CUUCGGUCuuAAcA--------UCCUCGG- -5' |
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| 33261 | 3' | -50 | NC_007603.1 | + | 24785 | 0.68 | 0.796343 |
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Target: 5'- gGUAGUGAAGCUgauAGuuucgcuucucaGGUUGguuuuUAGGAGCCa -3' miRNA: 3'- -UAUCGCUUCGG---UC------------UUAAC-----AUCCUCGG- -5' |
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| 33261 | 3' | -50 | NC_007603.1 | + | 9056 | 1.11 | 0.001813 |
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Target: 5'- uAUAGCGAAGCCAGAAUUGUAGGAGCCu -3' miRNA: 3'- -UAUCGCUUCGGUCUUAACAUCCUCGG- -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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