miRNA: 3'- cGUCGGACUGUGGCAG-----CCCGAGc---AGU- -5'
miRNA: 3'- -CGUCGGa----CUGUGGCAGCcCGaGCAGU- -5'
miRNA: 3'- -CGUCGG-ACUGUGG---CAGC---------CCGAGCAGu -5'
miRNA: 3'- -CGU-CGGACUGUGGCaGCC-CGa---GCAGU- -5'
miRNA: 3'- -CGUCGGACUGUGGCAGCCCGAGCAGU- -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 | |||||||
| 22963 | 3' | -58.4 | NC_005137.2 | + | 98372 | 0.66 | 0.796672 |
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Target: 5'- cCGGUUUGGCGCCGUCgcgacGGGCUUuuuaUCAa -3' miRNA: 3'- cGUCGGACUGUGGCAG-----CCCGAGc---AGU- -5' |
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| 22963 | 3' | -58.4 | NC_005137.2 | + | 51690 | 0.66 | 0.787676 |
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Target: 5'- cGCAGUUguugcGGCACCGUUGcGCgCGUCGg -3' miRNA: 3'- -CGUCGGa----CUGUGGCAGCcCGaGCAGU- -5' |
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| 22963 | 3' | -58.4 | NC_005137.2 | + | 104059 | 0.67 | 0.711506 |
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Target: 5'- uGUGGCCgUGGCGCCuucGUCGugcuuggccGGCUCGUUg -3' miRNA: 3'- -CGUCGG-ACUGUGG---CAGC---------CCGAGCAGu -5' |
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| 22963 | 3' | -58.4 | NC_005137.2 | + | 22413 | 0.71 | 0.492373 |
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Target: 5'- gGCGcGCCUGACGCUG-CGGaGCgucaCGUCGg -3' miRNA: 3'- -CGU-CGGACUGUGGCaGCC-CGa---GCAGU- -5' |
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| 22963 | 3' | -58.4 | NC_005137.2 | + | 109397 | 1.1 | 0.001302 |
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Target: 5'- uGCAGCCUGACACCGUCGGGCUCGUCAa -3' miRNA: 3'- -CGUCGGACUGUGGCAGCCCGAGCAGU- -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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