miRNA: 3'- -GGGGUGUCGa--------------GUG-GGCa-----UCGuCCUCU- -5'
miRNA: 3'- -GGGGUG---UCGagUGGg--CAUCGUCCUCU- -5'
miRNA: 3'- -GGGgUGUCGAGUGGGCauCGUCCUCU- -5'
miRNA: 3'- -GGGGUGUCGAGUGGGCAUCGUCCUCU- -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 | |||||||
| 8597 | 5' | -57.7 | NC_002198.2 | + | 2420 | 0.66 | 0.091981 |
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Target: 5'- gCCCCGCGGUgaucaugggaauaccCACgCCGgcgucgAGCuGGAGAg -3' miRNA: 3'- -GGGGUGUCGa--------------GUG-GGCa-----UCGuCCUCU- -5' |
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| 8597 | 5' | -57.7 | NC_002198.2 | + | 363 | 0.68 | 0.070065 |
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Target: 5'- aCCCCACcugAGUagAUCaggGUAGUAGGAGAu -3' miRNA: 3'- -GGGGUG---UCGagUGGg--CAUCGUCCUCU- -5' |
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| 8597 | 5' | -57.7 | NC_002198.2 | + | 1048 | 0.71 | 0.035394 |
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Target: 5'- gCUUgAUGGCUCGCCCGguGCGGGGGGa -3' miRNA: 3'- -GGGgUGUCGAGUGGGCauCGUCCUCU- -5' |
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| 8597 | 5' | -57.7 | NC_002198.2 | + | 374 | 1.11 | 1.2e-05 |
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Target: 5'- cCCCCACAGCUCACCCGUAGCAGGAGAa -3' miRNA: 3'- -GGGGUGUCGAGUGGGCAUCGUCCUCU- -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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