miRNA: 3'- -CGGgAGCAUCA---GCACGCGUA----GGCUCU- -5'
miRNA: 3'- -CGGGAgCaUCAGcACGCGUaGGCUCU- -5'
miRNA: 3'- -CG-GGAGCaucAGCaCGCGUAGGCUCU- -5'
miRNA: 3'- -CGGGAGCaUCAGCa---CGCG------UAGGCUCU- -5'
miRNA: 3'- -CGGGAGCAUCAGCACGCGUAGGCUCU- -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 | |||||||
| 33589 | 5' | -55.7 | NC_007605.1 | + | 90284 | 0.67 | 0.918733 |
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Target: 5'- gGCUgUUGUGGUuucCGUGUGCGUcgugCCGGGGc -3' miRNA: 3'- -CGGgAGCAUCA---GCACGCGUA----GGCUCU- -5' |
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| 33589 | 5' | -55.7 | NC_007605.1 | + | 158627 | 0.67 | 0.900911 |
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Target: 5'- uGCUCUgG-GGUC-UGCGCA-CCGAGAc -3' miRNA: 3'- -CGGGAgCaUCAGcACGCGUaGGCUCU- -5' |
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| 33589 | 5' | -55.7 | NC_007605.1 | + | 159455 | 0.68 | 0.881057 |
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Target: 5'- uGCuCCUUGcgcUUGaGCGCGUCCGAGAg -3' miRNA: 3'- -CG-GGAGCaucAGCaCGCGUAGGCUCU- -5' |
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| 33589 | 5' | -55.7 | NC_007605.1 | + | 153893 | 0.74 | 0.567355 |
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Target: 5'- gGCCCUCGgGGUUGagggGCGCccaggcGUCCGGGGa -3' miRNA: 3'- -CGGGAGCaUCAGCa---CGCG------UAGGCUCU- -5' |
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| 33589 | 5' | -55.7 | NC_007605.1 | + | 134850 | 1.11 | 0.002941 |
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Target: 5'- gGCCCUCGUAGUCGUGCGCAUCCGAGAg -3' miRNA: 3'- -CGGGAGCAUCAGCACGCGUAGGCUCU- -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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