miRNA: 3'- -UCCGUGAaCGGG-GGu-CAGCAGGAGCu -5'
miRNA: 3'- -UCCGUGa--------------ACGGGGGUCaGCA--GGAGCu -5'
miRNA: 3'- -UCCGUGaaCGGGGG-----------UCAGCAGGAGCu -5'
miRNA: 3'- ucCGUGaa----CGGGGGUCaGCAGGAGCU- -5'
miRNA: 3'- -UCCGUgAACGGGGGUCAGCAGGAGCU- -5'
Results 21 - 25 of 25 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 | |||||||
| 25678 | 5' | -59 | NC_005337.1 | + | 15211 | 0.71 | 0.448737 |
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Target: 5'- cAGGCGCUcGUUCuCCucGUCGUCCUCGu -3' miRNA: 3'- -UCCGUGAaCGGG-GGu-CAGCAGGAGCu -5' |
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| 25678 | 5' | -59 | NC_005337.1 | + | 24208 | 0.72 | 0.422945 |
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Target: 5'- gAGGCGCgcgucgagguggagcUGCCCCCGGcCGUggCCUCGc -3' miRNA: 3'- -UCCGUGa--------------ACGGGGGUCaGCA--GGAGCu -5' |
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| 25678 | 5' | -59 | NC_005337.1 | + | 79785 | 0.72 | 0.388045 |
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Target: 5'- cAGGCGCggGUCCUUcacggugccgaGGUCGUCCUCGu -3' miRNA: 3'- -UCCGUGaaCGGGGG-----------UCAGCAGGAGCu -5' |
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| 25678 | 5' | -59 | NC_005337.1 | + | 59377 | 0.74 | 0.318365 |
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Target: 5'- -cGCGCcaucacGCCCCCGG-CGUCCUCGGu -3' miRNA: 3'- ucCGUGaa----CGGGGGUCaGCAGGAGCU- -5' |
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| 25678 | 5' | -59 | NC_005337.1 | + | 40913 | 0.96 | 0.010328 |
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Target: 5'- cAGGCA-UUGCCCCCAGUCGUCCUCGAc -3' miRNA: 3'- -UCCGUgAACGGGGGUCAGCAGGAGCU- -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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