miRNA: 3'- -GGUGGUCCCGA---GUAuACCGca--CCCGc -5'
miRNA: 3'- -GGugGuCCCGAGUauACCGCACCCGc -5'
miRNA: 3'- -GGUGGUCccg---AGUAUACCGCACCCGc -5'
miRNA: 3'- -GGUGGUCCCGAGUAUACCGCACCCGC- -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 | |||||||
| 31602 | 3' | -58 | NC_006875.1 | + | 2840 | 0.71 | 0.050129 |
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Target: 5'- aCCGCCAGGGCUggcUAUcUGGCagcgGGGUu -3' miRNA: 3'- -GGUGGUCCCGA---GUAuACCGca--CCCGc -5' |
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| 31602 | 3' | -58 | NC_006875.1 | + | 6317 | 0.75 | 0.023167 |
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Target: 5'- gCCugCcGGGUUCGc-UGGCGUGGGCc -3' miRNA: 3'- -GGugGuCCCGAGUauACCGCACCCGc -5' |
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| 31602 | 3' | -58 | NC_006875.1 | + | 3485 | 0.76 | 0.017088 |
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Target: 5'- uUCGCCGGauaccaUCAUGUGGCGUGGGCu -3' miRNA: 3'- -GGUGGUCccg---AGUAUACCGCACCCGc -5' |
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| 31602 | 3' | -58 | NC_006875.1 | + | 3421 | 1.1 | 2e-05 |
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Target: 5'- uCCACCAGGGCUCAUAUGGCGUGGGCGa -3' miRNA: 3'- -GGUGGUCCCGAGUAUACCGCACCCGC- -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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