miRNA: 3'- guAGGUGUaGCc-GAAGCGACUGCUGG- -5'
miRNA: 3'- guaGGUG---UAGCCGAAGCGAC-UGCU-GG- -5'
miRNA: 3'- gUAGG----------UGU---AGCCGAa-----GCGACugCUGG- -5'
miRNA: 3'- -GUAGGU-GUAGCCGAAGCGa-CugC-UGG- -5'
miRNA: 3'- -GUAGGUGUAGCCGAAGCGACUGCUGG- -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 | |||||||
| 17623 | 3' | -53.1 | NC_004466.2 | + | 1844 | 0.67 | 0.758933 |
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Target: 5'- -cUCUACAaCGacCUUUGUUGGCGACCc -3' miRNA: 3'- guAGGUGUaGCc-GAAGCGACUGCUGG- -5' |
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| 17623 | 3' | -53.1 | NC_004466.2 | + | 16434 | 0.68 | 0.682796 |
|
Target: 5'- --gCCGCugaGUUGGCUUCGUUGaAUGAgCCa -3' miRNA: 3'- guaGGUG---UAGCCGAAGCGAC-UGCU-GG- -5' |
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| 17623 | 3' | -53.1 | NC_004466.2 | + | 38140 | 0.71 | 0.515849 |
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Target: 5'- gGUCCaguuucuguaGCAgguUCGGCUgguggcUGCUGugGACCa -3' miRNA: 3'- gUAGG----------UGU---AGCCGAa-----GCGACugCUGG- -5' |
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| 17623 | 3' | -53.1 | NC_004466.2 | + | 37599 | 0.72 | 0.453172 |
|
Target: 5'- gCAUCUGcCAUCGGCUUCGUcgGugGuACUa -3' miRNA: 3'- -GUAGGU-GUAGCCGAAGCGa-CugC-UGG- -5' |
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| 17623 | 3' | -53.1 | NC_004466.2 | + | 37248 | 1.12 | 0.000835 |
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Target: 5'- aCAUCCACAUCGGCUUCGCUGACGACCu -3' miRNA: 3'- -GUAGGUGUAGCCGAAGCGACUGCUGG- -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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