miRNA: 3'- aGCCGcaUGUC-C-CAGUUCAUGGCGaa -5'
miRNA: 3'- agCCGCa----UGUCCCAGU----UCAugGCGaa -5'
miRNA: 3'- aGCCGCa-----UGUCcCAGUUCa-UGGCGAA- -5'
miRNA: 3'- -AGCCgCA--UGUCC-CAGU---UCAUGGCGAa -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 | |||||||
| 23487 | 5' | -55 | NC_005259.1 | + | 60582 | 0.66 | 0.779997 |
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Target: 5'- gCGGCccACGGcGaGUCGGGUGCCGUc- -3' miRNA: 3'- aGCCGcaUGUC-C-CAGUUCAUGGCGaa -5' |
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| 23487 | 5' | -55 | NC_005259.1 | + | 28002 | 0.66 | 0.759855 |
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Target: 5'- -gGGUGccgggGCGGGGUCGccggGGUugCGCg- -3' miRNA: 3'- agCCGCa----UGUCCCAGU----UCAugGCGaa -5' |
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| 23487 | 5' | -55 | NC_005259.1 | + | 68591 | 0.69 | 0.587514 |
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Target: 5'- cCGGCGgccaccGCAGcGUCAAGgaACCGCUUg -3' miRNA: 3'- aGCCGCa-----UGUCcCAGUUCa-UGGCGAA- -5' |
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| 23487 | 5' | -55 | NC_005259.1 | + | 53610 | 0.72 | 0.432413 |
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Target: 5'- gUCGGgGUcaGCAGGcGUCGagcGGUGCCGUUg -3' miRNA: 3'- -AGCCgCA--UGUCC-CAGU---UCAUGGCGAa -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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