miRNA: 3'- ugGGGGCAGCCuGC--------CCGCAGaCAGGU- -5'
miRNA: 3'- uGGGGGCAGccUGCCCG---CAGACAGGU- -5'
miRNA: 3'- uGGG-GGCAGCCu-----GCCcGCaGACAGGU- -5'
miRNA: 3'- -UGgGGGCAGcCUGCCCgCA-------GACAGGU- -5'
miRNA: 3'- -UGGGGGCAGCCUGCCCGCAGACAGGU- -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 | |||||||
| 27537 | 5' | -62.5 | NC_005879.1 | + | 13783 | 0.66 | 0.296688 |
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Target: 5'- -aCUCCGUCGG-CGcaggguuuGGCGUC-GUCCAu -3' miRNA: 3'- ugGGGGCAGCCuGC--------CCGCAGaCAGGU- -5' |
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| 27537 | 5' | -62.5 | NC_005879.1 | + | 9965 | 0.66 | 0.289583 |
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Target: 5'- cUUCCCGUUu-GCGGGUaggGUCUGUCCAu -3' miRNA: 3'- uGGGGGCAGccUGCCCG---CAGACAGGU- -5' |
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| 27537 | 5' | -62.5 | NC_005879.1 | + | 39185 | 0.67 | 0.269069 |
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Target: 5'- uCCCaCCGUCGGcgauauCGGuCGgCUGUCCAg -3' miRNA: 3'- uGGG-GGCAGCCu-----GCCcGCaGACAGGU- -5' |
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| 27537 | 5' | -62.5 | NC_005879.1 | + | 39284 | 0.72 | 0.110136 |
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Target: 5'- gACgCCCGUCcGACGGGgGUucgcggcCUGUCCAg -3' miRNA: 3'- -UGgGGGCAGcCUGCCCgCA-------GACAGGU- -5' |
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| 27537 | 5' | -62.5 | NC_005879.1 | + | 39225 | 1.07 | 0.000217 |
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Target: 5'- aACCCCCGUCGGACGGGCGUCUGUCCAc -3' miRNA: 3'- -UGGGGGCAGCCUGCCCGCAGACAGGU- -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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