miRNA: 3'- -GUUCGGU--GUUGAGc---CGCC------UCUCUCCG- -5'
miRNA: 3'- -GUUCGGuGUuGaGCCGCCU-CU-CUCCG- -5'
miRNA: 3'- -GUUCGGUG-----UUGAGCCGccuCUCUCCG- -5'
miRNA: 3'- gUUCGGU----GUUGaGCCG-CCUCu---CUCCG- -5'
miRNA: 3'- -GUUCGGUGUUGAGCCGCCUCUCUCCG- -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 | |||||||
| 17643 | 3' | -55.8 | NC_004466.2 | + | 41657 | 0.66 | 0.631397 |
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Target: 5'- uCGAGCCGauCGGCUUaccuGCGGcacgccAGGGAGGCc -3' miRNA: 3'- -GUUCGGU--GUUGAGc---CGCC------UCUCUCCG- -5' |
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| 17643 | 3' | -55.8 | NC_004466.2 | + | 37565 | 0.67 | 0.575849 |
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Target: 5'- aCGAGCC-CAuCcCGGUGGAaGGuGGGGCg -3' miRNA: 3'- -GUUCGGuGUuGaGCCGCCU-CU-CUCCG- -5' |
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| 17643 | 3' | -55.8 | NC_004466.2 | + | 37850 | 0.68 | 0.500266 |
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Target: 5'- cCGGGCUAUcgaggAACUCGGCcuuGAGGGGUa -3' miRNA: 3'- -GUUCGGUG-----UUGAGCCGccuCUCUCCG- -5' |
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| 17643 | 3' | -55.8 | NC_004466.2 | + | 44869 | 0.71 | 0.34759 |
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Target: 5'- uGGGCCAgggcCAGC-CGGCgGGAGccuuGAGGCa -3' miRNA: 3'- gUUCGGU----GUUGaGCCG-CCUCu---CUCCG- -5' |
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| 17643 | 3' | -55.8 | NC_004466.2 | + | 21770 | 1.12 | 0.000425 |
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Target: 5'- uCAAGCCACAACUCGGCGGAGAGAGGCg -3' miRNA: 3'- -GUUCGGUGUUGAGCCGCCUCUCUCCG- -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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