miRNA: 3'- uACCCCGUAaaCGGU--GUaUAGCGGGC- -5'
miRNA: 3'- uaCCCCGuaaACGgUGUAUAGCGGgc -5'
miRNA: 3'- -UACCCCG----UAAAC---------------GGUGUAUAGCGGGC- -5'
miRNA: 3'- -UACCCCGUAAACGGUGUAUAGCGGGC- -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 | |||||||
| 30424 | 5' | -54.5 | NC_006548.1 | + | 34330 | 0.66 | 0.588066 |
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Target: 5'- uUGGGGUAUccGCCAauCGcGUUGCCUGc -3' miRNA: 3'- uACCCCGUAaaCGGU--GUaUAGCGGGC- -5' |
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| 30424 | 5' | -54.5 | NC_006548.1 | + | 9355 | 0.66 | 0.576624 |
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Target: 5'- -aGGGGUgc-UGCgGCAUGUUGCCg- -3' miRNA: 3'- uaCCCCGuaaACGgUGUAUAGCGGgc -5' |
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| 30424 | 5' | -54.5 | NC_006548.1 | + | 37571 | 0.72 | 0.30339 |
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Target: 5'- uGUGGGGCcacgGUUUGagccugucgcagcuaUCGCGUAUCGCUCGa -3' miRNA: 3'- -UACCCCG----UAAAC---------------GGUGUAUAGCGGGC- -5' |
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| 30424 | 5' | -54.5 | NC_006548.1 | + | 9382 | 1.08 | 0.000715 |
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Target: 5'- gAUGGGGCAUUUGCCACAUAUCGCCCGg -3' miRNA: 3'- -UACCCCGUAAACGGUGUAUAGCGGGC- -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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