miRNA: 3'- gUGCAaUCGU----GCACCGACCC--ACUCUu -5'
miRNA: 3'- -GUGCAauCGUGCa------CCGA--------------CCCACUCUU- -5'
miRNA: 3'- -GUgCAa-UCGUGCa--CCGACCCACUcuu -5'
miRNA: 3'- -GUGCAAUCGUGCACCGACCCACUCUU- -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 | |||||||
| 2674 | 3' | -54.7 | NC_001491.2 | + | 20618 | 0.66 | 0.917669 |
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Target: 5'- gACGUaGGCGuaguUGUGGUUGGGguUGAGGu -3' miRNA: 3'- gUGCAaUCGU----GCACCGACCC--ACUCUu -5' |
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| 2674 | 3' | -54.7 | NC_001491.2 | + | 11468 | 0.68 | 0.836204 |
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Target: 5'- aCACGUgcGCGCGgcugcggGGCUgccuggccccucugGGGUGGGGGu -3' miRNA: 3'- -GUGCAauCGUGCa------CCGA--------------CCCACUCUU- -5' |
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| 2674 | 3' | -54.7 | NC_001491.2 | + | 5516 | 0.73 | 0.570389 |
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Target: 5'- gCAgGUcgGGCGCGgcgGGCUGGGUGAa-- -3' miRNA: 3'- -GUgCAa-UCGUGCa--CCGACCCACUcuu -5' |
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| 2674 | 3' | -54.7 | NC_001491.2 | + | 69153 | 1.06 | 0.005262 |
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Target: 5'- cCACGUUAGCACGUGGCUGGGUGAGAAc -3' miRNA: 3'- -GUGCAAUCGUGCACCGACCCACUCUU- -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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