miRNA: 3'- cuCGGCCa---CUGCauAGCCCu---CGGCGU- -5'
miRNA: 3'- -CUCGgCCACuGCauag-CCCUCGGCGu -5'
miRNA: 3'- cUCGGCC-------------ACUGCa--UAGCC-CUCGGCGu -5'
miRNA: 3'- -CUCGGCCACUGCAUAGCCCUCGGCGU- -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 | |||||||
| 28137 | 3' | -59.2 | NC_005887.1 | + | 17271 | 0.66 | 0.432777 |
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Target: 5'- -uGCCGGgcgaGACG--UCGGGcggcGCCGCGc -3' miRNA: 3'- cuCGGCCa---CUGCauAGCCCu---CGGCGU- -5' |
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| 28137 | 3' | -59.2 | NC_005887.1 | + | 15063 | 0.67 | 0.395523 |
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Target: 5'- gGGGCaGGUGuCGccgaaGGGAGCCGCc -3' miRNA: 3'- -CUCGgCCACuGCauag-CCCUCGGCGu -5' |
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| 28137 | 3' | -59.2 | NC_005887.1 | + | 1926 | 0.67 | 0.359554 |
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Target: 5'- cAGCCGGgcggcgucaugcgUGACGgcgAUCGGuGGGUCGUg -3' miRNA: 3'- cUCGGCC-------------ACUGCa--UAGCC-CUCGGCGu -5' |
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| 28137 | 3' | -59.2 | NC_005887.1 | + | 16016 | 1.08 | 0.000324 |
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Target: 5'- cGAGCCGGUGACGUAUCGGGAGCCGCAg -3' miRNA: 3'- -CUCGGCCACUGCAUAGCCCUCGGCGU- -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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