miRNA: 3'- auGGGAGAACUCUg--CCCA----UCGGAgUu -5'
miRNA: 3'- aUGGGAGaa------CUCUGC--------------CCAUCGGAGuu -5'
miRNA: 3'- aUGGGAGAACU-CUGCC-CA-----------UCGGAguu -5'
miRNA: 3'- -AUGGGAGAACUCUGCCCAUCGGAGUU- -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 | |||||||
| 28423 | 3' | -55.8 | NC_005946.1 | + | 44901 | 0.66 | 0.788936 |
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Target: 5'- -uCCCUCUUGAGGuagGGGUugacGGCCUgGu -3' miRNA: 3'- auGGGAGAACUCUg--CCCA----UCGGAgUu -5' |
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| 28423 | 3' | -55.8 | NC_005946.1 | + | 63748 | 0.67 | 0.766519 |
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Target: 5'- gACCCUCcuccccugGAGGCGacgcugucugggauGGUGGCCUCc- -3' miRNA: 3'- aUGGGAGaa------CUCUGC--------------CCAUCGGAGuu -5' |
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| 28423 | 3' | -55.8 | NC_005946.1 | + | 62726 | 0.7 | 0.548559 |
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Target: 5'- gGCCCUCUUGAcGACGGcGUcguccuucuucAGCCUg-- -3' miRNA: 3'- aUGGGAGAACU-CUGCC-CA-----------UCGGAguu -5' |
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| 28423 | 3' | -55.8 | NC_005946.1 | + | 80500 | 1.04 | 0.003396 |
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Target: 5'- cUACCCUCUUGAGACGGGUAGCCUCAAc -3' miRNA: 3'- -AUGGGAGAACUCUGCCCAUCGGAGUU- -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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