miRNA: 3'- aGGGUuu--UGGGGGCACC-----UCACCu-UGU- -5'
miRNA: 3'- -AGGGuUUUGGGGGcACCUCACCUUgU- -5'
miRNA: 3'- -AGGgUUUUGGGGGCACCUc----ACCUUgU- -5'
miRNA: 3'- -AGGGuuu----UGGGGGCaCCUCACCUUgU- -5'
miRNA: 3'- -AGGGUUUUGGGGGCACCUCACCUUGU- -5'
Results 21 - 25 of 25 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 | |||||||
| 27240 | 5' | -54.5 | NC_005832.1 | + | 78455 | 0.71 | 0.661082 |
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Target: 5'- cCCCAucauGCCCCUGUGGcggugAGUGGccACAa -3' miRNA: 3'- aGGGUuu--UGGGGGCACC-----UCACCu-UGU- -5' |
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| 27240 | 5' | -54.5 | NC_005832.1 | + | 66164 | 0.71 | 0.650523 |
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Target: 5'- uUCCCuGAACCUCU-UGGGGUGGGAgGg -3' miRNA: 3'- -AGGGuUUUGGGGGcACCUCACCUUgU- -5' |
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| 27240 | 5' | -54.5 | NC_005832.1 | + | 20523 | 0.72 | 0.58715 |
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Target: 5'- cUCUgAGGGCCCCCGUGGAcccucUGGGAgGa -3' miRNA: 3'- -AGGgUUUUGGGGGCACCUc----ACCUUgU- -5' |
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| 27240 | 5' | -54.5 | NC_005832.1 | + | 7628 | 0.73 | 0.555823 |
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Target: 5'- gUCCCucaccucAUCCCCG-GGAGUGGAGgGg -3' miRNA: 3'- -AGGGuuu----UGGGGGCaCCUCACCUUgU- -5' |
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| 27240 | 5' | -54.5 | NC_005832.1 | + | 104873 | 1.09 | 0.002724 |
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Target: 5'- gUCCCAAAACCCCCGUGGAGUGGAACAc -3' miRNA: 3'- -AGGGUUUUGGGGGCACCUCACCUUGU- -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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