miRNA: 3'- -UGUCU--UGCUACCG-GAGAGau----GGCGGU- -5'
miRNA: 3'- -UGUcu-UGCUa--------CCGGAGA-GAUGGCGGU- -5'
miRNA: 3'- ugUCUUGCUACcGGag---AGAUGGCGGU- -5'
miRNA: 3'- -UGUCUUGCUACCGGAGAGAUGGCGGU- -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 | |||||||
| 579 | 5' | -55.2 | AC_000015.1 | + | 25991 | 0.66 | 0.57274 |
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Target: 5'- aGCAGGagAUGAUGGCaUUCUUaugcccCCGCCAg -3' miRNA: 3'- -UGUCU--UGCUACCG-GAGAGau----GGCGGU- -5' |
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| 579 | 5' | -55.2 | AC_000015.1 | + | 10342 | 0.67 | 0.527951 |
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Target: 5'- cGCGuacGCGAguuuccucgGGCUUCUaCUACCGCCGc -3' miRNA: 3'- -UGUcu-UGCUa--------CCGGAGA-GAUGGCGGU- -5' |
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| 579 | 5' | -55.2 | AC_000015.1 | + | 7548 | 0.69 | 0.384417 |
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Target: 5'- -aGGAAUGAUGaCCaaagaUCUACCGCCAg -3' miRNA: 3'- ugUCUUGCUACcGGag---AGAUGGCGGU- -5' |
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| 579 | 5' | -55.2 | AC_000015.1 | + | 10226 | 1.08 | 0.000577 |
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Target: 5'- uACAGAACGAUGGCCUCUCUACCGCCAa -3' miRNA: 3'- -UGUCUUGCUACCGGAGAGAUGGCGGU- -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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