miRNA: 3'- -CGa------CCUUG-UCUCGaga---UUGUCAUGGa -5'
miRNA: 3'- -CGACCuuGUC-UCGa-----GAUUGUCaUGGa -5'
miRNA: 3'- -CGACCU----UGUCU-CGAGAuu-GUCAUg---GA- -5'
miRNA: 3'- -CGACCUUGUCUCGAGAUUGUCAUGGA- -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 | |||||||
| 627 | 3' | -49.7 | AC_000017.1 | + | 19263 | 0.66 | 0.872713 |
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Target: 5'- aGCgccuuugGGGGCuAGAGCguuguaGGCAGUGCCg -3' miRNA: 3'- -CGa------CCUUG-UCUCGaga---UUGUCAUGGa -5' |
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| 627 | 3' | -49.7 | AC_000017.1 | + | 17679 | 0.66 | 0.855153 |
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Target: 5'- uGCUGGggUGGuAGCgcgcugUUGGCAGcACCa -3' miRNA: 3'- -CGACCuuGUC-UCGa-----GAUUGUCaUGGa -5' |
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| 627 | 3' | -49.7 | AC_000017.1 | + | 27052 | 0.68 | 0.785683 |
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Target: 5'- cGCUGGAagacGCGGAgGCUCUcuuCAGUAaauaCUg -3' miRNA: 3'- -CGACCU----UGUCU-CGAGAuu-GUCAUg---GA- -5' |
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| 627 | 3' | -49.7 | AC_000017.1 | + | 1762 | 1.1 | 0.001717 |
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Target: 5'- uGCUGGAACAGAGCUCUAACAGUACCUc -3' miRNA: 3'- -CGACCUUGUCUCGAGAUUGUCAUGGA- -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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