miRNA: 3'- -AGUcACUAC-CUCGcCUCaCGGGUCGa -5'
miRNA: 3'- agUCACUACCUCG-CCU------------C--------------ACGGGUCGa -5'
miRNA: 3'- aGUCaCUACCUCg-----CCUCAC-----GGGUCGa -5'
miRNA: 3'- -AGUCACUACCUCGCCUCACGGGUCGA- -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 | |||||||
| 13009 | 3' | -57.7 | NC_003390.1 | + | 31469 | 0.66 | 0.535161 |
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Target: 5'- aUCAuUGAUGaGGGCuGGG-GCCCAGUg -3' miRNA: 3'- -AGUcACUAC-CUCGcCUCaCGGGUCGa -5' |
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| 13009 | 3' | -57.7 | NC_003390.1 | + | 17453 | 0.66 | 0.531949 |
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Target: 5'- -aAGUGAUGGGGCaGGAaaucggaaccucGgacgauacggucauUGCCCGGCa -3' miRNA: 3'- agUCACUACCUCG-CCU------------C--------------ACGGGUCGa -5' |
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| 13009 | 3' | -57.7 | NC_003390.1 | + | 26144 | 0.66 | 0.513885 |
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Target: 5'- cCAG-GAUGGGGguuccaGGGGUGugguaCCCAGCa -3' miRNA: 3'- aGUCaCUACCUCg-----CCUCAC-----GGGUCGa -5' |
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| 13009 | 3' | -57.7 | NC_003390.1 | + | 2600 | 1.08 | 0.000466 |
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Target: 5'- cUCAGUGAUGGAGCGGAGUGCCCAGCUg -3' miRNA: 3'- -AGUCACUACCUCGCCUCACGGGUCGA- -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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