miRNA: 3'- gCGGGUCGUGUUACGG-----UACU------------ACCGuu -5'
miRNA: 3'- gCGg--GUCGUGUuaCG--GUACUACCGuu -5'
miRNA: 3'- gCGG---GUCGUGUUaCGGUACUACcguu -5'
miRNA: 3'- gCGGGUCGUGUuACGguACUACCGUU- -5'
miRNA: 3'- -GCGGGUCGUGUUACGGUACUACCGUU- -5'
Results 1 - 5 of 5 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 | |||||||
| 31557 | 3' | -55 | NC_006820.1 | + | 16473 | 0.66 | 0.940881 |
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Target: 5'- uGCCUGGCACGAUGCUcacauGUGAcacucuucaaacUGGUc- -3' miRNA: 3'- gCGGGUCGUGUUACGG-----UACU------------ACCGuu -5' |
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| 31557 | 3' | -55 | NC_006820.1 | + | 12282 | 0.66 | 0.925595 |
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Target: 5'- gGCauaCAGCACAggGCauCGUGAUGGUu- -3' miRNA: 3'- gCGg--GUCGUGUuaCG--GUACUACCGuu -5' |
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| 31557 | 3' | -55 | NC_006820.1 | + | 115435 | 0.67 | 0.901768 |
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Target: 5'- uGCCucgCAGCACGA-GCCAUGAUGa--- -3' miRNA: 3'- gCGG---GUCGUGUUaCGGUACUACcguu -5' |
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| 31557 | 3' | -55 | NC_006820.1 | + | 179039 | 0.71 | 0.722397 |
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Target: 5'- uGCUCAGCACGcUGU--UGGUGGCGAu -3' miRNA: 3'- gCGGGUCGUGUuACGguACUACCGUU- -5' |
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| 31557 | 3' | -55 | NC_006820.1 | + | 24148 | 1.07 | 0.004875 |
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Target: 5'- cCGCCCAGCACAAUGCCAUGAUGGCAAg -3' miRNA: 3'- -GCGGGUCGUGUUACGGUACUACCGUU- -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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