miRNA: 3'- -GCCAGUUAAGUUUCC---GUg---GCU-----AACGU- -5'
miRNA: 3'- gCCAGUuaAGU---UUCCGUGGCU----AACGU- -5'
miRNA: 3'- gCCAGuuaAGUUuCCGUGGCUAa---CGU- -5'
miRNA: 3'- -GCCAGUUAAGUUUCCGUGGCUAACGU- -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 | |||||||
| 32271 | 5' | -48.2 | NC_007022.1 | + | 73119 | 0.66 | 0.999428 |
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Target: 5'- cCGGUCAGUUCGGAGGaaaCAauaaCGAagaagUUGUAu -3' miRNA: 3'- -GCCAGUUAAGUUUCC---GUg---GCU-----AACGU- -5' |
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| 32271 | 5' | -48.2 | NC_007022.1 | + | 31733 | 0.69 | 0.995532 |
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Target: 5'- gGGUCGc-UCAgucGAGGUGCCGAgcaaUUGCAu -3' miRNA: 3'- gCCAGUuaAGU---UUCCGUGGCU----AACGU- -5' |
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| 32271 | 5' | -48.2 | NC_007022.1 | + | 132051 | 0.69 | 0.994777 |
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Target: 5'- uGGUUuaaUCAAcGGCACCGGUaucgGCAc -3' miRNA: 3'- gCCAGuuaAGUUuCCGUGGCUAa---CGU- -5' |
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| 32271 | 5' | -48.2 | NC_007022.1 | + | 163758 | 1.1 | 0.014515 |
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Target: 5'- cCGGUCAAUUCAAAGGCACCGAUUGCAa -3' miRNA: 3'- -GCCAGUUAAGUUUCCGUGGCUAACGU- -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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