miRNA: 3'- gauacuaCCCua----UCAGCCGGCCU--UUG- -5'
miRNA: 3'- -GAUACuaCCCUAUCa--------GCCGGCCUUug -5'
miRNA: 3'- gauacuaCCCU--AUCAGCCGGCCUUUG- -5'
miRNA: 3'- -GAUACUACCCUAUCAGCCGGCCUUUG- -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 | |||||||
| 20449 | 5' | -50.8 | NC_004688.1 | + | 88237 | 0.66 | 0.983116 |
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Target: 5'- ------aGGGuuacgaGGUCGGCCGGGcuGACg -3' miRNA: 3'- gauacuaCCCua----UCAGCCGGCCU--UUG- -5' |
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| 20449 | 5' | -50.8 | NC_004688.1 | + | 77797 | 0.67 | 0.960174 |
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Target: 5'- gCUGUGgcGGGGUGGaggcaugacCGGUCGGAGu- -3' miRNA: 3'- -GAUACuaCCCUAUCa--------GCCGGCCUUug -5' |
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| 20449 | 5' | -50.8 | NC_004688.1 | + | 93841 | 0.81 | 0.335395 |
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Target: 5'- ------cGGGGcuUAGUCGGCCGGAAACg -3' miRNA: 3'- gauacuaCCCU--AUCAGCCGGCCUUUG- -5' |
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| 20449 | 5' | -50.8 | NC_004688.1 | + | 30002 | 1.09 | 0.006169 |
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Target: 5'- uCUAUGAUGGGAUAGUCGGCCGGAAACc -3' miRNA: 3'- -GAUACUACCCUAUCAGCCGGCCUUUG- -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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