miRNA: 3'- -CCGGU--UGUGCUAAGccaCGUCGaGUg -5'
miRNA: 3'- -CC-GGUUG-UGCUa---AGCCa-----CGUCGaGUG- -5'
miRNA: 3'- -CCGgU-------------UGUGCUA-AGCCA-CGu---CGAGUG- -5'
miRNA: 3'- -CCGGUUGuGCU--------------AAgCC----ACGUCGAGUg -5'
Results 21 - 24 of 24 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 | |||||||
| 1336 | 3' | -53.2 | NC_001335.1 | + | 13226 | 0.67 | 0.762918 |
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Target: 5'- cGGCCAucGCACGGUUCcagGUAGC-CAa -3' miRNA: 3'- -CCGGU--UGUGCUAAGccaCGUCGaGUg -5' |
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| 1336 | 3' | -53.2 | NC_001335.1 | + | 50738 | 0.66 | 0.783507 |
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Target: 5'- aGGcCCAGCgACGAgucgUCGGccggggGCGGCgCACc -3' miRNA: 3'- -CC-GGUUG-UGCUa---AGCCa-----CGUCGaGUG- -5' |
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| 1336 | 3' | -53.2 | NC_001335.1 | + | 13016 | 0.66 | 0.792563 |
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Target: 5'- aGGCgGauagacaaucgggGCGCGGUgUCGGUcGCucgcGCUCACg -3' miRNA: 3'- -CCGgU-------------UGUGCUA-AGCCA-CGu---CGAGUG- -5' |
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| 1336 | 3' | -53.2 | NC_001335.1 | + | 19846 | 0.65 | 0.819795 |
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Target: 5'- uGGCCGGCcCGAagaugauccacaccUUgGGgaacUGCAGCUCGg -3' miRNA: 3'- -CCGGUUGuGCU--------------AAgCC----ACGUCGAGUg -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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