miRNA: 3'- -CACGGCCG-------------UCaGUa---CAACUGGUUucc -5'
miRNA: 3'- caCGGCCGU--CAGUacaACUGGUuUCC- -5'
miRNA: 3'- cACGG------------CCGuCAGUaCAACUGGUuUCC- -5'
miRNA: 3'- caCGGcCGUCAGUACAACUGguUUCC- -5'
miRNA: 3'- -CACGGCCGUCAGUACAACUGGUUUCC- -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 | |||||||
| 30960 | 5' | -51.6 | NC_006556.1 | + | 14624 | 0.66 | 0.61305 |
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Target: 5'- aGUGCCGGUguagauacgggugGGcCAgccgGUUGACCAAc-- -3' miRNA: 3'- -CACGGCCG-------------UCaGUa---CAACUGGUUucc -5' |
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| 30960 | 5' | -51.6 | NC_006556.1 | + | 10959 | 0.66 | 0.602119 |
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Target: 5'- -aGUCGGCAacGUCA---UGACCAuAGGc -3' miRNA: 3'- caCGGCCGU--CAGUacaACUGGUuUCC- -5' |
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| 30960 | 5' | -51.6 | NC_006556.1 | + | 2451 | 0.67 | 0.590006 |
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Target: 5'- aUGCCcuauugggucaaGGC-GUCG-GUUGACCAuAGGa -3' miRNA: 3'- cACGG------------CCGuCAGUaCAACUGGUuUCC- -5' |
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| 30960 | 5' | -51.6 | NC_006556.1 | + | 6127 | 0.67 | 0.565918 |
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Target: 5'- -gGCC-GCAGUUGUGUUGAC--GGGGu -3' miRNA: 3'- caCGGcCGUCAGUACAACUGguUUCC- -5' |
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| 30960 | 5' | -51.6 | NC_006556.1 | + | 13151 | 1.1 | 0.000539 |
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Target: 5'- uGUGCCGGCAGUCAUGUUGACCAAAGGc -3' miRNA: 3'- -CACGGCCGUCAGUACAACUGGUUUCC- -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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