miRNA: 3'- gaGGACCUGG---ACCACU---UGUAagaCGU- -5'
miRNA: 3'- gAGGACCUGgACCa------CUUGUA---AGACGU- -5'
miRNA: 3'- -GAGG-ACCugGACCAC---------------UUGua--AGACGU- -5'
miRNA: 3'- gaGGACCUGGACCAcUUGUAAGacgu -5'
miRNA: 3'- -GAGGACCUGGACCACUUGUAAGACGU- -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 | |||||||
| 385 | 5' | -52.6 | AC_000011.1 | + | 12353 | 0.66 | 0.727807 |
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Target: 5'- -aCCUGGACCgcaUGGUGAccgACGUgc-GCGa -3' miRNA: 3'- gaGGACCUGG---ACCACU---UGUAagaCGU- -5' |
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| 385 | 5' | -52.6 | AC_000011.1 | + | 5875 | 0.68 | 0.612378 |
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Target: 5'- uUCCUGGAUgUGGacgagggGGACAUgugUUUGCAu -3' miRNA: 3'- gAGGACCUGgACCa------CUUGUA---AGACGU- -5' |
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| 385 | 5' | -52.6 | AC_000011.1 | + | 16860 | 0.68 | 0.582196 |
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Target: 5'- cCUCCaUGGugCUGGUGcugggcuugaucaugGGCucggUCUGCGu -3' miRNA: 3'- -GAGG-ACCugGACCAC---------------UUGua--AGACGU- -5' |
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| 385 | 5' | -52.6 | AC_000011.1 | + | 22237 | 0.69 | 0.55461 |
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Target: 5'- -aUCUGGGCCUGGUcGGCGUUCa--- -3' miRNA: 3'- gaGGACCUGGACCAcUUGUAAGacgu -5' |
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| 385 | 5' | -52.6 | AC_000011.1 | + | 11513 | 1.09 | 0.000944 |
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Target: 5'- gCUCCUGGACCUGGUGAACAUUCUGCAg -3' miRNA: 3'- -GAGGACCUGGACCACUUGUAAGACGU- -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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