miRNA: 3'- ucaGAGCGaCCG-----GCUG-AGUUUGAGGC- -5'
miRNA: 3'- -UCAGAGCGACCGGc---------UGAGU----UUGAGGC- -5'
miRNA: 3'- -UCAG--AGCGAC-CGGCUGAGUU--------------UGAGGC- -5'
miRNA: 3'- ucAGAGCGACCGGCU----------GAGUU---------UGAGGC- -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 | |||||||
| 22183 | 5' | -55 | NC_004927.1 | + | 38768 | 0.66 | 0.81574 |
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Target: 5'- --gCUUGCgGGCuucguCGGCgUCGAACUCCGa -3' miRNA: 3'- ucaGAGCGaCCG-----GCUG-AGUUUGAGGC- -5' |
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| 22183 | 5' | -55 | NC_004927.1 | + | 59539 | 0.68 | 0.706329 |
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Target: 5'- uGGUUUCGUUGGCUcagacgaccaGCUCGaaauGACUCCGu -3' miRNA: 3'- -UCAGAGCGACCGGc---------UGAGU----UUGAGGC- -5' |
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| 22183 | 5' | -55 | NC_004927.1 | + | 70541 | 0.72 | 0.442194 |
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Target: 5'- cGGUCguUCGUUGaGCCGAUUCAGgaacaggcggauauGCUCCGc -3' miRNA: 3'- -UCAG--AGCGAC-CGGCUGAGUU--------------UGAGGC- -5' |
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| 22183 | 5' | -55 | NC_004927.1 | + | 27473 | 0.75 | 0.339191 |
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Target: 5'- -aUCUCGCUGGCUGAuuacguccguCUCGAagucaccgcACUCCGa -3' miRNA: 3'- ucAGAGCGACCGGCU----------GAGUU---------UGAGGC- -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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