miRNA: 3'- -UGUCGG-AGGGcaUCAGCCGCGUGaga -5'
miRNA: 3'- uguCGGaG-GGCAUCAGCCGcGUGAGa -5'
miRNA: 3'- -UGUCGG-AGGGCA-----------UCA-GCCGCGUG-AGa -5'
miRNA: 3'- -UGUCGGAGGGCAUCAGCCGCGUGAGA- -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 | |||||||
| 28363 | 5' | -59 | NC_005946.1 | + | 96155 | 0.67 | 0.64299 |
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Target: 5'- cGCAGUCgUCCC--AGUCGGCGUAUg-- -3' miRNA: 3'- -UGUCGG-AGGGcaUCAGCCGCGUGaga -5' |
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| 28363 | 5' | -59 | NC_005946.1 | + | 22316 | 0.67 | 0.622341 |
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Target: 5'- --cGCUcCuCCGUAGUCGGCaCACUCc -3' miRNA: 3'- uguCGGaG-GGCAUCAGCCGcGUGAGa -5' |
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| 28363 | 5' | -59 | NC_005946.1 | + | 9707 | 0.71 | 0.391324 |
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Target: 5'- gACGGCCaUCCUGUugucgggggugAGUgCGGCGCACgUCa -3' miRNA: 3'- -UGUCGG-AGGGCA-----------UCA-GCCGCGUG-AGa -5' |
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| 28363 | 5' | -59 | NC_005946.1 | + | 22528 | 1.07 | 0.001188 |
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Target: 5'- gACAGCCUCCCGUAGUCGGCGCACUCUg -3' miRNA: 3'- -UGUCGGAGGGCAUCAGCCGCGUGAGA- -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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