miRNA: 3'- -GCCUCUCCUaGCAGg----CUCUGUC-CUGU- -5'
miRNA: 3'- -GCC-UCUCCua-GCa--GGCU-CUGUCCUGU- -5'
miRNA: 3'- gCCUCUC--CUAGCAGGcuCUGUCCUgu -5'
miRNA: 3'- gCCU--CUCC----UAGCa---GGCUCUGUCCUgU- -5'
miRNA: 3'- -GCCU--CUCCU------AGCAGGCUCugUCCuGu -5'
Results 41 - 45 of 45 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. |
strand
|
Start Position | R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 16002 | 3' | -55.7 | NC_004065.1 | + | 176463 | 0.7 | 0.865507 |
|
Target: 5'- uCGGGGAGGGaUGUCgggcaGAGGCGGaGGCAc -3' miRNA: 3'- -GCCUCUCCUaGCAGg----CUCUGUC-CUGU- -5' |
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| 16002 | 3' | -55.7 | NC_004065.1 | + | 139860 | 0.69 | 0.872656 |
|
Target: 5'- aCGGcGGAGGcggCGgagCCGGcGGCAGGACGg -3' miRNA: 3'- -GCC-UCUCCua-GCa--GGCU-CUGUCCUGU- -5' |
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| 16002 | 3' | -55.7 | NC_004065.1 | + | 115394 | 0.69 | 0.892879 |
|
Target: 5'- aGGAGGGauGAUCGUCCccGGCGGGGu- -3' miRNA: 3'- gCCUCUC--CUAGCAGGcuCUGUCCUgu -5' |
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| 16002 | 3' | -55.7 | NC_004065.1 | + | 143290 | 0.68 | 0.916853 |
|
Target: 5'- aGGGccGAGGcggcGUCGggggCCGGGGCAGGAgGg -3' miRNA: 3'- gCCU--CUCC----UAGCa---GGCUCUGUCCUgU- -5' |
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| 16002 | 3' | -55.7 | NC_004065.1 | + | 207499 | 0.66 | 0.973284 |
|
Target: 5'- cCGGAacGGGGAauaccgUUGUCCGGGugGGG-Cu -3' miRNA: 3'- -GCCU--CUCCU------AGCAGGCUCugUCCuGu -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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