miRNA: 3'- cUGUGc--CACCUGuC----------UGCGGGCAGGCU- -5'
miRNA: 3'- cuGUGCC------------ACCUGUCU---GCGG---GCAGGCU- -5'
miRNA: 3'- -CUGUGCCACCUGUCU-GCGggCA--GGCU- -5'
miRNA: 3'- -CUGUGCCACCUGUCUgcGGGCaGGcu -5'
miRNA: 3'- -CUGUGCCACCUGUCUGCGGGCAGGCU- -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 | |||||||
| 27521 | 3' | -58.8 | NC_005879.1 | + | 28354 | 0.67 | 0.414732 |
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Target: 5'- aGCGCcaaGUGGACuGguaagaaaauACGCCUGUCCGGa -3' miRNA: 3'- cUGUGc--CACCUGuC----------UGCGGGCAGGCU- -5' |
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| 27521 | 3' | -58.8 | NC_005879.1 | + | 19175 | 0.67 | 0.396384 |
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Target: 5'- -cCACGGacagauuguugaUGGACAGAauuCGCCgauUGUCCGAc -3' miRNA: 3'- cuGUGCC------------ACCUGUCU---GCGG---GCAGGCU- -5' |
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| 27521 | 3' | -58.8 | NC_005879.1 | + | 39185 | 0.74 | 0.138884 |
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Target: 5'- gGACACGGUGGACAGGcCGCaaGUagCUGGa -3' miRNA: 3'- -CUGUGCCACCUGUCU-GCGggCA--GGCU- -5' |
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| 27521 | 3' | -58.8 | NC_005879.1 | + | 39153 | 0.75 | 0.11439 |
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Target: 5'- gGACACGGUGGACAGA--CCCG-CCa- -3' miRNA: 3'- -CUGUGCCACCUGUCUgcGGGCaGGcu -5' |
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| 27521 | 3' | -58.8 | NC_005879.1 | + | 39298 | 1.08 | 0.00042 |
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Target: 5'- gGACACGGUGGACAGACGCCCGUCCGAc -3' miRNA: 3'- -CUGUGCCACCUGUCUGCGGGCAGGCU- -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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