miRNA: 3'- -CGGCUUGuCGUggcCGCGCUCGC------CCU- -5'
miRNA: 3'- -CGG--CUUGucGUGGCCGCGC-----UCGCCcu -5'
miRNA: 3'- -CGGCUUG-------------UCGUG-GCCGCGcuCGCCcu -5'
miRNA: 3'- -CGGCUUGUCGUGGCCGCGCUCGCCCU- -5'
Results 41 - 44 of 44 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. |
strand
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Start Position | R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 24854 | 3' | -60.9 | NC_005284.1 | + | 46548 | 0.66 | 0.441972 |
|
Target: 5'- uGCCGAGCcGCA---GCGCGAGCGacaucaGGAa -3' miRNA: 3'- -CGGCUUGuCGUggcCGCGCUCGC------CCU- -5' |
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| 24854 | 3' | -60.9 | NC_005284.1 | + | 17701 | 0.66 | 0.451373 |
|
Target: 5'- cGCCcuGAAUcuCGCCGGCGCGucgauGGCGGu- -3' miRNA: 3'- -CGG--CUUGucGUGGCCGCGC-----UCGCCcu -5' |
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| 24854 | 3' | -60.9 | NC_005284.1 | + | 22079 | 0.66 | 0.459927 |
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Target: 5'- gGCCGGACugcgcgacggaaaAGCGCuUGGCGCuuGCGGu- -3' miRNA: 3'- -CGGCUUG-------------UCGUG-GCCGCGcuCGCCcu -5' |
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| 24854 | 3' | -60.9 | NC_005284.1 | + | 29744 | 1.1 | 0.000258 |
|
Target: 5'- cGCCGAACAGCACCGGCGCGAGCGGGAu -3' miRNA: 3'- -CGGCUUGUCGUGGCCGCGCUCGCCCU- -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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