miRNA: 3'- -UGGGCU-CCG------------GCC-UU---UAGCAGCCGCUa -5'
miRNA: 3'- uGGGCUc---CGGCCUUUAGCAGCCGcua -5'
miRNA: 3'- -UGGGC-UCCGGCCUUuaGCAGC-CGcua -5'
Results 21 - 23 of 23 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 | |||||||
| 23201 | 3' | -58.6 | NC_005259.1 | + | 14022 | 0.69 | 0.403575 |
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Target: 5'- uGCCCGAcGGCacgaucaucgagCGGcAGcgcAUCGUCGGCGAc -3' miRNA: 3'- -UGGGCU-CCG------------GCC-UU---UAGCAGCCGCUa -5' |
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| 23201 | 3' | -58.6 | NC_005259.1 | + | 43513 | 0.69 | 0.421601 |
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Target: 5'- cCUCGGaacuGCCGGAAAUCGUCGGUc-- -3' miRNA: 3'- uGGGCUc---CGGCCUUUAGCAGCCGcua -5' |
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| 23201 | 3' | -58.6 | NC_005259.1 | + | 62764 | 0.66 | 0.622725 |
|
Target: 5'- uACUCGuGGGCCGGAA--CGUCGcGCa-- -3' miRNA: 3'- -UGGGC-UCCGGCCUUuaGCAGC-CGcua -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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