miRNA: 3'- -CGACGa----GGU-CUUGCU---UGU---AGUCACGG- -5'
miRNA: 3'- -CG-ACGAGG---UCu---UGCU---------------UGUAGUCACGG- -5'
miRNA: 3'- cGACgaGGUCUUGcUUGUAGUCaCGG- -5'
miRNA: 3'- -CGACGAGGUCUUGCUUGUAGUCACGG- -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 | |||||||
| 4091 | 5' | -50.7 | NC_001655.1 | + | 6481 | 0.66 | 0.458326 |
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Target: 5'- aGCUGCaguggCCGuGGACGGcguACAgguUCAGUGUUa -3' miRNA: 3'- -CGACGa----GGU-CUUGCU---UGU---AGUCACGG- -5' |
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| 4091 | 5' | -50.7 | NC_001655.1 | + | 1818 | 0.69 | 0.272264 |
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Target: 5'- cGCaUGCUUCguaAGuguuGCGAgugucguuccacacuGCAUCAGUGCCc -3' miRNA: 3'- -CG-ACGAGG---UCu---UGCU---------------UGUAGUCACGG- -5' |
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| 4091 | 5' | -50.7 | NC_001655.1 | + | 5080 | 0.73 | 0.143244 |
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Target: 5'- uCUGggCCAGGACaGGCGUCAGcGCCg -3' miRNA: 3'- cGACgaGGUCUUGcUUGUAGUCaCGG- -5' |
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| 4091 | 5' | -50.7 | NC_001655.1 | + | 7607 | 1.14 | 0.000107 |
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Target: 5'- gGCUGCUCCAGAACGAACAUCAGUGCCc -3' miRNA: 3'- -CGACGAGGUCUUGCUUGUAGUCACGG- -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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