miRNA: 3'- -CGGCUU-AAGCu---GGUUG--AGUCAa---GCUu -5'
miRNA: 3'- -CGGCuuaaGCUGG-UUGAGUCaAGCUU- -5'
miRNA: 3'- -CGGCuuaaGCUGGUUGAGUC-AAGCuu -5'
miRNA: 3'- -CGGCUUAAGCUGGu---UGAGUcaaGCUu -5'
miRNA: 3'- -CGGCuua-AGCUGGU------UG---AGUCAAGCUu -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 | |||||||
| 12201 | 3' | -48.3 | NC_003309.1 | + | 3198 | 0.66 | 0.978797 |
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Target: 5'- cGCCGAAcUUCGcguuCCAGCcaUCGGUgaugCGAu -3' miRNA: 3'- -CGGCUU-AAGCu---GGUUG--AGUCAa---GCUu -5' |
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| 12201 | 3' | -48.3 | NC_003309.1 | + | 41274 | 0.66 | 0.973159 |
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Target: 5'- cGCUGg---CGGCCgGGCUCAGgUCGAGg -3' miRNA: 3'- -CGGCuuaaGCUGG-UUGAGUCaAGCUU- -5' |
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| 12201 | 3' | -48.3 | NC_003309.1 | + | 44881 | 0.67 | 0.958774 |
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Target: 5'- uGCCGuacaCGGCUGACUCAGgUUCGc- -3' miRNA: 3'- -CGGCuuaaGCUGGUUGAGUC-AAGCuu -5' |
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| 12201 | 3' | -48.3 | NC_003309.1 | + | 4932 | 0.68 | 0.939822 |
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Target: 5'- gGUCGAAUUCGGCCuguuGCUCGac-CGAc -3' miRNA: 3'- -CGGCUUAAGCUGGu---UGAGUcaaGCUu -5' |
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| 12201 | 3' | -48.3 | NC_003309.1 | + | 43317 | 0.72 | 0.765046 |
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Target: 5'- gGCCGugcgUCGACCAcgccuuGCccaUCAGUUCGAc -3' miRNA: 3'- -CGGCuua-AGCUGGU------UG---AGUCAAGCUu -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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