miRNA: 3'- gUCCGUUCCgGGUUCCguaUCAGAag -5'
miRNA: 3'- guCCGUUCCgGgUUCCGU-------------AUCAGAAG- -5'
miRNA: 3'- gUCCGU--UCCGGGUu-------CCGUA------UCAGAAG- -5'
miRNA: 3'- -GUCCGUUCCGGGUUCCGUAUCAGAAG- -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 | |||||||
| 9404 | 3' | -53.9 | NC_002519.1 | + | 31283 | 0.66 | 0.633166 |
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Target: 5'- aAGGCGGGGaCCAAGGgc-AGUCUg- -3' miRNA: 3'- gUCCGUUCCgGGUUCCguaUCAGAag -5' |
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| 9404 | 3' | -53.9 | NC_002519.1 | + | 12123 | 0.68 | 0.528787 |
|
Target: 5'- -uGGCAGGGgCaAGGGCAgauugguuucagaUGGUCUUCc -3' miRNA: 3'- guCCGUUCCgGgUUCCGU-------------AUCAGAAG- -5' |
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| 9404 | 3' | -53.9 | NC_002519.1 | + | 28902 | 0.69 | 0.433424 |
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Target: 5'- uGGGCAgaAGGUCCAccuaguguGGCAUacaaagGGUCUUCc -3' miRNA: 3'- gUCCGU--UCCGGGUu-------CCGUA------UCAGAAG- -5' |
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| 9404 | 3' | -53.9 | NC_002519.1 | + | 23309 | 1.1 | 0.000602 |
|
Target: 5'- aCAGGCAAGGCCCAAGGCAUAGUCUUCu -3' miRNA: 3'- -GUCCGUUCCGGGUUCCGUAUCAGAAG- -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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