miRNA: 3'- -AGGcCGUGaGGCCUACgCGCu---GAAGa -5'
miRNA: 3'- agGCCG---UGa-GGCCU-ACGCGCUGaaGa -5'
miRNA: 3'- -AGGCCGUGagGCCU-ACGCGCuGaAGA- -5'
miRNA: 3'- aGGc--CGUGAGGCCUACGCGCUG--------AAGa -5'
miRNA: 3'- -AGGCCGUGAGGCCUACGCGCUGAAGA- -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 | |||||||
| 12162 | 3' | -57.7 | NC_003309.1 | + | 33092 | 0.66 | 0.579989 |
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Target: 5'- aUCC-GCACaCCGGAUGgGCGcaucCUUCg -3' miRNA: 3'- -AGGcCGUGaGGCCUACgCGCu---GAAGa -5' |
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| 12162 | 3' | -57.7 | NC_003309.1 | + | 32914 | 0.68 | 0.46589 |
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Target: 5'- -aCGGCuauGCggCCGGAcUGCGCGACggCa -3' miRNA: 3'- agGCCG---UGa-GGCCU-ACGCGCUGaaGa -5' |
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| 12162 | 3' | -57.7 | NC_003309.1 | + | 11241 | 0.69 | 0.417935 |
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Target: 5'- cUCCGGUACg-CGGAcUGCGCGuCgUCUg -3' miRNA: 3'- -AGGCCGUGagGCCU-ACGCGCuGaAGA- -5' |
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| 12162 | 3' | -57.7 | NC_003309.1 | + | 49396 | 0.77 | 0.113318 |
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Target: 5'- gCCaucGCACUCCGGAUGCGCGAUcggugcauUUCg -3' miRNA: 3'- aGGc--CGUGAGGCCUACGCGCUG--------AAGa -5' |
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| 12162 | 3' | -57.7 | NC_003309.1 | + | 38019 | 1.07 | 0.000754 |
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Target: 5'- uUCCGGCACUCCGGAUGCGCGACUUCUu -3' miRNA: 3'- -AGGCCGUGAGGCCUACGCGCUGAAGA- -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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