miRNA: 3'- agGACCUACCCGUCa------CGCC-CUUa---CGa -5'
miRNA: 3'- -AGGACCUACCC-GUCaCGCCcuua-CGA- -5'
miRNA: 3'- aGGACCUa--CCCG---UCACGCCCUUacga -5'
miRNA: 3'- -AGGACCUACCCGUCACGCCCUUACGA- -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 | |||||||
| 11415 | 3' | -57.5 | NC_003085.1 | + | 28601 | 0.66 | 0.552014 |
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Target: 5'- -gCUGGGUGGGCGGcaccgcaGCGGcGAGcucgGCg -3' miRNA: 3'- agGACCUACCCGUCa------CGCC-CUUa---CGa -5' |
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| 11415 | 3' | -57.5 | NC_003085.1 | + | 4094 | 0.66 | 0.509337 |
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Target: 5'- gUUCUGGGUGGGcCGG-GCGGuccagGCUg -3' miRNA: 3'- -AGGACCUACCC-GUCaCGCCcuua-CGA- -5' |
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| 11415 | 3' | -57.5 | NC_003085.1 | + | 21107 | 0.67 | 0.468108 |
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Target: 5'- cCCUGGGacaGGGCggaGGUGUGGGAAa--- -3' miRNA: 3'- aGGACCUa--CCCG---UCACGCCCUUacga -5' |
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| 11415 | 3' | -57.5 | NC_003085.1 | + | 45625 | 1.07 | 0.00059 |
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Target: 5'- gUCCUGGAUGGGCAGUGCGGGAAUGCUc -3' miRNA: 3'- -AGGACCUACCCGUCACGCCCUUACGA- -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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