miRNA: 3'- auuACG-----UGCA--UGUU-GUAUACCAGCGG- -5'
miRNA: 3'- aUUAC-GUGCAUgu---UGUAuaCCAGCGG- -5'
miRNA: 3'- auuaCGUGca--UGUUG----UAUACCAGCGG- -5'
miRNA: 3'- -AUUACgUGCAUGUUGUa-------------UACCAGCGG- -5'
miRNA: 3'- -AUUACGUGCAUGUUGUAUACCAGCGG- -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 | |||||||
| 16898 | 3' | -46.7 | NC_004305.1 | + | 6287 | 0.67 | 0.971318 |
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Target: 5'- --uUGUuucaaACGUugGCGAuUAUAUGGUCGCUa -3' miRNA: 3'- auuACG-----UGCA--UGUU-GUAUACCAGCGG- -5' |
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| 16898 | 3' | -46.7 | NC_004305.1 | + | 12478 | 0.67 | 0.967851 |
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Target: 5'- cAGUGuCGCGUAagaauACGUugGGUUGCCa -3' miRNA: 3'- aUUAC-GUGCAUgu---UGUAuaCCAGCGG- -5' |
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| 16898 | 3' | -46.7 | NC_004305.1 | + | 27810 | 0.68 | 0.946039 |
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Target: 5'- ---cGCACccacGCAAUcuugAUAUGGUUGCCg -3' miRNA: 3'- auuaCGUGca--UGUUG----UAUACCAGCGG- -5' |
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| 16898 | 3' | -46.7 | NC_004305.1 | + | 3792 | 0.71 | 0.816893 |
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Target: 5'- gUAGUGgGCGUGCAACGcuuuuaagacacgcAUGGUUGUCg -3' miRNA: 3'- -AUUACgUGCAUGUUGUa-------------UACCAGCGG- -5' |
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| 16898 | 3' | -46.7 | NC_004305.1 | + | 16089 | 1.13 | 0.002964 |
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Target: 5'- uUAAUGCACGUACAACAUAUGGUCGCCa -3' miRNA: 3'- -AUUACGUGCAUGUUGUAUACCAGCGG- -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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