miRNA: 3'- uGCCACcGCCaUUACCUga----GGCUACG- -5'
miRNA: 3'- -UGCCACCGCCA---UUACcUGA-----GGCU-ACG- -5'
miRNA: 3'- ugC-CACCGCCAUUACCUGA--GGCU-----------ACG- -5'
miRNA: 3'- -UGCCACCGCCAUUACCUGAGGCUACG- -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 | |||||||
| 25984 | 3' | -54.4 | NC_005340.1 | + | 12257 | 0.67 | 0.538668 |
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Target: 5'- uUGGUGaCGGcGGUGGAaaacugCCGGUGCc -3' miRNA: 3'- uGCCACcGCCaUUACCUga----GGCUACG- -5' |
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| 25984 | 3' | -54.4 | NC_005340.1 | + | 4710 | 0.7 | 0.365245 |
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Target: 5'- aGCGGUGGUGGUggcGAUGaGCUgcugaCCGAcUGCu -3' miRNA: 3'- -UGCCACCGCCA---UUACcUGA-----GGCU-ACG- -5' |
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| 25984 | 3' | -54.4 | NC_005340.1 | + | 15853 | 0.75 | 0.193064 |
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Target: 5'- -aGcGUGGCGGUAAUGGGCUugUCGAccgcccacaugUGCg -3' miRNA: 3'- ugC-CACCGCCAUUACCUGA--GGCU-----------ACG- -5' |
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| 25984 | 3' | -54.4 | NC_005340.1 | + | 10168 | 1.11 | 0.000466 |
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Target: 5'- cACGGUGGCGGUAAUGGACUCCGAUGCc -3' miRNA: 3'- -UGCCACCGCCAUUACCUGAGGCUACG- -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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