miRNA: 3'- -UCAU----GGCGu-CGCCG----------CUACCGACGCua -5'
miRNA: 3'- -UC-AUGgCGUCGCCGCU-------ACCGaCGCua -5'
miRNA: 3'- ucaUGGCGuCGCCGcuACCGACGCUa -5'
miRNA: 3'- -UCAUGGCGUCGCCGCUACCGACGCUA- -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 | |||||||
| 27366 | 5' | -59.1 | NC_005857.1 | + | 15922 | 0.67 | 0.408319 |
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Target: 5'- aGGUGcuccCCGCuuGCGGCaggucgaugcGGUGGCUGCGc- -3' miRNA: 3'- -UCAU----GGCGu-CGCCG----------CUACCGACGCua -5' |
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| 27366 | 5' | -59.1 | NC_005857.1 | + | 9695 | 0.67 | 0.398224 |
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Target: 5'- cGGaUACgGCAGCGGCGAuaaaaaaUGGCgGUGu- -3' miRNA: 3'- -UC-AUGgCGUCGCCGCU-------ACCGaCGCua -5' |
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| 27366 | 5' | -59.1 | NC_005857.1 | + | 13411 | 0.71 | 0.209257 |
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Target: 5'- --cGCCGCuGCGGUacUGGUUGCGAg -3' miRNA: 3'- ucaUGGCGuCGCCGcuACCGACGCUa -5' |
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| 27366 | 5' | -59.1 | NC_005857.1 | + | 13345 | 1.05 | 0.000644 |
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Target: 5'- cAGUACCGCAGCGGCGAUGGCUGCGAUu -3' miRNA: 3'- -UCAUGGCGUCGCCGCUACCGACGCUA- -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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