miRNA: 3'- aCcUCGGaCUGCCG----------GCUUC-AACUCCU- -5'
miRNA: 3'- aCCUCGGaCUGcCGGCUUCa-ACU---CCU- -5'
miRNA: 3'- aCCucGGACUgCCGGCUUCaACUC-CU- -5'
miRNA: 3'- aCCUCGgaCUGCCG--GCUUCAACU-CCu -5'
miRNA: 3'- -ACCUCGGACUGCCGGCUUCAACUCCU- -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 | |||||||
| 8163 | 3' | -56.6 | NC_001978.2 | + | 39297 | 0.66 | 0.549225 |
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Target: 5'- aGaAGCCgGACGGCacgccgaccaCGAAGaUUGAGGGu -3' miRNA: 3'- aCcUCGGaCUGCCG----------GCUUC-AACUCCU- -5' |
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| 8163 | 3' | -56.6 | NC_001978.2 | + | 36772 | 0.66 | 0.549225 |
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Target: 5'- cGGAGCC-GAC-GCCGGAGccUGAgccGGAg -3' miRNA: 3'- aCCUCGGaCUGcCGGCUUCa-ACU---CCU- -5' |
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| 8163 | 3' | -56.6 | NC_001978.2 | + | 1997 | 0.68 | 0.4347 |
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Target: 5'- cGGu-CCUGGgGGCCGAAGcUGGGuGAg -3' miRNA: 3'- aCCucGGACUgCCGGCUUCaACUC-CU- -5' |
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| 8163 | 3' | -56.6 | NC_001978.2 | + | 41406 | 0.68 | 0.415364 |
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Target: 5'- gGGGGCggGGCGGCucCGAAGUUGGcGGc -3' miRNA: 3'- aCCUCGgaCUGCCG--GCUUCAACU-CCu -5' |
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| 8163 | 3' | -56.6 | NC_001978.2 | + | 7389 | 1.09 | 0.000466 |
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Target: 5'- aUGGAGCCUGACGGCCGAAGUUGAGGAa -3' miRNA: 3'- -ACCUCGGACUGCCGGCUUCAACUCCU- -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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