miRNA: 3'- uagCCAAUg---GCCAUGCCGGCaGUaaa -5'
miRNA: 3'- -UAGCCaaUGGCCAUG--CCggCAGUaaa -5'
miRNA: 3'- -UAGCCaaUGGCCa-----------UGCCGGCAGUaaa -5'
miRNA: 3'- -UAGCCAAUGGCCAUGCCGGCAGUAAA- -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 | |||||||
| 25205 | 3' | -53.5 | NC_005336.1 | + | 92902 | 0.66 | 0.955432 |
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Target: 5'- --aGGUUGacgaUGGUGCGGCCG-CAg-- -3' miRNA: 3'- uagCCAAUg---GCCAUGCCGGCaGUaaa -5' |
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| 25205 | 3' | -53.5 | NC_005336.1 | + | 94184 | 0.66 | 0.937525 |
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Target: 5'- gGUCGGc-GCCGGUGCggGGuuGUCGc-- -3' miRNA: 3'- -UAGCCaaUGGCCAUG--CCggCAGUaaa -5' |
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| 25205 | 3' | -53.5 | NC_005336.1 | + | 6216 | 0.73 | 0.624667 |
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Target: 5'- cGUCGGcgGCCGGcgcgcgagcacgGCGGCCGUCGc-- -3' miRNA: 3'- -UAGCCaaUGGCCa-----------UGCCGGCAGUaaa -5' |
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| 25205 | 3' | -53.5 | NC_005336.1 | + | 47472 | 1.04 | 0.008814 |
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Target: 5'- uAUCGGUUACCGGUACGGCCGUCAUUUa -3' miRNA: 3'- -UAGCCAAUGGCCAUGCCGGCAGUAAA- -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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