miRNA: 3'- -CCU----UCGGGUA---UCCUaa-----------GGUGG-AGGGU- -5'
miRNA: 3'- -CCuuCGGGUau-CCU---AAGGUGGaGg---GU- -5'
miRNA: 3'- -CCUUC-GGGUA-UCCUAAGG-------------UGGAG-GGU- -5'
miRNA: 3'- -CCUUCGGGUAUCCUAAGGUGGAGGGU- -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 | |||||||
| 15606 | 5' | -54.1 | NC_004050.1 | + | 2733 | 0.66 | 0.080741 |
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Target: 5'- gGGGcgaaGGCCCAUgaaAGGAggugguggcggacCCGCCaUCCCAc -3' miRNA: 3'- -CCU----UCGGGUA---UCCUaa-----------GGUGG-AGGGU- -5' |
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| 15606 | 5' | -54.1 | NC_004050.1 | + | 1451 | 0.66 | 0.079567 |
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Target: 5'- cGGggGCCCAaucGGAgagUUCCACC-CagaaCAg -3' miRNA: 3'- -CCuuCGGGUau-CCU---AAGGUGGaGg---GU- -5' |
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| 15606 | 5' | -54.1 | NC_004050.1 | + | 1387 | 0.66 | 0.076422 |
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Target: 5'- cGGGAGuCCCAUaAGGAUUCCcugacgaacggucACUUCaCUAc -3' miRNA: 3'- -CCUUC-GGGUA-UCCUAAGG-------------UGGAG-GGU- -5' |
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| 15606 | 5' | -54.1 | NC_004050.1 | + | 2443 | 1.1 | 0.000009 |
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Target: 5'- gGGAAGCCCAUAGGAUUCCACCUCCCAc -3' miRNA: 3'- -CCUUCGGGUAUCCUAAGGUGGAGGGU- -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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