miRNA: 3'- caGGUCGAUGAACg----CCGGACa--------GGUGg -5'
miRNA: 3'- caGGUCGaugaACGCCGGACa----GGUGG- -5'
miRNA: 3'- -CAGGUCGaugaa---CG-CCGGACAGGUGG- -5'
miRNA: 3'- -CAGGUCGAUGAACGCCGGACAGGUGG- -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 | |||||||
| 27521 | 5' | -56.4 | NC_005879.1 | + | 16373 | 0.67 | 0.450538 |
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Target: 5'- -aCUGGCUGCUUGgccaaGGCCUGguauuacagCCACa -3' miRNA: 3'- caGGUCGAUGAACg----CCGGACa--------GGUGg -5' |
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| 27521 | 5' | -56.4 | NC_005879.1 | + | 10914 | 0.69 | 0.356506 |
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Target: 5'- -cUCGGCag--UGCGGCCUGaaccgCCGCCg -3' miRNA: 3'- caGGUCGaugaACGCCGGACa----GGUGG- -5' |
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| 27521 | 5' | -56.4 | NC_005879.1 | + | 39228 | 0.76 | 0.127882 |
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Target: 5'- uGUCCAGUgcaguaugGCgGGUCUGUCCACCg -3' miRNA: 3'- -CAGGUCGaugaa---CG-CCGGACAGGUGG- -5' |
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| 27521 | 5' | -56.4 | NC_005879.1 | + | 39256 | 1.12 | 0.000275 |
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Target: 5'- uGUCCAGCUACUUGCGGCCUGUCCACCg -3' miRNA: 3'- -CAGGUCGAUGAACGCCGGACAGGUGG- -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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