miRNA: 3'- gGGUCCCU-----UGUUG--GGUAA--GGACUUAG- -5'
miRNA: 3'- -GGGUCCCUUGuug------GGUA-----------AGGACUUag -5'
miRNA: 3'- gGGUcCCUUGUUGGGu-----AAGGACUUag -5'
miRNA: 3'- -GGGUCCCUUGUUGGGUAAGGACUUAG- -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 | |||||||
| 658 | 5' | -50.5 | AC_000017.1 | + | 14296 | 0.66 | 0.846989 |
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Target: 5'- aCCGGGGGgagaaACAGCauCCGUUacUCUGAGUUg -3' miRNA: 3'- gGGUCCCU-----UGUUG--GGUAA--GGACUUAG- -5' |
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| 658 | 5' | -50.5 | AC_000017.1 | + | 20705 | 0.66 | 0.828166 |
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Target: 5'- uCCUAGGGAGCuuugcaggaCCAUguuaacaucuuUCCUGAAg- -3' miRNA: 3'- -GGGUCCCUUGuug------GGUA-----------AGGACUUag -5' |
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| 658 | 5' | -50.5 | AC_000017.1 | + | 22274 | 0.67 | 0.798205 |
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Target: 5'- aCCA-GGAACAGCUCuacagcUUCCUGGAg- -3' miRNA: 3'- gGGUcCCUUGUUGGGu-----AAGGACUUag -5' |
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| 658 | 5' | -50.5 | AC_000017.1 | + | 33861 | 1.13 | 0.000978 |
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Target: 5'- uCCCAGGGAACAACCCAUUCCUGAAUCa -3' miRNA: 3'- -GGGUCCCUUGUUGGGUAAGGACUUAG- -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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