miRNA: 3'- aCCAACGGUGGUa--------------GCUGcUCCa-CCGc -5'
miRNA: 3'- -ACCaACGGUGGUag---CUGCUCCaCCGC- -5'
miRNA: 3'- acCAACG-GUGGU--AGCuGCU-CCACCGc -5'
miRNA: 3'- -ACCAACGGUGGUAGCUGCUCCACCGC- -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 | |||||||
| 738 | 5' | -56.9 | AC_000020.1 | + | 27313 | 0.66 | 0.486742 |
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Target: 5'- gGGUUGCCACCAaagcuccgcucugcaCGGCaAGGccGGCa -3' miRNA: 3'- aCCAACGGUGGUa--------------GCUGcUCCa-CCGc -5' |
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| 738 | 5' | -56.9 | AC_000020.1 | + | 11122 | 0.7 | 0.272054 |
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Target: 5'- aUGG-UGCCAUUAggcggGACGAGGgGGCGg -3' miRNA: 3'- -ACCaACGGUGGUag---CUGCUCCaCCGC- -5' |
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| 738 | 5' | -56.9 | AC_000020.1 | + | 14323 | 0.7 | 0.258116 |
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Target: 5'- -cGUUGCgCGCCAccUCGuCGAuGGUGGCa -3' miRNA: 3'- acCAACG-GUGGU--AGCuGCU-CCACCGc -5' |
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| 738 | 5' | -56.9 | AC_000020.1 | + | 14259 | 1.08 | 0.000386 |
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Target: 5'- aUGGUUGCCACCAUCGACGAGGUGGCGc -3' miRNA: 3'- -ACCAACGGUGGUAGCUGCUCCACCGC- -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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