miRNA: 3'- cauGCCGCG-------UGGCgCGCAGGCUu---GUG- -5'
miRNA: 3'- caUGCCGCGuGGC--------GCGCa------GGCUUGUG- -5'
miRNA: 3'- caUGCCGCG--UGGC---------------GCGCaGGCUUGUG- -5'
miRNA: 3'- -CAUGCCGCGUGGCGCGCAGGCUUGUG- -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 | |||||||
| 22090 | 5' | -58.3 | NC_004927.1 | + | 28423 | 0.67 | 0.575106 |
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Target: 5'- --uCGGUGUgguaagaGCCGgGCGUCCGGuuccCACa -3' miRNA: 3'- cauGCCGCG-------UGGCgCGCAGGCUu---GUG- -5' |
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| 22090 | 5' | -58.3 | NC_004927.1 | + | 52840 | 0.68 | 0.514603 |
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Target: 5'- -gGCGGCGCuCCGgugaaggaCGCGaccacuaCCGAGCGCg -3' miRNA: 3'- caUGCCGCGuGGC--------GCGCa------GGCUUGUG- -5' |
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| 22090 | 5' | -58.3 | NC_004927.1 | + | 12663 | 0.69 | 0.48875 |
|
Target: 5'- -aGCGGCGUgaGCCGgucgaaccgaguugaUGCG-CCGAACGCc -3' miRNA: 3'- caUGCCGCG--UGGC---------------GCGCaGGCUUGUG- -5' |
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| 22090 | 5' | -58.3 | NC_004927.1 | + | 67125 | 1.1 | 0.000704 |
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Target: 5'- aGUACGGCGCACCGCGCGUCCGAACACa -3' miRNA: 3'- -CAUGCCGCGUGGCGCGCAGGCUUGUG- -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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