miRNA: 3'- uacUGUUugCGACCGC-A---------------CGGCUACGa -5'
miRNA: 3'- uaCUGuuugCGACCGCACGGCUA-CGa -5'
miRNA: 3'- -UACUGuuug--CGACCGC-ACGGC-UACGA- -5'
miRNA: 3'- -UACUGUUUGCGACCGCACGGCUACGA- -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 | |||||||
| 21140 | 3' | -54.8 | NC_004775.1 | + | 9469 | 0.67 | 0.523057 |
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Target: 5'- --aGCAGugGCUGGCGaUggccugacagcaacuGCCGAUGUg -3' miRNA: 3'- uacUGUUugCGACCGC-A---------------CGGCUACGa -5' |
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| 21140 | 3' | -54.8 | NC_004775.1 | + | 12151 | 0.7 | 0.34911 |
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Target: 5'- -cGACcg--GUUGGCGUGCCGAUaGCa -3' miRNA: 3'- uaCUGuuugCGACCGCACGGCUA-CGa -5' |
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| 21140 | 3' | -54.8 | NC_004775.1 | + | 8939 | 0.72 | 0.269476 |
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Target: 5'- uGUGAUuuaugaGCUGGCGaUGCCGuAUGCUg -3' miRNA: 3'- -UACUGuuug--CGACCGC-ACGGC-UACGA- -5' |
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| 21140 | 3' | -54.8 | NC_004775.1 | + | 1080 | 1.06 | 0.0009 |
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Target: 5'- cAUGACAAACGCUGGCGUGCCGAUGCUa -3' miRNA: 3'- -UACUGUUUGCGACCGCACGGCUACGA- -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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