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miRNA: 3'- -CAACGUAGGAACCGAGCGCACCGACA- -5'
miRNA: 3'- caaCGuaGGAACCGa--------------GCGCACCGACA- -5'
miRNA: 3'- -CAACG----UAGGAac--CGAGCGCA-CCGaca -5'
miRNA: 3'- caaCGUAGGAacCGAGCgCACCGAca -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#
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P value |
| Predicted miRNA align pattern | |||||||
| 23224 | 5' | -55.7 | NC_005259.1 | + | 50949 | 1.07 | 0.001362 |
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Target: 5'- cGUUGCAUCCUUGGCUCGCGUGGCUGUc -3' miRNA: 3'- -CAACGUAGGAACCGAGCGCACCGACA- -5' |
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| 23224 | 5' | -55.7 | NC_005259.1 | + | 58450 | 0.67 | 0.624521 |
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Target: 5'- --gGUggCCUUGGUgaucgcggccaccagUGCGUGGCUGUc -3' miRNA: 3'- caaCGuaGGAACCGa--------------GCGCACCGACA- -5' |
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| 23224 | 5' | -55.7 | NC_005259.1 | + | 36779 | 0.67 | 0.656385 |
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Target: 5'- cGUUGCcgccGUCCUgaccGCUCGCGUcGGCa-- -3' miRNA: 3'- -CAACG----UAGGAac--CGAGCGCA-CCGaca -5' |
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| 23224 | 5' | -55.7 | NC_005259.1 | + | 3263 | 0.66 | 0.732006 |
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Target: 5'- --gGCAUCCU--GCUCGgGUGGUUu- -3' miRNA: 3'- caaCGUAGGAacCGAGCgCACCGAca -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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