miRNA: 3'- -GCGA----CACuGACGUGg---UAACUGAUGGu -5'
miRNA: 3'- gCGACacUGACG-UGGUAACUG--AUGGU- -5'
miRNA: 3'- gCGACACUGACG-UGGU---AACUGAU---GGU- -5'
miRNA: 3'- -GCGACACUGACGUGGUAACUGAUGGU- -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 | |||||||
| 23553 | 3' | -51.7 | NC_005260.1 | + | 22618 | 0.66 | 0.993836 |
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Target: 5'- gCGCUcgaaGUG-CUGCGCacauGUUGACUACUu -3' miRNA: 3'- -GCGA----CACuGACGUGg---UAACUGAUGGu -5' |
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| 23553 | 3' | -51.7 | NC_005260.1 | + | 209924 | 0.69 | 0.970743 |
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Target: 5'- aGUUGguGCUGCuGCCGUUGACacUGCCAa -3' miRNA: 3'- gCGACacUGACG-UGGUAACUG--AUGGU- -5' |
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| 23553 | 3' | -51.7 | NC_005260.1 | + | 81920 | 0.73 | 0.850904 |
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Target: 5'- gGCUGUGGCUGCuGCCGcuuUUGGCUGuacUCAg -3' miRNA: 3'- gCGACACUGACG-UGGU---AACUGAU---GGU- -5' |
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| 23553 | 3' | -51.7 | NC_005260.1 | + | 222181 | 1.09 | 0.010752 |
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Target: 5'- uCGCUGUGACUGCACCAUUGACUACCAc -3' miRNA: 3'- -GCGACACUGACGUGGUAACUGAUGGU- -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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