miRNA: 3'- -GUCCuUGUAguAGUGACGGC--UUCUCc -5'
miRNA: 3'- -GUCCU--UGuaGUAGUGACGGCU---UCUCc -5'
miRNA: 3'- -GUCCUU---GUAGUagUGACGgCU-UCUCC- -5'
miRNA: 3'- -GUCCUUGUAGUAGUGACGGCUUCUCC- -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 | |||||||
| 15441 | 3' | -50.2 | NC_003930.1 | + | 5437 | 0.66 | 0.543396 |
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Target: 5'- gCAGGuGCGU--UUACUGCCGccGAGAGa -3' miRNA: 3'- -GUCCuUGUAguAGUGACGGC--UUCUCc -5' |
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| 15441 | 3' | -50.2 | NC_003930.1 | + | 8793 | 0.67 | 0.482648 |
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Target: 5'- cCAGGAcuGCugCAUUACUGCUGAaccAGAGa -3' miRNA: 3'- -GUCCU--UGuaGUAGUGACGGCU---UCUCc -5' |
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| 15441 | 3' | -50.2 | NC_003930.1 | + | 359 | 0.69 | 0.352421 |
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Target: 5'- cCAGGAAacuCGUCAggGCUGUgGAgAGAGGa -3' miRNA: 3'- -GUCCUU---GUAGUagUGACGgCU-UCUCC- -5' |
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| 15441 | 3' | -50.2 | NC_003930.1 | + | 4309 | 1.12 | 0.000249 |
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Target: 5'- aCAGGAACAUCAUCACUGCCGAAGAGGa -3' miRNA: 3'- -GUCCUUGUAGUAGUGACGGCUUCUCC- -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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