miRNA: 3'- -AACGGGUUUGAGUCGUGGCUCUUCAA- -5'
miRNA: 3'- aaCGGGuu------UGAGUCGUGGCUCUUCaa -5'
miRNA: 3'- aaCGGGUU-UGaGUCGUGGc-UCUUCAa -5'
miRNA: 3'- aACGGGUuu--GAGUCGuGGCUCU----UCAa -5'
miRNA: 3'- aaCGGGUu----UGAgUCGUggCUCUUCAa -5'
Results 1 - 5 of 5 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 | |||||||
| 358 | 3' | -52.9 | AC_000011.1 | + | 11656 | 1.03 | 0.00171 |
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Target: 5'- cUUGCCCAAACUCAGCACCGAGAAGUUg -3' miRNA: 3'- -AACGGGUUUGAGUCGUGGCUCUUCAA- -5' |
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| 358 | 3' | -52.9 | AC_000011.1 | + | 12941 | 0.8 | 0.084467 |
|
Target: 5'- -cGCCCcaguacgcGCUCAGCACCGAGGAGg- -3' miRNA: 3'- aaCGGGuu------UGAGUCGUGGCUCUUCaa -5' |
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| 358 | 3' | -52.9 | AC_000011.1 | + | 16802 | 0.68 | 0.536615 |
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Target: 5'- -aGCCCAGcAC-CAGCACCauGGAGGUg -3' miRNA: 3'- aaCGGGUU-UGaGUCGUGGc-UCUUCAa -5' |
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| 358 | 3' | -52.9 | AC_000011.1 | + | 22918 | 0.66 | 0.630694 |
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Target: 5'- cUGCCCAucguCUCGGC-CUGGGAgaagGGUa -3' miRNA: 3'- aACGGGUuu--GAGUCGuGGCUCU----UCAa -5' |
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| 358 | 3' | -52.9 | AC_000011.1 | + | 13458 | 0.66 | 0.654457 |
|
Target: 5'- -cGCCCGcgcuuGCUgGGCGaaGAGGAGUa -3' miRNA: 3'- aaCGGGUu----UGAgUCGUggCUCUUCAa -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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