miRNA: 3'- -UGGgCGGugCGAC-GCCAauu-----CGCUCG- -5'
miRNA: 3'- uGGGCGGUGCGACGCcaauUCGC---UCG- -5'
miRNA: 3'- -UGGGCGG---UGCG---ACGCCaa-------UUCGCUCG- -5'
miRNA: 3'- -UGGG-CGGug---CGA--CGCCAa-UUCGCUCG- -5'
miRNA: 3'- -UGGGCGGUGCGACGCCAAUUCGCUCG- -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 | |||||||
| 1029 | 3' | -57.5 | NC_000924.1 | + | 26751 | 0.66 | 0.585044 |
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Target: 5'- uACCgGUUugGCUGuCGGUgccuuucuGUGGGCu -3' miRNA: 3'- -UGGgCGGugCGAC-GCCAauu-----CGCUCG- -5' |
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| 1029 | 3' | -57.5 | NC_000924.1 | + | 36202 | 0.67 | 0.54257 |
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Target: 5'- cCCCGUCACGCUGUGu---GGUGuacGGCu -3' miRNA: 3'- uGGGCGGUGCGACGCcaauUCGC---UCG- -5' |
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| 1029 | 3' | -57.5 | NC_000924.1 | + | 31614 | 0.68 | 0.511392 |
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Target: 5'- aGCCCGCUcugAUGCcuaUGCGGaacaaaucaAGGCGGGCc -3' miRNA: 3'- -UGGGCGG---UGCG---ACGCCaa-------UUCGCUCG- -5' |
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| 1029 | 3' | -57.5 | NC_000924.1 | + | 21094 | 0.7 | 0.386747 |
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Target: 5'- cGCCCgGCCcuuuaGCUcaGUGGUgaGAGCGAGCg -3' miRNA: 3'- -UGGG-CGGug---CGA--CGCCAa-UUCGCUCG- -5' |
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| 1029 | 3' | -57.5 | NC_000924.1 | + | 56476 | 1.1 | 0.000571 |
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Target: 5'- cACCCGCCACGCUGCGGUUAAGCGAGCc -3' miRNA: 3'- -UGGGCGGUGCGACGCCAAUUCGCUCG- -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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