miRNA: 3'- aUCGGCGCACCGgUCAC-C-UGGca-AGa -5'
miRNA: 3'- auCGGCGCaCCGG-------------UCACCUGGcaaga -5'
miRNA: 3'- -AUCGGCGCa---CCGGUCACCU-------GGCaAGa -5'
miRNA: 3'- aUCGgCGCAC--CGG----UCACC---UGGCAAGa -5'
miRNA: 3'- aUCGG-CGCa--CCGGUCACCUgGCaAGa -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 | |||||||
| 30887 | 5' | -59.3 | NC_006552.1 | + | 47897 | 0.66 | 0.538546 |
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Target: 5'- cGGCCGCGUGGC-GGUGaGuACCuggUCg -3' miRNA: 3'- aUCGGCGCACCGgUCAC-C-UGGca-AGa -5' |
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| 30887 | 5' | -59.3 | NC_006552.1 | + | 7231 | 0.66 | 0.50669 |
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Target: 5'- -uGCCGCG-GGCCugcgccaucaacuGGUGGACCu---- -3' miRNA: 3'- auCGGCGCaCCGG-------------UCACCUGGcaaga -5' |
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| 30887 | 5' | -59.3 | NC_006552.1 | + | 64450 | 0.68 | 0.401271 |
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Target: 5'- cUGGCCGUGguggGGCUGGUGGAgacauucCCGaUCa -3' miRNA: 3'- -AUCGGCGCa---CCGGUCACCU-------GGCaAGa -5' |
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| 30887 | 5' | -59.3 | NC_006552.1 | + | 39780 | 0.68 | 0.393274 |
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Target: 5'- cAGCgGCGUGucGCCcgcaGGUGGcaaGCCGUUCa -3' miRNA: 3'- aUCGgCGCAC--CGG----UCACC---UGGCAAGa -5' |
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| 30887 | 5' | -59.3 | NC_006552.1 | + | 32705 | 0.72 | 0.219962 |
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Target: 5'- cGGCCgGCGcggGGCCGGUGGAgCGcUCg -3' miRNA: 3'- aUCGG-CGCa--CCGGUCACCUgGCaAGa -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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