miRNA: 3'- -AAUCuuCuu---AAGCGGCCa-GG----------CCAUGG- -5'
miRNA: 3'- -AAUCUUCUUAAGCGGCCAGGCCAUGG- -5'
miRNA: 3'- aAUCUu-----CUUAAGCGGCcaGGCCaUGG- -5'
miRNA: 3'- aAUCuuCUUAAGCGGCCag-----GCCAuGG- -5'
miRNA: 3'- aaucuucuuaAGCGGC-CAGGCC--AUGG- -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 |
| Predicted miRNA align pattern | |||||||
| 1301 | 3' | -50.8 | NC_001331.1 | + | 1089 | 0.68 | 0.2621 |
|
Target: 5'- gUUGGggGcguucUUCGCCGGcgCCuucaucaccgGGUACCg -3' miRNA: 3'- -AAUCuuCuu---AAGCGGCCa-GG----------CCAUGG- -5' |
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| 1301 | 3' | -50.8 | NC_001331.1 | + | 1157 | 1.09 | 0.000158 |
|
Target: 5'- gUUAGAAGAAUUCGCCGGUCCGGUACCc -3' miRNA: 3'- -AAUCUUCUUAAGCGGCCAGGCCAUGG- -5' |
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| 1301 | 3' | -50.8 | NC_001331.1 | + | 2256 | 0.66 | 0.343151 |
|
Target: 5'- gUGGGuuccuuGAGUUCGCCG--CCGGgGCCu -3' miRNA: 3'- aAUCUu-----CUUAAGCGGCcaGGCCaUGG- -5' |
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| 1301 | 3' | -50.8 | NC_001331.1 | + | 4616 | 0.67 | 0.305049 |
|
Target: 5'- gUGGucGAGUUCGCCGGcuacgaaUGGU-CCa -3' miRNA: 3'- aAUCuuCUUAAGCGGCCag-----GCCAuGG- -5' |
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| 1301 | 3' | -50.8 | NC_001331.1 | + | 6613 | 0.66 | 0.363448 |
|
Target: 5'- ---------gUCGCCGuGUCCGGacUGCCg -3' miRNA: 3'- aaucuucuuaAGCGGC-CAGGCC--AUGG- -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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