miRNA: 3'- aaUCGuAGACGCGACUa-----------AGGUUCCGg -5'
miRNA: 3'- aauCGUAGACGCgacua-----AGGUUCCGg -5'
miRNA: 3'- aAUCGUAGaCGCGacuaAGGUuCCGG- -5'
miRNA: 3'- aaUCGuAGACGCGACUa----------AGGU--UCCGG- -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 |
| Predicted miRNA align pattern | |||||||
| 32354 | 5' | -52.1 | NC_007024.1 | + | 40706 | 0.76 | 0.286349 |
|
Target: 5'- -aAGC-UCUGCGCUGAgccucuguggagUCCAAGGUa -3' miRNA: 3'- aaUCGuAGACGCGACUa-----------AGGUUCCGg -5' |
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| 32354 | 5' | -52.1 | NC_007024.1 | + | 37116 | 0.66 | 0.844192 |
|
Target: 5'- --cGUAUCUGCGagcggcaaggUCCGAGGCa -3' miRNA: 3'- aauCGUAGACGCgacua-----AGGUUCCGg -5' |
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| 32354 | 5' | -52.1 | NC_007024.1 | + | 22042 | 0.7 | 0.602691 |
|
Target: 5'- aUGGCAUCaGCGUgc--UCCAuGGCCg -3' miRNA: 3'- aAUCGUAGaCGCGacuaAGGUuCCGG- -5' |
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| 32354 | 5' | -52.1 | NC_007024.1 | + | 5813 | 0.72 | 0.480285 |
|
Target: 5'- -gGGC-UCUGCGCUGAaaaucgcauuaUCCGcuGGGCCu -3' miRNA: 3'- aaUCGuAGACGCGACUa----------AGGU--UCCGG- -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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