miRNA: 3'- -ACgaCGUCCCGUGgU-UACCAgG--------------ACUG- -5'
miRNA: 3'- -ACGAC-GUCCCGUGGUu--------ACCAGgACUG- -5'
miRNA: 3'- aCGACG----UCCCGugGu--UACCA--GGACUG- -5'
miRNA: 3'- -ACGACGUCCCGUGGUUACCAGGACUG- -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
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| Predicted miRNA align pattern | |||||||
| 16921 | 3' | -57 | NC_004313.1 | + | 26408 | 0.65 | 0.50156 |
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Target: 5'- cUGgaGCAGGGCGCgGaAUGGUgCagucuguuucagcgUGACa -3' miRNA: 3'- -ACgaCGUCCCGUGgU-UACCAgG--------------ACUG- -5' |
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| 16921 | 3' | -57 | NC_004313.1 | + | 2344 | 0.68 | 0.366352 |
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Target: 5'- uUGUUGcCGGGGCGCUGugcauguucUGGUCgUGGCu -3' miRNA: 3'- -ACGAC-GUCCCGUGGUu--------ACCAGgACUG- -5' |
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| 16921 | 3' | -57 | NC_004313.1 | + | 37145 | 0.71 | 0.236654 |
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Target: 5'- cGCUGUuugaAGGGUugCuguGUGGUucCCUGACc -3' miRNA: 3'- aCGACG----UCCCGugGu--UACCA--GGACUG- -5' |
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| 16921 | 3' | -57 | NC_004313.1 | + | 11454 | 1.1 | 0.000286 |
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Target: 5'- cUGCUGCAGGGCACCAAUGGUCCUGACg -3' miRNA: 3'- -ACGACGUCCCGUGGUUACCAGGACUG- -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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