miRNA: 3'- -ACCUCUGUcACAGAGG---------UCUC--------------CCCGCa -5'
miRNA: 3'- -ACCUCUGUCACAGa----GGU-CUCC--------CCGCA- -5'
miRNA: 3'- -ACCUCUGUCACa---Ga---GGUCU-CCCCGCa -5'
miRNA: 3'- -ACCUCUGUCACAGAGGUCUCCCCGCA- -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 | |||||||
| 259 | 5' | -58.2 | AC_000008.1 | + | 17544 | 0.69 | 0.2874 |
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Target: 5'- cUGGAGACAcUGUCUCCacggccgguGGAGgcuccucuacgggaGGGCGg -3' miRNA: 3'- -ACCUCUGUcACAGAGG---------UCUC--------------CCCGCa -5' |
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| 259 | 5' | -58.2 | AC_000008.1 | + | 15197 | 0.71 | 0.200107 |
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Target: 5'- gUGGAGGCGGUGUUgugggCCAuGGGGaagaagguGGCGUa -3' miRNA: 3'- -ACCUCUGUCACAGa----GGU-CUCC--------CCGCA- -5' |
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| 259 | 5' | -58.2 | AC_000008.1 | + | 11803 | 0.73 | 0.135662 |
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Target: 5'- gUGGAGGCGGUGguggCgaacUCAGAgGGGGCGg -3' miRNA: 3'- -ACCUCUGUCACa---Ga---GGUCU-CCCCGCa -5' |
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| 259 | 5' | -58.2 | AC_000008.1 | + | 18342 | 1.08 | 0.000341 |
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Target: 5'- gUGGAGACAGUGUCUCCAGAGGGGCGUg -3' miRNA: 3'- -ACCUCUGUCACAGAGGUCUCCCCGCA- -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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