Hi I ran RNAplfold as RNAplfold -W 60 -u 11 < trial.fa on a sequence of length 71, it gives me an output of matrix(in the file with extension '_lunp'), with 71 rows and 11 columns, however I didn't quiet get the concept.According to the documentation it says that it will calculate the average probability over each u of 11 length over sliding window of length 60, if that's the case then why is it that in the matrix the first 10 rows have NA in their 11 length windows:

```
#i$ l=1 2 3 4 5 6 7 8 9 10 11
1 0.9469881 NA NA NA NA NA NA NA NA NA NA
2 0.7428546 0.7108948 NA NA NA NA NA NA NA NA NA
3 0.7833689 0.6985533 0.6691537 NA NA NA NA NA NA NA NA
4 0.8540909 0.7242232 0.655665 0.6532912 NA NA NA NA NA NA NA
5 0.8320361 0.7807689 0.686046 0.6210906 0.6206707 NA NA NA NA NA NA
6 0.9145157 0.7697201 0.7289685 0.6372758 0.5771261 0.5777204 NA NA NA NA NA
7 0.9481671 0.9134377 0.7694369 0.7286978 0.6370939 0.5769615 0.5775573 NA NA NA NA
8 0.9930493 0.9427189 0.9119256 0.7681018 0.7271193 0.6369164 0.5768006 0.577397 NA NA NA
9 0.996136 0.9919387 0.9416257 0.9109458 0.7673214 0.7262351 0.6367918 0.5766883 0.5772853 NA NA
10 0.5856886 0.5843086 0.5835655 0.5382947 0.5172792 0.4713382 0.4463127 0.4205373 0.3834285 0.3872539 NA
```

and also why would the last row contain average probabilities over 11 nucleotides when 71st sequence is the last one?

```
71 0.0572429 0.006454323 0.005939727 0.005937336 0.005934025 0.005908198 0.005830827 0.005815964 0.005814055 0.005804212 0.005767331
```

Thanks

So does that mean that for the probability of the first 11 mer being unpaired would be under 11 th row and 11 the column i.e at 11-11+1...11? for instance

11 0.6214644 0.5804635 0.5794147 0.5787987 0.5336643 0.512956 0.4683483 0.4437102 0.4185386 0.381642

0.3854975The last one will be the probability of first 11 mer being unpaired correct?

Yes, it seems so.....