%!PS-Adobe-3.0 EPSF-3.0
%%Title: RNA Dot Plot
%%Creator: ViennaRNA-2.2.10
%%CreationDate: Tue Dec 19 19:42:58 2017
%%BoundingBox: 66 211 518 662
%%DocumentFonts: Helvetica
%%Pages: 1
%%EndComments

%Options: 
% 
%This file contains the square roots of the base pair probabilities in the form
% i  j  sqrt(p(i,j)) ubox

%%BeginProlog
/DPdict 100 dict def
DPdict begin
/logscale false def
/lpmin 1e-05 log def

/box { %size x y box - draws box centered on x,y
   2 index 0.5 mul sub            % x -= 0.5
   exch 2 index 0.5 mul sub exch  % y -= 0.5
   3 -1 roll dup rectfill
} bind def

/ubox {
   logscale {
      log dup add lpmin div 1 exch sub dup 0 lt { pop 0 } if
   } if
   3 1 roll
   exch len exch sub 1 add box
} bind def

/lbox {
   3 1 roll
   len exch sub 1 add box
} bind def

/drawseq {
% print sequence along all 4 sides
[ [0.7 -0.3 0 ]
  [0.7 0.7 len add 0]
  [-0.3 len sub -0.4 -90]
  [-0.3 len sub 0.7 len add -90]
] {
   gsave
    aload pop rotate translate
    0 1 len 1 sub {
     dup 0 moveto
     sequence exch 1 getinterval
     show
    } for
   grestore
  } forall
} bind def

/drawgrid{
  0.01 setlinewidth
  len log 0.9 sub cvi 10 exch exp  % grid spacing
  dup 1 gt {
     dup dup 20 div dup 2 array astore exch 40 div setdash
  } { [0.3 0.7] 0.1 setdash } ifelse
  0 exch len {
     dup dup
     0 moveto
     len lineto
     dup
     len exch sub 0 exch moveto
     len exch len exch sub lineto
     stroke
  } for
  [] 0 setdash
  0.04 setlinewidth
  currentdict /cutpoint known {
    cutpoint 1 sub
    dup dup -1 moveto len 1 add lineto
    len exch sub dup
    -1 exch moveto len 1 add exch lineto
    stroke
  } if
  0.5 neg dup translate
} bind def

end
%%EndProlog
DPdict begin
%delete next line to get rid of title
270 665 moveto /Helvetica findfont 14 scalefont setfont (Anolis_caro_chrUn_GL343207.trna3_AlaAGC) show

/sequence { (\
GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA\
) } def
/len { sequence length } bind def

72 216 translate
72 6 mul len 1 add div dup scale
/Helvetica findfont 0.95 scalefont setfont

drawseq
0.5 dup translate
% draw diagonal
0.04 setlinewidth
0 len moveto len 0 lineto stroke

/min { 2 copy gt { exch } if pop } bind def

/utri{ % i j prob utri
  gsave
  1 min 2 div
  0.85 mul 0.15 add 0.95  0.33
  3 1 roll % prepare hsb color
  sethsbcolor
  % now produce the coordinates for lines
  exch 1 sub dup len exch sub dup 4 -1 roll dup 3 1 roll dup len exch sub
  moveto lineto lineto closepath fill
  grestore
} bind def
/uHmotif{ % i j uHmotif
  gsave
  1 min 2 div
  0.85 mul 0.15 add 0.95  0.99
  3 1 roll % prepare hsb color
  sethsbcolor
  % now produce the coordinates for lines
  exch 1 sub dup len exch sub dup 4 -1 roll dup 3 1 roll dup len exch sub
  moveto lineto lineto closepath fill
  grestore
} bind def
/lHmotif{ % i j lHmotif
  gsave
  1 min 2 div
  0.85 mul 0.15 add 0.95  0.99
  3 1 roll % prepare hsb color
  sethsbcolor
  % now produce the coordinates for lines
  dup len exch sub dup 4 -1 roll 1 sub dup 3 1 roll dup len exch sub
  moveto lineto lineto closepath fill
  grestore
} bind def
/uImotif{ % i j k l uImotif
  gsave
  1 min 2 div
  0.85 mul 0.15 add 0.95  0.99
  3 1 roll % prepare hsb color
  sethsbcolor
  % now produce the coordinates for lines
  1 sub dup 5 1 roll exch len exch sub dup 5 1 roll 3 -1 roll dup
  5 1 roll exch 4 1 roll 3 1 roll exch 1 sub len exch sub dup 3 1 roll
  moveto lineto lineto lineto closepath fill
  grestore
} bind def
/lImotif{ % i j k l lImotif
  gsave
  1 min 2 div
  0.85 mul 0.15 add 0.95  0.99
  3 1 roll % prepare hsb color
  sethsbcolor
  % now produce the coordinates for lines
  4 -1 roll 1 sub dup 5 1 roll exch 1 sub len exch sub dup 3 -1 roll exch
  5 -1 roll len exch sub dup 6 -1 roll dup 3 1 roll 7 4 roll
  moveto lineto lineto lineto closepath fill
  grestore
} bind def

%data starts here

%start of quadruplex data

%start of Hmotif data

%start of Imotif data

%draw the grid
drawgrid

%start of base pair probability data
1 71 0.011137621 ubox
1 72 0.998618513 ubox
2 70 0.011249479 ubox
2 71 0.999343269 ubox
2 72 0.029380302 ubox
3 69 0.016278852 ubox
3 70 0.998657995 ubox
3 71 0.029349731 ubox
3 72 0.013044031 ubox
4 68 0.015570075 ubox
4 69 0.999660285 ubox
4 70 0.006500567 ubox
4 71 0.013063530 ubox
5 67 0.017184802 ubox
5 68 0.995393993 ubox
5 70 0.012116272 ubox
6 20 0.003683136 ubox
6 47 0.007871866 ubox
6 67 0.961997835 ubox
6 68 0.010641824 ubox
7 19 0.003963646 ubox
7 22 0.016669769 ubox
7 23 0.006395271 ubox
7 26 0.010803708 ubox
7 45 0.003325342 ubox
7 46 0.008388346 ubox
7 66 0.889354167 ubox
8 18 0.004993356 ubox
8 21 0.043576199 ubox
8 22 0.009051039 ubox
8 23 0.003412982 ubox
8 26 0.053349931 ubox
8 44 0.006391561 ubox
8 45 0.009575801 ubox
8 46 0.006511628 ubox
8 48 0.044296110 ubox
8 66 0.051228716 ubox
9 17 0.005076838 ubox
9 20 0.044973880 ubox
9 47 0.045851242 ubox
9 67 0.006907131 ubox
10 20 0.031947572 ubox
10 25 0.993218795 ubox
10 47 0.003684611 ubox
10 61 0.005362683 ubox
11 18 0.045881626 ubox
11 19 0.032788757 ubox
11 22 0.010762380 ubox
11 24 0.996351171 ubox
11 43 0.031784396 ubox
11 45 0.044997253 ubox
11 46 0.003273388 ubox
11 60 0.005393685 ubox
12 18 0.028759750 ubox
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12 42 0.031993047 ubox
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12 58 0.005409282 ubox
13 18 0.016589428 ubox
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13 22 0.996158882 ubox
13 41 0.032010508 ubox
13 43 0.044839517 ubox
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14 20 0.079642667 ubox
14 56 0.005446527 ubox
15 20 0.129735024 ubox
15 55 0.005085787 ubox
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17 37 0.052295806 ubox
17 39 0.003520191 ubox
17 42 0.004660118 ubox
17 52 0.004889289 ubox
18 25 0.005375323 ubox
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27 46 0.039850990 ubox
28 34 0.019643833 ubox
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28 45 0.024434496 ubox
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29 45 0.003166236 ubox
30 36 0.012434123 ubox
30 40 0.998065717 ubox
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31 35 0.012393915 ubox
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31 43 0.003645699 ubox
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32 39 0.013599795 ubox
32 42 0.003678913 ubox
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33 37 0.102337630 ubox
33 39 0.003720007 ubox
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47 64 0.003785455 ubox
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56 60 0.024269416 ubox
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53 61 0.9500000 lbox
showpage
end
%%EOF