clear; clf; 
hold on;
%% Plotting the boundaries for Scer chr11
plot([645000,671445],[-5000,-5000],'k-');
plot([645000,645000],[-4500,-5500],'k-');
plot([671445,671445],[-4500,-5500],'k-');
%% Text at position 671445,-5300:  Scer chr11
h = text(671445.0, -5300.0, 'Scer chr11');
set(h,'VerticalAlignment','top')
set(h,'HorizontalAlignment','right')
set(h,'Interpreter','none')
set(h,'FontName','Times')
set(h,'FontSize',8)
%% Hooks at the end of Scer chr11
plot([645000,645000,645000],[-5500,-5500,-5400],'k-');
plot([671445,671445,671445],[-4500,-4500,-4600],'k-');
%% 
%% Arrow from [645985,649494] to [-5000,-5000].  Width 300, indent 400, length 3509
fill([645985.00,649094.00,649494.00,649094.00,645985.00,645985.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'b-');
%% Text at position 647739,-4700:  YKR102W (FLO10)
h = text(647739.0, -4700.0, 'YKR102W (FLO10)');
set(h,'VerticalAlignment','middle')
set(h,'HorizontalAlignment','left')
set(h,'Interpreter','none')
set(h,'FontName','Times')
set(h,'FontSize',8)
set(h,'Rotation',90)
%% 
%% Arrow from [652709,656365] to [-5000,-5000].  Width 300, indent 400, length 3656
fill([652709.00,655965.00,656365.00,655965.00,652709.00,652709.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'b-');
%% Text at position 654537,-4700:  YKR103W
h = text(654537.0, -4700.0, 'YKR103W');
set(h,'VerticalAlignment','middle')
set(h,'HorizontalAlignment','left')
set(h,'Interpreter','none')
set(h,'FontName','Times')
set(h,'FontSize',8)
set(h,'Rotation',90)
%% 
%% Arrow from [656465,657385] to [-5000,-5000].  Width 300, indent 400, length 920
fill([656465.00,656985.00,657385.00,656985.00,656465.00,656465.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'b-');
%% Text at position 656925,-4700:  YKR104W
h = text(656925.0, -4700.0, 'YKR104W');
set(h,'VerticalAlignment','middle')
set(h,'HorizontalAlignment','left')
set(h,'Interpreter','none')
set(h,'FontName','Times')
set(h,'FontSize',8)
set(h,'Rotation',90)
%% 
%% Arrow from [660093,658345] to [-5000,-5000].  Width 300, indent 400, length 1748
fill([660093.00,658745.00,658345.00,658745.00,660093.00,660093.00], ...
	[-4700.00,-4700.00,-5000.00,-5300.00,-5300.00,-4700.00], 'r-');
%% Text at position 659219,-4700:  YKR105C
h = text(659219.0, -4700.0, 'YKR105C');
set(h,'VerticalAlignment','middle')
set(h,'HorizontalAlignment','left')
set(h,'Interpreter','none')
set(h,'FontName','Times')
set(h,'FontSize',8)
set(h,'Rotation',90)
%% 
%% Arrow from [661071,662918] to [-5000,-5000].  Width 300, indent 400, length 1847
fill([661071.00,662518.00,662918.00,662518.00,661071.00,661071.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'b-');
%% Text at position 661994,-4700:  YKR106W
h = text(661994.0, -4700.0, 'YKR106W');
set(h,'VerticalAlignment','middle')
set(h,'HorizontalAlignment','left')
set(h,'Interpreter','none')
set(h,'FontName','Times')
set(h,'FontSize',8)
set(h,'Rotation',90)
%% 
%% Arrow from [665059,665297] to [-5000,-5000].  Width 300, indent 214.2, length 238
fill([665059.00,665082.80,665297.00,665082.80,665059.00,665059.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'm-');
%% Text at position 665178,-4700:  YKRWOMEGA1
h = text(665178.0, -4700.0, 'YKRWOMEGA1');
set(h,'VerticalAlignment','middle')
set(h,'HorizontalAlignment','left')
set(h,'Interpreter','none')
set(h,'FontName','Times')
set(h,'FontSize',8)
set(h,'Rotation',90)
%% Plotting the boundaries for Spar contig403
plot([647172,663161],[-10000,-10000],'k-');
plot([647172,647172],[-9500,-10500],'k-');
plot([663161,663161],[-9500,-10500],'k-');
%% Text at position 663161,-10300:  Spar contig403
h = text(663161.0, -10300.0, 'Spar contig403');
set(h,'VerticalAlignment','top')
set(h,'HorizontalAlignment','right')
set(h,'Interpreter','none')
set(h,'FontName','Times')
set(h,'FontSize',8)
%% Hooks at the end of Spar contig403
plot([647172,646839,646839],[-10500,-10500,-10400],'k-');
plot([663161,663455,663455],[-9500,-9500,-9600],'k-');
%% 
%% Arrow from [650012,649836] to [-10000,-10000].  Width 300, indent 158.4, length 176
fill([650012.00,649994.40,649836.00,649994.40,650012.00,650012.00], ...
	[-9700.00,-9700.00,-10000.00,-10300.00,-10300.00,-9700.00], 'w-');
%% Text at position 649924,-9700:  NoHit12910
h = text(649924.0, -9700.0, 'NoHit12910');
set(h,'VerticalAlignment','middle')
set(h,'HorizontalAlignment','left')
set(h,'Interpreter','none')
set(h,'FontName','Times')
set(h,'FontSize',8)
set(h,'Rotation',90)
%% 
%% Arrow from [651832,651626] to [-10000,-10000].  Width 300, indent 185.4, length 206
fill([651832.00,651811.40,651626.00,651811.40,651832.00,651832.00], ...
	[-9700.00,-9700.00,-10000.00,-10300.00,-10300.00,-9700.00], 'w-');
%% Text at position 651729,-9700:  NoHit12908
h = text(651729.0, -9700.0, 'NoHit12908');
set(h,'VerticalAlignment','middle')
set(h,'HorizontalAlignment','left')
set(h,'Interpreter','none')
set(h,'FontName','Times')
set(h,'FontSize',8)
set(h,'Rotation',90)
%% 
%% Arrow from [652645,657327] to [-10000,-10000].  Width 300, indent 400, length 4682
fill([652645.00,656927.00,657327.00,656927.00,652645.00,652645.00], ...
	[-10300.00,-10300.00,-10000.00,-9700.00,-9700.00,-10300.00], 'b-');
%% Text at position 654986,-9700:  YKR103W
h = text(654986.0, -9700.0, 'YKR103W');
set(h,'VerticalAlignment','middle')
set(h,'HorizontalAlignment','left')
set(h,'Interpreter','none')
set(h,'FontName','Times')
set(h,'FontSize',8)
set(h,'Rotation',90)
%% 
%% Arrow from [657727,657885] to [-10000,-10000].  Width 300, indent 142.2, length 158
fill([657727.00,657742.80,657885.00,657742.80,657727.00,657727.00], ...
	[-10300.00,-10300.00,-10000.00,-9700.00,-9700.00,-10300.00], 'w-');
%% Text at position 657806,-9700:  NoHit12901
h = text(657806.0, -9700.0, 'NoHit12901');
set(h,'VerticalAlignment','middle')
set(h,'HorizontalAlignment','left')
set(h,'Interpreter','none')
set(h,'FontName','Times')
set(h,'FontSize',8)
set(h,'Rotation',90)
%% 
%% Arrow from [660093,658345] to [-10000,-10000].  Width 300, indent 400, length 1748
fill([660093.00,658745.00,658345.00,658745.00,660093.00,660093.00], ...
	[-9700.00,-9700.00,-10000.00,-10300.00,-10300.00,-9700.00], 'r-');
%% Text at position 659219,-9700:  
h = text(659219.0, -9700.0, '');
set(h,'VerticalAlignment','middle')
set(h,'HorizontalAlignment','left')
set(h,'Interpreter','none')
set(h,'FontName','Times')
set(h,'FontSize',8)
set(h,'Rotation',90)
%% 
%% Arrow from [661083,662930] to [-10000,-10000].  Width 300, indent 400, length 1847
fill([661083.00,662530.00,662930.00,662530.00,661083.00,661083.00], ...
	[-10300.00,-10300.00,-10000.00,-9700.00,-9700.00,-10300.00], 'g-');
%% Text at position 662007,-9700:  YKR106W
h = text(662007.0, -9700.0, 'YKR106W');
set(h,'VerticalAlignment','middle')
set(h,'HorizontalAlignment','left')
set(h,'Interpreter','none')
set(h,'FontName','Times')
set(h,'FontSize',8)
set(h,'Rotation',90)
%% Plotting the boundaries for Smik contig124
plot([646573.0,662620.0],[-15000,-15000],'k-');
plot([646573.0,646573.0],[-14500,-15500],'k-');
plot([662620.0,662620.0],[-14500,-15500],'k-');
%% Text at position 662620.0,-15300:  Smik contig124
h = text(662620.0, -15300.0, 'Smik contig124');
set(h,'VerticalAlignment','top')
set(h,'HorizontalAlignment','right')
set(h,'Interpreter','none')
set(h,'FontName','Times')
set(h,'FontSize',8)
%% Hooks at the end of Smik contig124
plot([646573.0,644772.0,644772.0],[-15500,-15500,-15400],'k-');
plot([662620.0,663042.0,663042.0],[-14500,-14500,-14600],'k-');
%% 
%% Arrow from [649128.0,648637.0] to [-15000,-15000].  Width 300, indent 400, length 491
fill([649128.00,649037.00,648637.00,649037.00,649128.00,649128.00], ...
	[-14700.00,-14700.00,-15000.00,-15300.00,-15300.00,-14700.00], 'b-');
%% Text at position 648882.0,-14700:  YAL064W-B
h = text(648882.0, -14700.0, 'YAL064W-B');
set(h,'VerticalAlignment','middle')
set(h,'HorizontalAlignment','left')
set(h,'Interpreter','none')
set(h,'FontName','Times')
set(h,'FontSize',8)
set(h,'Rotation',90)
%% 
%% Arrow from [652584.0,657371.0] to [-15000,-15000].  Width 300, indent 400, length 4787
fill([652584.00,656971.00,657371.00,656971.00,652584.00,652584.00], ...
	[-15300.00,-15300.00,-15000.00,-14700.00,-14700.00,-15300.00], 'b-');
%% Text at position 654977.0,-14700:  YKR103W
h = text(654977.0, -14700.0, 'YKR103W');
set(h,'VerticalAlignment','middle')
set(h,'HorizontalAlignment','left')
set(h,'Interpreter','none')
set(h,'FontName','Times')
set(h,'FontSize',8)
set(h,'Rotation',90)
%% 
%% Arrow from [660090.0,658348.0] to [-15000,-15000].  Width 300, indent 400, length 1742
fill([660090.00,658748.00,658348.00,658748.00,660090.00,660090.00], ...
	[-14700.00,-14700.00,-15000.00,-15300.00,-15300.00,-14700.00], 'r-');
%% Text at position 659219.0,-14700:  
h = text(659219.0, -14700.0, '');
set(h,'VerticalAlignment','middle')
set(h,'HorizontalAlignment','left')
set(h,'Interpreter','none')
set(h,'FontName','Times')
set(h,'FontSize',8)
set(h,'Rotation',90)
%% 
%% Arrow from [661068.0,662075.0] to [-15000,-15000].  Width 300, indent 400, length 1007
fill([661068.00,661675.00,662075.00,661675.00,661068.00,661068.00], ...
	[-15300.00,-15300.00,-15000.00,-14700.00,-14700.00,-15300.00], 'b-');
%% Text at position 661571.0,-14700:  YKR106W
h = text(661571.0, -14700.0, 'YKR106W');
set(h,'VerticalAlignment','middle')
set(h,'HorizontalAlignment','left')
set(h,'Interpreter','none')
set(h,'FontName','Times')
set(h,'FontSize',8)
set(h,'Rotation',90)
%% 
%% Arrow from [662029.0,662619.0] to [-15000,-15000].  Width 300, indent 400, length 590
fill([662029.00,662219.00,662619.00,662219.00,662029.00,662029.00], ...
	[-15300.00,-15300.00,-15000.00,-14700.00,-14700.00,-15300.00], 'b-');
%% Text at position 662324.0,-14700:  YKR106W
h = text(662324.0, -14700.0, 'YKR106W');
set(h,'VerticalAlignment','middle')
set(h,'HorizontalAlignment','left')
set(h,'Interpreter','none')
set(h,'FontName','Times')
set(h,'FontSize',8)
set(h,'Rotation',90)
%% 
%% 
%% Plot x_dashed vs. y_dashed
%% 
%% 
%% Seting variable x_dashed.  3 values, [min,avg,max]=[661068.0..661074.0..661083]
x_dashed = [...
	661071,661083,661068.0];
%% Seting variable y_dashed.  3 values, [min,avg,max]=[-15000..-10000..-5000]
y_dashed = [...
	-5000,-10000,-15000];
plot(x_dashed, y_dashed, 'k.:')
%% 
%% 
%% Plot x_dashed vs. y_dashed
%% 
%% 
%% Seting variable x_dashed.  3 values, [min,avg,max]=[662619.0..662822.333333..662930]
x_dashed = [...
	662918,662930,662619.0];
%% Seting variable y_dashed.  3 values, [min,avg,max]=[-15000..-10000..-5000]
y_dashed = [...
	-5000,-10000,-15000];
plot(x_dashed, y_dashed, 'k.:')
%% 
%% 
%% Plot x_dashed vs. y_dashed
%% 
%% 
%% Seting variable x_dashed.  3 values, [min,avg,max]=[660090.0..660092.0..660093]
x_dashed = [...
	660093,660093,660090.0];
%% Seting variable y_dashed.  3 values, [min,avg,max]=[-15000..-10000..-5000]
y_dashed = [...
	-5000,-10000,-15000];
plot(x_dashed, y_dashed, 'k.:')
%% 
%% 
%% Plot x_dashed vs. y_dashed
%% 
%% 
%% Seting variable x_dashed.  3 values, [min,avg,max]=[658345..658346.0..658348.0]
x_dashed = [...
	  658345,  658345,658348.0];
%% Seting variable y_dashed.  3 values, [min,avg,max]=[-15000..-10000..-5000]
y_dashed = [...
	-5000,-10000,-15000];
plot(x_dashed, y_dashed, 'k.:')
%% 
%% 
%% Plot x_dashed vs. y_dashed
%% 
%% 
%% Seting variable x_dashed.  3 values, [min,avg,max]=[652584.0..652646.0..652709]
x_dashed = [...
	652709,652645,652584.0];
%% Seting variable y_dashed.  3 values, [min,avg,max]=[-15000..-10000..-5000]
y_dashed = [...
	-5000,-10000,-15000];
plot(x_dashed, y_dashed, 'k.:')
%% 
%% 
%% Plot x_dashed vs. y_dashed
%% 
%% 
%% Seting variable x_dashed.  3 values, [min,avg,max]=[656365..657021.0..657371.0]
x_dashed = [...
	  656365,  657327,657371.0];
%% Seting variable y_dashed.  3 values, [min,avg,max]=[-15000..-10000..-5000]
y_dashed = [...
	-5000,-10000,-15000];
plot(x_dashed, y_dashed, 'k.:')
ax = axis;
axis([ax(1),ax(2),ax(3),0]);
h = gcf;
h2 = get(h,'CurrentAxes');
set(h2,'YAxisLocation','right');
title('Scer ChrXI tile 14 positions 650kbp to 666kbp aligned against Spar Smik Sbay');
