clear; clf; 
hold on;
%% Plotting the boundaries for Scer chr17
plot([45000,90779],[-5000,-5000],'k-');
plot([45000,45000],[-4500,-5500],'k-');
plot([90779,90779],[-4500,-5500],'k-');
%% Text at position 90779,-5300:  Scer chr17
h = text(90779.0, -5300.0, 'Scer chr17');
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 chr17
plot([45000,45000,45000],[-5500,-5500,-5400],'k-');
plot([90779,90779,90779],[-4500,-4500,-4600],'k-');
%% 
%% Arrow from [46723,46953] to [-5000,-5000].  Width 300, indent 207.0, length 230
fill([46723.00,46746.00,46953.00,46746.00,46723.00,46723.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'w-');
%% Text at position 46838,-4700:  Q0130 (OLI1)
h = text(46838.0, -4700.0, 'Q0130 (OLI1)');
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 [48201,48290] to [-5000,-5000].  Width 300, indent 80.1, length 89
fill([48201.00,48209.90,48290.00,48209.90,48201.00,48201.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'c-');
%% Text at position 48245,-4700:  tS(UGA)Q2 (TS(UGA)Q2)
h = text(48245.0, -4700.0, 'tS(UGA)Q2 (TS(UGA)Q2)');
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 [48901,50097] to [-5000,-5000].  Width 300, indent 400, length 1196
fill([48901.00,49697.00,50097.00,49697.00,48901.00,48901.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'b-');
%% Text at position 49499,-4700:  Q0140 (VAR1)
h = text(49499.0, -4700.0, 'Q0140 (VAR1)');
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 [51052,51228] to [-5000,-5000].  Width 300, indent 158.4, length 176
fill([51052.00,51069.60,51228.00,51069.60,51052.00,51052.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'w-');
%% Text at position 51140,-4700:  Q0142
h = text(51140.0, -4700.0, 'Q0142');
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 [51277,51429] to [-5000,-5000].  Width 300, indent 136.8, length 152
fill([51277.00,51292.20,51429.00,51292.20,51277.00,51277.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'w-');
%% Text at position 51353,-4700:  Q0143
h = text(51353.0, -4700.0, 'Q0143');
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 [54109,54438] to [-5000,-5000].  Width 300, indent 296.1, length 329
fill([54109.00,54141.90,54438.00,54141.90,54109.00,54109.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'w-');
%% Text at position 54273,-4700:  Q0144
h = text(54273.0, -4700.0, 'Q0144');
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 [58009,60724] to [-5000,-5000].  Width 300, indent 400, length 2715
fill([58009.00,60324.00,60724.00,60324.00,58009.00,58009.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'm-');
%% Text at position 59366,-4700:  21S_rRNA_3 (21S_RRNA_3)
h = text(59366.0, -4700.0, '21S_rRNA_3 (21S_RRNA_3)');
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 [61022,61729] to [-5000,-5000].  Width 300, indent 400, length 707
fill([61022.00,61329.00,61729.00,61329.00,61022.00,61022.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'w-');
%% Text at position 61375,-4700:  Q0160 (SCEI)
h = text(61375.0, -4700.0, 'Q0160 (SCEI)');
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 [61868,62447] to [-5000,-5000].  Width 300, indent 400, length 579
fill([61868.00,62047.00,62447.00,62047.00,61868.00,61868.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'm-');
%% Text at position 62157,-4700:  21S_rRNA_4 (21S_RRNA_4)
h = text(62157.0, -4700.0, '21S_rRNA_4 (21S_RRNA_4)');
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 [63862,63937] to [-5000,-5000].  Width 300, indent 67.5, length 75
fill([63862.00,63869.50,63937.00,63869.50,63862.00,63862.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'c-');
%% Text at position 63899,-4700:  tT(UGU)Q1 (TT(UGU)Q1)
h = text(63899.0, -4700.0, 'tT(UGU)Q1 (TT(UGU)Q1)');
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 [64415,64490] to [-5000,-5000].  Width 300, indent 67.5, length 75
fill([64415.00,64422.50,64490.00,64422.50,64415.00,64415.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'c-');
%% Text at position 64452,-4700:  tC(GCA)Q (TC(GCA)Q)
h = text(64452.0, -4700.0, 'tC(GCA)Q (TC(GCA)Q)');
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 [64596,64670] to [-5000,-5000].  Width 300, indent 66.6, length 74
fill([64596.00,64603.40,64670.00,64603.40,64596.00,64596.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'c-');
%% Text at position 64633,-4700:  tH(GUG)Q (TH(GUG)Q)
h = text(64633.0, -4700.0, 'tH(GUG)Q (TH(GUG)Q)');
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 [65770,66174] to [-5000,-5000].  Width 300, indent 363.6, length 404
fill([65770.00,65810.40,66174.00,65810.40,65770.00,65770.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'w-');
%% Text at position 65972,-4700:  Q0182
h = text(65972.0, -4700.0, 'Q0182');
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 [66095,66179] to [-5000,-5000].  Width 300, indent 75.6, length 84
fill([66095.00,66103.40,66179.00,66103.40,66095.00,66095.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'c-');
%% Text at position 66137,-4700:  tL(UAA)Q (TL(UAA)Q)
h = text(66137.0, -4700.0, 'tL(UAA)Q (TL(UAA)Q)');
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 [66210,66285] to [-5000,-5000].  Width 300, indent 67.5, length 75
fill([66210.00,66217.50,66285.00,66217.50,66210.00,66210.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'c-');
%% Text at position 66247,-4700:  tQ(UUG)Q (TQ(UUG)Q)
h = text(66247.0, -4700.0, 'tQ(UUG)Q (TQ(UUG)Q)');
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 [67061,67134] to [-5000,-5000].  Width 300, indent 65.7, length 73
fill([67061.00,67068.30,67134.00,67068.30,67061.00,67061.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'c-');
%% Text at position 67097,-4700:  tK(UUU)Q (TK(UUU)Q)
h = text(67097.0, -4700.0, 'tK(UUU)Q (TK(UUU)Q)');
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 [67309,67381] to [-5000,-5000].  Width 300, indent 64.8, length 72
fill([67309.00,67316.20,67381.00,67316.20,67309.00,67309.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'c-');
%% Text at position 67345,-4700:  tR(UCU)Q1 (TR(UCU)Q1)
h = text(67345.0, -4700.0, 'tR(UCU)Q1 (TR(UCU)Q1)');
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 [67468,67542] to [-5000,-5000].  Width 300, indent 66.6, length 74
fill([67468.00,67475.40,67542.00,67475.40,67468.00,67468.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'c-');
%% Text at position 67505,-4700:  tG(UCC)Q (TG(UCC)Q)
h = text(67505.0, -4700.0, 'tG(UCC)Q (TG(UCC)Q)');
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 [68322,68396] to [-5000,-5000].  Width 300, indent 66.6, length 74
fill([68322.00,68329.40,68396.00,68329.40,68322.00,68322.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'c-');
%% Text at position 68359,-4700:  tD(GUC)Q (TD(GUC)Q)
h = text(68359.0, -4700.0, 'tD(GUC)Q (TD(GUC)Q)');
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 [69203,69288] to [-5000,-5000].  Width 300, indent 76.5, length 85
fill([69203.00,69211.50,69288.00,69211.50,69203.00,69203.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'c-');
%% Text at position 69245,-4700:  tS(GCU)Q1 (TS(GCU)Q1)
h = text(69245.0, -4700.0, 'tS(GCU)Q1 (TS(GCU)Q1)');
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 [69289,69362] to [-5000,-5000].  Width 300, indent 65.7, length 73
fill([69289.00,69296.30,69362.00,69296.30,69289.00,69289.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'c-');
%% Text at position 69325,-4700:  tR(ACG)Q2 (TR(ACG)Q2)
h = text(69325.0, -4700.0, 'tR(ACG)Q2 (TR(ACG)Q2)');
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 [69846,69921] to [-5000,-5000].  Width 300, indent 67.5, length 75
fill([69846.00,69853.50,69921.00,69853.50,69846.00,69846.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'c-');
%% Text at position 69883,-4700:  tA(UGC)Q (TA(UGC)Q)
h = text(69883.0, -4700.0, 'tA(UGC)Q (TA(UGC)Q)');
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 [70162,70237] to [-5000,-5000].  Width 300, indent 67.5, length 75
fill([70162.00,70169.50,70237.00,70169.50,70162.00,70162.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'c-');
%% Text at position 70199,-4700:  tI(GAU)Q (TI(GAU)Q)
h = text(70199.0, -4700.0, 'tI(GAU)Q (TI(GAU)Q)');
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 [70824,70907] to [-5000,-5000].  Width 300, indent 74.7, length 83
fill([70824.00,70832.30,70907.00,70832.30,70824.00,70824.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'c-');
%% Text at position 70865,-4700:  tY(GUA)Q (TY(GUA)Q)
h = text(70865.0, -4700.0, 'tY(GUA)Q (TY(GUA)Q)');
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 [71433,71503] to [-5000,-5000].  Width 300, indent 63.0, length 70
fill([71433.00,71440.00,71503.00,71440.00,71433.00,71433.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'c-');
%% Text at position 71468,-4700:  tN(GUU)Q (TN(GUU)Q)
h = text(71468.0, -4700.0, 'tN(GUU)Q (TN(GUU)Q)');
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 [72630,72705] to [-5000,-5000].  Width 300, indent 67.5, length 75
fill([72630.00,72637.50,72705.00,72637.50,72630.00,72630.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'c-');
%% Text at position 72667,-4700:  TM(CAU)Q1 (TM(CAU)Q1)
h = text(72667.0, -4700.0, 'TM(CAU)Q1 (TM(CAU)Q1)');
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 [73758,74513] to [-5000,-5000].  Width 300, indent 400, length 755
fill([73758.00,74113.00,74513.00,74113.00,73758.00,73758.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'w-');
%% Text at position 74135,-4700:  Q0250 (COX2)
h = text(74135.0, -4700.0, 'Q0250 (COX2)');
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 [74495,75984] to [-5000,-5000].  Width 300, indent 400, length 1489
fill([74495.00,75584.00,75984.00,75584.00,74495.00,74495.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'w-');
%% Text at position 75239,-4700:  Q0255
h = text(75239.0, -4700.0, 'Q0255');
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 [77431,77505] to [-5000,-5000].  Width 300, indent 66.6, length 74
fill([77431.00,77438.40,77505.00,77438.40,77431.00,77431.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'c-');
%% Text at position 77468,-4700:  tF(GAA)Q (TF(GAA)Q)
h = text(77468.0, -4700.0, 'tF(GAA)Q (TF(GAA)Q)');
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 [78162,78089] to [-5000,-5000].  Width 300, indent 65.7, length 73
fill([78162.00,78154.70,78089.00,78154.70,78162.00,78162.00], ...
	[-4700.00,-4700.00,-5000.00,-5300.00,-5300.00,-4700.00], 'c-');
%% Text at position 78125,-4700:  tT(XXX)Q2 (TT(XXX)Q2)
h = text(78125.0, -4700.0, 'tT(XXX)Q2 (TT(XXX)Q2)');
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 [78533,78608] to [-5000,-5000].  Width 300, indent 67.5, length 75
fill([78533.00,78540.50,78608.00,78540.50,78533.00,78533.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'c-');
%% Text at position 78570,-4700:  tV(UAC)Q (TV(UAC)Q)
h = text(78570.0, -4700.0, 'tV(UAC)Q (TV(UAC)Q)');
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 [79213,80022] to [-5000,-5000].  Width 300, indent 400, length 809
fill([79213.00,79622.00,80022.00,79622.00,79213.00,79213.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'w-');
%% Text at position 79617,-4700:  Q0275 (COX3)
h = text(79617.0, -4700.0, 'Q0275 (COX3)');
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 [85035,85112] to [-5000,-5000].  Width 300, indent 69.3, length 77
fill([85035.00,85042.70,85112.00,85042.70,85035.00,85035.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'c-');
%% Text at position 85073,-4700:  tM(CAU)Q2 (TM(CAU)Q2)
h = text(85073.0, -4700.0, 'tM(CAU)Q2 (TM(CAU)Q2)');
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 [85290,85779] to [-5000,-5000].  Width 300, indent 400, length 489
fill([85290.00,85379.00,85779.00,85379.00,85290.00,85290.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'm-');
%% Text at position 85534,-4700:  9S_rRNA_5 (9S_RRNA_5)
h = text(85534.0, -4700.0, '9S_rRNA_5 (9S_RRNA_5)');
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 [85554,85709] to [-5000,-5000].  Width 300, indent 139.5, length 155
fill([85554.00,85569.50,85709.00,85569.50,85554.00,85554.00], ...
	[-5300.00,-5300.00,-5000.00,-4700.00,-4700.00,-5300.00], 'w-');
%% Text at position 85631,-4700:  Q0297
h = text(85631.0, -4700.0, 'Q0297');
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 contig1544
plot([46242,48378],[-10000,-10000],'k-');
plot([46242,46242],[-9500,-10500],'k-');
plot([48378,48378],[-9500,-10500],'k-');
%% Text at position 48378,-10300:  Smik contig1544
h = text(48378.0, -10300.0, 'Smik contig1544');
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 contig1544
plot([46242,46242,46242],[-10500,-10500,-10400],'k-');
plot([48378,48378,48378],[-9500,-9500,-9600],'k-');
%% 
%% Arrow from [46723,46953] to [-10000,-10000].  Width 300, indent 207.0, length 230
fill([46723.00,46746.00,46953.00,46746.00,46723.00,46723.00], ...
	[-10300.00,-10300.00,-10000.00,-9700.00,-9700.00,-10300.00], 'r-');
%% Text at position 46838,-9700:  
h = text(46838.0, -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 [46243,47553] to [-10000,-10000].  Width 300, indent 400, length 1310
fill([46243.00,47153.00,47553.00,47153.00,46243.00,46243.00], ...
	[-10300.00,-10300.00,-10000.00,-9700.00,-9700.00,-10300.00], 'm-');
%% Text at position 46898,-9700:  TyElmt_64 hits at 54%
h = text(46898.0, -9700.0, 'TyElmt_64 hits at 54%');
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 [47596,48378] to [-10000,-10000].  Width 300, indent 400, length 782
fill([47596.00,47978.00,48378.00,47978.00,47596.00,47596.00], ...
	[-10300.00,-10300.00,-10000.00,-9700.00,-9700.00,-10300.00], 'm-');
%% Text at position 47987,-9700:  TyElmt_86 hits at 55%
h = text(47987.0, -9700.0, 'TyElmt_86 hits at 55%');
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 contig7
plot([48552,49426],[-12500,-12500],'k-');
plot([48552,48552],[-12000,-13000],'k-');
plot([49426,49426],[-12000,-13000],'k-');
%% Text at position 49426,-12800:  Smik contig7
h = text(49426.0, -12800.0, 'Smik contig7');
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 contig7
plot([48552,48355,48355],[-13000,-13000,-12900],'k-');
plot([49426,51051,51051],[-12000,-12000,-12100],'k-');
%% 
%% Arrow from [48801,49424] to [-12500,-12500].  Width 300, indent 400, length 623
fill([48801.00,49024.00,49424.00,49024.00,48801.00,48801.00], ...
	[-12800.00,-12800.00,-12500.00,-12200.00,-12200.00,-12800.00], 'b-');
%% Text at position 49112,-12200:  YBR112C
h = text(49112.0, -12200.0, 'YBR112C');
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 [48901,49425] to [-12500,-12500].  Width 300, indent 400, length 524
fill([48901.00,49025.00,49425.00,49025.00,48901.00,48901.00], ...
	[-12800.00,-12800.00,-12500.00,-12200.00,-12200.00,-12800.00], 'r-');
%% Text at position 49163,-12200:  
h = text(49163.0, -12200.0, '');
set(h,'VerticalAlignment','middle')
set(h,'HorizontalAlignment','left')
set(h,'Interpreter','none')
set(h,'FontName','Times')
set(h,'FontSize',8)
set(h,'Rotation',90)
%% Plotting the boundaries for Sbay contig957
plot([61532,105779],[-17500,-17500],'k-');
plot([61532,61532],[-17000,-18000],'k-');
plot([105779,105779],[-17000,-18000],'k-');
%% Text at position 105779,-17800:  Sbay contig957
h = text(105779.0, -17800.0, 'Sbay contig957');
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 Sbay contig957
plot([61532,61532,61532],[-18000,-18000,-17900],'k-');
plot([105779,105779,105779],[-17000,-17000,-17100],'k-');
%% 
%% Arrow from [68838,68425] to [-17500,-17500].  Width 300, indent 371.7, length 413
fill([68838.00,68796.70,68425.00,68796.70,68838.00,68838.00], ...
	[-17200.00,-17200.00,-17500.00,-17800.00,-17800.00,-17200.00], 'm-');
%% Text at position 68632,-17200:  TyElmt_28 hits at 62%
h = text(68632.0, -17200.0, 'TyElmt_28 hits at 62%');
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 [70542,70285] to [-17500,-17500].  Width 300, indent 231.3, length 257
fill([70542.00,70516.30,70285.00,70516.30,70542.00,70542.00], ...
	[-17200.00,-17200.00,-17500.00,-17800.00,-17800.00,-17200.00], 'm-');
%% Text at position 70414,-17200:  TyElmt_4 hits at 56%
h = text(70414.0, -17200.0, 'TyElmt_4 hits at 56%');
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 [78827,78490] to [-17500,-17500].  Width 300, indent 303.3, length 337
fill([78827.00,78793.30,78490.00,78793.30,78827.00,78827.00], ...
	[-17200.00,-17200.00,-17500.00,-17800.00,-17800.00,-17200.00], 'm-');
%% Text at position 78659,-17200:  TyElmt_6 hits at 55%
h = text(78659.0, -17200.0, 'TyElmt_6 hits at 55%');
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 [65434,67614] to [-17500,-17500].  Width 300, indent 400, length 2180
fill([65434.00,67214.00,67614.00,67214.00,65434.00,65434.00], ...
	[-17800.00,-17800.00,-17500.00,-17200.00,-17200.00,-17800.00], 'r-');
%% Text at position 66524,-17200:  YAR014C
h = text(66524.0, -17200.0, 'YAR014C');
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 [69282,69007] to [-17500,-17500].  Width 300, indent 247.5, length 275
fill([69282.00,69254.50,69007.00,69254.50,69282.00,69282.00], ...
	[-17200.00,-17200.00,-17500.00,-17800.00,-17800.00,-17200.00], 'w-');
%% Text at position 69145,-17200:  NoHit383
h = text(69145.0, -17200.0, 'NoHit383');
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 [69017,69595] to [-17500,-17500].  Width 300, indent 400, length 578
fill([69017.00,69195.00,69595.00,69195.00,69017.00,69017.00], ...
	[-17800.00,-17800.00,-17500.00,-17200.00,-17200.00,-17800.00], 'w-');
%% Text at position 69306,-17200:  NoHit382
h = text(69306.0, -17200.0, 'NoHit382');
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 [71250,71029] to [-17500,-17500].  Width 300, indent 198.9, length 221
fill([71250.00,71227.90,71029.00,71227.90,71250.00,71250.00], ...
	[-17200.00,-17200.00,-17500.00,-17800.00,-17800.00,-17200.00], 'w-');
%% Text at position 71140,-17200:  NoHit380
h = text(71140.0, -17200.0, 'NoHit380');
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 [71636,72382] to [-17500,-17500].  Width 300, indent 400, length 746
fill([71636.00,71982.00,72382.00,71982.00,71636.00,71636.00], ...
	[-17800.00,-17800.00,-17500.00,-17200.00,-17200.00,-17800.00], 'g-');
%% Text at position 72009,-17200:  YAR028W
h = text(72009.0, -17200.0, 'YAR028W');
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 [72466,72681] to [-17500,-17500].  Width 300, indent 193.5, length 215
fill([72466.00,72487.50,72681.00,72487.50,72466.00,72466.00], ...
	[-17800.00,-17800.00,-17500.00,-17200.00,-17200.00,-17800.00], 'w-');
%% Text at position 72574,-17200:  NoHit378
h = text(72574.0, -17200.0, 'NoHit378');
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 [72937,73134] to [-17500,-17500].  Width 300, indent 177.3, length 197
fill([72937.00,72956.70,73134.00,72956.70,72937.00,72937.00], ...
	[-17800.00,-17800.00,-17500.00,-17200.00,-17200.00,-17800.00], 'w-');
%% Text at position 73036,-17200:  NoHit374
h = text(73036.0, -17200.0, 'NoHit374');
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 [73386,73640] to [-17500,-17500].  Width 300, indent 228.6, length 254
fill([73386.00,73411.40,73640.00,73411.40,73386.00,73386.00], ...
	[-17800.00,-17800.00,-17500.00,-17200.00,-17200.00,-17800.00], 'g-');
%% Text at position 73513,-17200:  YAR027W
h = text(73513.0, -17200.0, 'YAR027W');
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 [74495,74653] to [-17500,-17500].  Width 300, indent 142.2, length 158
fill([74495.00,74510.80,74653.00,74510.80,74495.00,74495.00], ...
	[-17800.00,-17800.00,-17500.00,-17200.00,-17200.00,-17800.00], 'r-');
%% Text at position 74574,-17200:  
h = text(74574.0, -17200.0, '');
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 [76463,75561] to [-17500,-17500].  Width 300, indent 400, length 902
fill([76463.00,75961.00,75561.00,75961.00,76463.00,76463.00], ...
	[-17200.00,-17200.00,-17500.00,-17800.00,-17800.00,-17200.00], 'r-');
%% Text at position 76012,-17200:  YAR008W
h = text(76012.0, -17200.0, 'YAR008W');
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 [76743,78608] to [-17500,-17500].  Width 300, indent 400, length 1865
fill([76743.00,78208.00,78608.00,78208.00,76743.00,76743.00], ...
	[-17800.00,-17800.00,-17500.00,-17200.00,-17200.00,-17800.00], 'r-');
%% Text at position 77676,-17200:  YAR007C
h = text(77676.0, -17200.0, 'YAR007C');
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 [80417,79131] to [-17500,-17500].  Width 300, indent 400, length 1286
fill([80417.00,79531.00,79131.00,79531.00,80417.00,80417.00], ...
	[-17200.00,-17200.00,-17500.00,-17800.00,-17800.00,-17200.00], 'r-');
%% Text at position 79774,-17200:  YAR003W
h = text(79774.0, -17200.0, 'YAR003W');
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 [80693,81352] to [-17500,-17500].  Width 300, indent 400, length 659
fill([80693.00,80952.00,81352.00,80952.00,80693.00,80693.00], ...
	[-17800.00,-17800.00,-17500.00,-17200.00,-17200.00,-17800.00], 'r-');
%% Text at position 81023,-17200:  YAR002C-A
h = text(81023.0, -17200.0, 'YAR002C-A');
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 [83180,81540] to [-17500,-17500].  Width 300, indent 400, length 1640
fill([83180.00,81940.00,81540.00,81940.00,83180.00,83180.00], ...
	[-17200.00,-17200.00,-17500.00,-17800.00,-17800.00,-17200.00], 'r-');
%% Text at position 82360,-17200:  YAR002W
h = text(82360.0, -17200.0, 'YAR002W');
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.  2 values, [min,avg,max]=[46723..46723..46723]
x_dashed = [...
	46723,46723];
%% Seting variable y_dashed.  2 values, [min,avg,max]=[-10000..-7500..-5000]
y_dashed = [...
	-5000,-10000];
plot(x_dashed, y_dashed, 'k.:')
%% 
%% 
%% Plot x_dashed vs. y_dashed
%% 
%% 
%% Seting variable x_dashed.  2 values, [min,avg,max]=[46953..46953..46953]
x_dashed = [...
	46953,46953];
%% Seting variable y_dashed.  2 values, [min,avg,max]=[-10000..-7500..-5000]
y_dashed = [...
	-5000,-10000];
plot(x_dashed, y_dashed, 'k.:')
%% 
%% 
%% Plot x_dashed vs. y_dashed
%% 
%% 
%% Seting variable x_dashed.  2 values, [min,avg,max]=[74495..74495..74495]
x_dashed = [...
	74495,74495];
%% Seting variable y_dashed.  2 values, [min,avg,max]=[-17500..-11250..-5000]
y_dashed = [...
	-5000,-17500];
plot(x_dashed, y_dashed, 'k.:')
%% 
%% 
%% Plot x_dashed vs. y_dashed
%% 
%% 
%% Seting variable x_dashed.  2 values, [min,avg,max]=[74653..75318..75984]
x_dashed = [...
	75984,74653];
%% Seting variable y_dashed.  2 values, [min,avg,max]=[-17500..-11250..-5000]
y_dashed = [...
	-5000,-17500];
plot(x_dashed, y_dashed, 'k.:')
%% 
%% 
%% Plot x_dashed vs. y_dashed
%% 
%% 
%% Seting variable x_dashed.  2 values, [min,avg,max]=[48901..48901..48901]
x_dashed = [...
	48901,48901];
%% Seting variable y_dashed.  2 values, [min,avg,max]=[-12500..-8750..-5000]
y_dashed = [...
	-5000,-12500];
plot(x_dashed, y_dashed, 'k.:')
%% 
%% 
%% Plot x_dashed vs. y_dashed
%% 
%% 
%% Seting variable x_dashed.  2 values, [min,avg,max]=[49425..49761..50097]
x_dashed = [...
	50097,49425];
%% Seting variable y_dashed.  2 values, [min,avg,max]=[-12500..-8750..-5000]
y_dashed = [...
	-5000,-12500];
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 Chr17 tile 2 positions 50kbp to 85kbp aligned against Spar Smik Sbay');
