HD<-c(12192251,12239831,12216907,12189857,12203793,12177421,12201025,12183817,12181987,12183275,12177969,12179119,12175367,12175389,12176001,12173605,12171505,12167213,12164469,12161603,12156373,12154459,12150079,12149733,12146237,12143695,12141105,12136531,12134337,12130071,12128347,12123763,12121549,12120240,12116736,12115590,12113718,12111994,12110908,12108522,12109034,12106460,12105817,12104500,12104534,12100606,12099834,12100248,12097059,12094902,12093235,12092954,12089997,12088576,12087006,12085512,12085738,12082822,12081325,12078721,12078748,12076230,12074775,12072559,12072788,12070486,12068420,12066934,12065978,12062808,12062499,12060246,12057516,12056940,12055458,12052739,12051647,12050374,12047338,12046274,12044793,12042734,12042402,12038264,12037576,12037991,12035218,12034352,12032938,12030116,12028412,12027959,12026605,12024555,12022301,12021941,12020729,12018541,12017327,12016470,12015450,12011558,12012401,12010705,12011665,12008961,12007574,12006906,12006233,12005296,12003561,12003200,12001224,12002784,12001290,11999799,12000279,11998879,11999269,11998245,11996463,11997649,11997917,11998732,11996344,11995604,11996514,11996770,11997534,11995484,11998396,11996926,11998116,11997668,11998271,11998693,12000087,12000214,12003267,11999888,12003736,12002806,12002944,12004194,12005231,12005801,12007112,12006874,12009328,12011752,12010593,12012601,12014719,12014575,12017224,12018587,12017890,12019934,12020986,12022107,12024578,12026906,12026930,12029206,12032231,12032675,12035085,12036331,12037717,12041597,12040851,12043722,12044024,12047642,12048037,12050223,12052942,12055166,12056027,12059881,12062467,12062861,12065393,12067685,12070199,12072245,12072853,12076171,12076673,12079338,12081691,12082322,12084983,12088378,12090046,12092272,12093696,12096474,12097840,12100540,12103135,12104317,12107760,12110070,12111412,12113293,12115575,12118173,12120061,12122491,12123283,12126465,12127997,12130269,12132539,12134317,12135823,12140748,12139568,12141253,12143961,12145407,12147048,12150630,12150944,12153543,12154699,12157586,12158612,12160759,12160934,12163203,12166302,12165534,12167904,12168912,12170956,12172017,12173419,12176356,12176914,12179036,12179216,12182650,12182364,12184790,12186156,12188189,12188968,12190343,12191885,12192326,12195208,12195315,12197585,12199525,12199238,12201063,12202413,12204035,12206298,12207970,12208141,12210898,12211686,12213898,12214202,12215403,12216201,12216721,12217737,12218753,12220769,12221458,12222707,12223848,12224882,12226239,12228019,12229901,12228547,12230037,12231715,12232095,12233731,12235621,12235282,12237536,12237604,12240045,12240221,12242185,12242413,12242949,12244063,12245105,12246415,12247427,12248081,12249626,12249254,12251117,12251543,12252289,12252218,12254270,12254412,12256784,12257159,12256402,12257098,12259328,12259261,12259585,12261713,12261465,12263737,12265709,12264147,12266407,12265195,12267377,12266967,12268021,12268269,12269359,12271249,12271321,12273085,12272179,12272876,12273358,12273964,12274388,12274970,12275947,12277391,12277331,12277241,12278707,12279019,12281098,12281243,12281205,12282391,12283843,12281875,12283683,12284021,12285117,12285711,12285430,12285432,12286962,12287761,12287743,12288011,12288578,12290439,12290417,12290867,12293107,12291379,12293739,12292480,12292842,12294082,12294480,12295054,12295786,12295652,12296962,12297362,12298033,12297249,12298103,12297830,12300909,12299741,12300058,12301300,12300829,12301788,12303244,12302119,12303129,12303837,12304911,12304509,12306373,12305589,12306879,12306233,12305825,12307979,12307851,12308471,12308477,12308873,12309177,12310535,12311239,12311597,12311289,12310941,12313277,12312815,12314431,12314518,12312892,12313478,12315416,12315533,12317173,12315890,12316312,12316630,12316648,12318137,12318804,12319172,12318759,12320132,12320080,12319712,12321614,12322671,12321967,12322991,12322007,12323505,12323543,12323437,12324395,12324797,12325925,12326942,12325291,12327168,12327788,12328631,12328516,12328846,12330101,12330363,12330073,12331222,12332345,12331234,12331872,12332271,12333288,12334253,12332980,12333907,12334808,12335829,12334946,12336301,12338179,12336601,12338708,12337745,12337858,12339403,12340514,12340517,12339674,12341015,12340595,12341432,12341427,12342416,12343825,12343864,12343315,12344466,12345078,12346059,12345576,12346729,12346482,12346841,12346860,12349497,12348664,12348339,12351064,12349487,12351816,12351289,12352004,12351598,12351333,12353788,12353164,12353238,12353383,12355532,12355251,12356373,12356064,12356662,12357757,12357323,12358525,12357445,12359137,12359897,12359199,12360372,12359443,12361995,12361061,12361183,12361856,12362244,12362057,12361959,12363239,12362913,12364005,12364659,12366073,12365813,12366371,12364975,12365922,12367264,12367295,12367297,12368767,12368029,12369131,12369463,12370999,12370411,12370819,12371269,12372477,12372160,12372476,12372742,12372944,12374703,12373153,12375053,12373885,12375038,12374972,12375403,12375695,12376671,12376253,12377746,12379123,12378962,12378664,12378952,12379845,12380213,12380217,12380202,12381162,12380798,12381751,12382292,12381546,12382552,12382975,12382531,12384392,12384292,12384028,12384749,12383645,12385023,12386330,12386140,12385898,12385941,12386391,12386694,12388117,12388453,12388917,12388085,12389593,12388321,12389117,12389518,12391966,12390463,12390943,12390764,12390231,12393494,12391377,12393159,12393204,12393529,12393304,12393371,12393926,12393803,12394513,12395921,12395654,12395316,12395948,12397063,12396193,12396454,12398143,12396798,12397394,12397886,12398084,12398095,12398563,12399966,12399822,12399073,12400811,12401190,12400669,12400776,12401052,12400050,12400947,12402603,12401761,12401744,12402740,12402801,12402559,12403647,12403765,12403650,12405157,12405685,12406044,12405498,12406062,12405148,12405858,12406899,12406918,12407586,12407653,12407716,12407050,12407948,12409945,12408195,12408520,12408214,12410022,12410077,12410015,12409387,12410061,12410723,12410733,12411829,12411757,12411845,12412121,12411779,12412329,12413791,12413321,12411235,12413963,12412841,12413071,12413253,12414523,12414503,12413535,12415761,12416020,12415536,12415875,12416039,12415365,12416604,12416936,12415332,12416879,12416385,12417223,12418687,12418169,12418653,12418305,12417661,12419173,12419355,12418763,12419483,12420127,12419403,12420295,12421024,12420796,12421534,12420662,12421564,12421554,12421498,12421570,12422030,12422482,12422608,12422920,12423672,12423791,12423239,12423622,12422538,12423808,12424774,12425420,12424028,12425131,12424767,12425325,12426333,12425737,12425129,12426327,12426341,12427223,12425835,12427575,12427633,12427915,12426473,12427531,12428651,12426685,12428905,12428107,12429941,12428801,12429135,12429569,12429303,12430083,12430432,12429856,12430302,12429896,12430890,12430866,12431654,12430052,12431420,12431696,12431086,12432252,12432761,12431936,12432654,12432578,12434206,12432884,12433080,12434263,12433507,12433587,12434263,12434419,12434451,12434705,12435025,12435233,12436205,12435767,12435426,12435372,12435854,12436574,12436310,12436934,12437578,12436820,12437474,12438792,12437678,12437646,12438614,12437752,12439164,12437910,12438226,12437472,12438108,12440081,12439837,12439769,12440143,12439880,12440636,12439142,12439166,12440030,12440342,12441344,12440352,12441422,12441114,12442764,12441598,12441820,12441799,12441909,12442385,12442704,12442906,12442443,12441831,12443402,12442078,12443461,12443081,12443260,12443592,12444052,12444958,12444158,12444550,12444886,12443880,12446318,12445022,12445083,12445881,12445029,12445707,12446765,12446905,12445973,12446355,12445236,12447010,12447394,12446820,12447652,12447626,12447346,12448226,12447670,12447491,12448867,12447975,12448367,12448349,12448367,12449472,12448256,12449022,12449584,12449806,12450184,12449661,12450153,12450669,12451041,12451292,12449883,12450269,12450261,12451519,12451173,12451569,12450818,12452080,12451808,12451652,12452044,12452878,12451962,12452646,12453278,12453232,12452424,12452534,12452824,12454048,12453122,12453672,12454511,12453299,12454656,12454310,12453934,12454956,12455592,12456142,12454444,12454642,12455625,12455382,12455729,12455484,12456611,12457031,12456964,12456170,12455658,12457097,12456597,12456941,12457191,12457213,12457401,12456659,12457273,12457823,12458941,12457979,12458861,12457919,12458421,12459103,12457909,12459555,12459367,12459461,12459923,12458829,12459763,12459651,12459543,12459503,12459415,12459777,12460536,12460518,12460416,12460686,12461217,12460697,12461457,12459923,12461145,12461705,12461791,12462063,12462433,12462343,12462311,12461675,12463069,12462081,12462935,12463011,12462671,12462909,12463941,12463093,12463883,12463370,12463440,12463496,12463286,12464249,12463583,12464266,12464514,12464555,12464877,12464046,12464988,12463955,12464587,12465379,12464685,12465341,12465345,12465145,12465240,12465558,12465936,12465952,12466358,12465663,12465659,12466333,12466299,12466255,12467671,12466081,12467472,12467785,12467433,12468365,12467559)

STRAND_SHIFT<-c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,518,519,520,521,522,523,524,525,526,527,528,529,530,531,532,533,534,535,536,537,538,539,540,541,542,543,544,545,546,547,548,549,550,551,552,553,554,555,556,557,558,559,560,561,562,563,564,565,566,567,568,569,570,571,572,573,574,575,576,577,578,579,580,581,582,583,584,585,586,587,588,589,590,591,592,593,594,595,596,597,598,599,600,601,602,603,604,605,606,607,608,609,610,611,612,613,614,615,616,617,618,619,620,621,622,623,624,625,626,627,628,629,630,631,632,633,634,635,636,637,638,639,640,641,642,643,644,645,646,647,648,649,650,651,652,653,654,655,656,657,658,659,660,661,662,663,664,665,666,667,668,669,670,671,672,673,674,675,676,677,678,679,680,681,682,683,684,685,686,687,688,689,690,691,692,693,694,695,696,697,698,699,700,701,702,703,704,705,706,707,708,709,710,711,712,713,714,715,716,717,718,719,720,721,722,723,724,725,726,727,728,729,730,731,732,733,734,735,736,737,738,739,740,741,742,743,744,745,746,747,748,749,750,751,752,753,754,755,756,757,758,759,760,761,762,763,764,765,766,767,768,769,770,771,772,773,774,775,776,777,778,779,780,781,782,783,784,785,786,787,788,789,790,791,792,793,794,795,796,797,798,799,800,801,802,803,804,805,806,807,808,809,810,811,812,813,814,815,816,817,818,819,820,821,822,823,824,825,826,827,828,829,830,831,832,833,834,835,836,837,838,839,840,841,842,843,844,845,846,847,848,849,850,851,852,853,854,855,856,857,858,859,860,861,862,863,864,865,866,867,868,869,870,871,872,873,874,875,876,877,878,879,880,881,882,883,884,885,886,887,888,889,890,891,892,893,894,895,896,897,898,899,900,901,902,903,904,905,906,907,908,909,910,911,912,913,914,915,916,917,918,919,920,921,922,923,924,925,926,927,928,929,930,931,932,933,934,935,936,937,938,939,940,941,942,943,944,945,946,947,948,949,950,951,952,953,954,955,956,957,958,959,960,961,962,963,964,965,966,967,968,969,970,971,972,973,974,975,976,977,978,979,980,981,982,983,984,985,986,987,988,989,990,991,992,993,994,995,996,997,998,999,1000)

RL<-36
RL<-STRAND_SHIFT[which(HD==min(HD[1:RL]))]
FL<-STRAND_SHIFT[which(HD==min(HD[(RL*2+1):(length(HD))]))]
MAX_HD<-max(HD)
HD_FL<-HD[which(STRAND_SHIFT==FL)]
HD_RL<-HD[which(STRAND_SHIFT==RL)]
RSC<-(MAX_HD-HD_FL)/(MAX_HD-HD_RL)
RSC<-format(RSC,digits=3,nsmall=3)
MAIN_PLOT<-paste("FL = ",FL,"|")
MAIN_PLOT<-paste(MAIN_PLOT,"RSC = ",RSC)
pdf("Hct116Pol24h8Rep1-Q-binding-characteristics.pdf",height=7,width=7)
plot(STRAND_SHIFT,HD,xlab="strand shift",ylab="hamming distance",type="l",main=MAIN_PLOT,cex.axis=1.3,cex.lab=1.5)
abline(v=FL,col="red",lty=2)
abline(h=HD_FL,lty=2,col="red")
abline(v=RL,lty=2,col="grey")
abline(h=HD_RL,lty=2,col="grey")
abline(h=MAX_HD,lty=2)
abline(v=0,lty=2)
dev.off()