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["Mapping of Polyadenylation Sites"]
["# minReadNum=2 #---minimum peak read number",{"$nulls":5},"major PAS refers to polyadenylation site with most reads"]
["# minUDRatio=0 #---minimum upstream to downstream average ratio"]
["# minCovAsGap=0 #---any position coverage lower than this value is considered as a gap"]
["# maxCovGapSize=30 #--- maximum gap size to be allowed between the cluster and the polyA"]
[{"$nulls":5},"positions of polyadenylation sites (PAS)"]
["gene ID","strand","3´-end of ORF","5´-end of ORF","Number of identified PAS-clusters","PAS closest to ORF (distance relative to ORF in nt)","PAS closest to ORF (genomic position)","PAS furthest to ORF (distance relative to ORF in nt)","PAS furthest to ORF (genomic position)","major PAS (distance relative to ORF in nt)","major PAS (genomic position)"]
["PF3D7_0100100","+",37126,29510,0,"null","null","null","null","null","null"]
["PF3D7_0100200","-",38982,40207,0,"null","null","null","null","null","null"]
["PF3D7_0100300","-",42367,46507,0,"null","null","null","null","null","null"]
["PF3D7_0100400","+",51636,50363,0,"null","null","null","null","null","null"]
["PF3D7_0100600","-",53778,55006,0,"null","null","null","null","null","null"]
["PF3D7_0100700","-",56690,56893,0,"null","null","null","null","null","null"]
["PF3D7_0100800","+",61003,59772,0,"null","null","null","null","null","null"]
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["PF3D7_0101000","-",65817,66989,0,"null","null","null","null","null","null"]
["PF3D7_0101100","-",69304,70417,0,"null","null","null","null","null","null"]
["PF3D7_0101200","+",72426,71624,0,"null","null","null","null","null","null"]
["PF3D7_0101300","+",75366,74563,0,"null","null","null","null","null","null"]
["PF3D7_0101600","-",81765,83106,0,"null","null","null","null","null","null"]
["PF3D7_0101800","-",87203,88177,0,"null","null","null","null","null","null"]
["PF3D7_0101900","-",90242,91420,0,"null","null","null","null","null","null"]
["PF3D7_0102200","+",102282,98819,2,400,102682,444,102726,444,102726]
["PF3D7_0102300","+",105209,104704,1,546,105755,546,105755,546,105755]
["PF3D7_0102500","-",110750,115799,1,452,110298,452,110298,452,110298]
["PF3D7_0102600","-",119041,121249,1,560,118481,560,118481,560,118481]
["PF3D7_0102700","+",125484,124517,0,"null","null","null","null","null","null"]
["PF3D7_0102800","-",126318,128141,0,"null","null","null","null","null","null"]
["PF3D7_0102900","-",128960,130840,3,330,128630,443,128517,365,128595]
["PF3D7_0103000","-",132086,133624,2,825,131261,1060,131026,825,131261]
["PF3D7_0103100","-",134353,139257,1,322,134031,322,134031,322,134031]
["PF3D7_0103200","-",140662,142219,2,410,140252,534,140128,410,140252]
["PF3D7_0103300","-",143640,146396,1,1653,141987,1653,141987,1653,141987]
["PF3D7_0103400","-",147915,152777,1,673,147242,673,147242,673,147242]
["PF3D7_0103500","+",160426,154176,0,"null","null","null","null","null","null"]
["PF3D7_0103600","+",166229,161131,1,344,166573,344,166573,344,166573]
["PF3D7_0103700","+",168687,166513,0,"null","null","null","null","null","null"]
["PF3D7_0103800","-",169079,171273,0,"null","null","null","null","null","null"]
["PF3D7_0103900","+",174591,172864,1,467,175058,467,175058,467,175058]
["PF3D7_0104000","+",176376,175609,0,"null","null","null","null","null","null"]
["PF3D7_0104100","+",180790,178087,2,826,181616,893,181683,893,181683]
["PF3D7_0104200","-",182822,184222,3,799,182023,1961,180861,1705,181117]
["PF3D7_0104300","+",201230,190269,2,501,201731,546,201776,546,201776]
["PF3D7_0104400","+",204143,202536,1,329,204472,329,204472,329,204472]
["PF3D7_0104500","-",204622,205389,2,241,204381,325,204297,241,204381]
["PF3D7_0104600","+",210189,206170,1,233,210422,233,210422,233,210422]
["PF3D7_0104700","+",213005,210870,0,"null","null","null","null","null","null"]
["PF3D7_0104800","+",217509,215776,1,535,218044,535,218044,535,218044]
["PF3D7_0105100","+",221633,221202,1,245,221878,245,221878,245,221878]
["PF3D7_0105200","-",222254,223960,2,613,221641,641,221613,641,221613]
["PF3D7_0105300","-",225110,225779,2,140,224970,171,224939,140,224970]
["PF3D7_0105400","-",226681,227285,2,569,226112,713,225968,569,226112]
["PF3D7_0105500","-",228485,229519,0,"null","null","null","null","null","null"]
["PF3D7_0105600","-",230289,234402,2,410,229879,671,229618,410,229879]
["PF3D7_0105700","+",247857,238666,1,367,248224,367,248224,367,248224]
["PF3D7_0105800","-",249231,252010,4,327,248904,738,248493,696,248535]
["PF3D7_0105900","+",254930,253584,2,451,255381,1123,256053,451,255381]
["PF3D7_0106000","-",255775,258543,2,378,255397,411,255364,411,255364]
["PF3D7_0106100","-",260658,261809,2,624,260034,1151,259507,624,260034]
["PF3D7_0106200","-",263340,264223,1,474,262866,474,262866,474,262866]
["PF3D7_0106300","-",265208,269173,2,551,264657,1484,263724,1484,263724]
["PF3D7_0106400","+",273404,272454,2,419,273823,459,273863,419,273823]
["PF3D7_0106500","+",278550,274315,1,191,278741,191,278741,191,278741]
["PF3D7_0106600","+",280014,279115,0,"null","null","null","null","null","null"]
["PF3D7_0106700","+",285459,281155,1,387,285846,387,285846,387,285846]
["PF3D7_0106800","+",288918,286951,2,846,289764,920,289838,920,289838]
["PF3D7_0106900","+",292590,290386,1,410,293000,410,293000,410,293000]
["PF3D7_0107000","+",294968,293642,3,23,294991,367,295335,23,294991]
["PF3D7_0107100","-",295300,296931,1,355,294945,355,294945,355,294945]
["PF3D7_0107200","+",299397,297362,2,251,299648,325,299722,251,299648]
["PF3D7_0107300","-",299562,300868,1,228,299334,228,299334,228,299334]
["PF3D7_0107400","+",303398,302937,2,599,303997,1268,304666,599,303997]
["PF3D7_0107500","-",304362,309257,3,394,303968,1063,303299,1063,303299]
["PF3D7_0107600","+",319405,314618,0,"null","null","null","null","null","null"]
["PF3D7_0107700","+",321508,320168,1,318,321826,318,321826,318,321826]
["PF3D7_0107800","+",326072,322371,1,417,326489,417,326489,417,326489]
["PF3D7_0107900","-",326397,327224,2,288,326109,324,326073,288,326109]
["PF3D7_0108000","-",328431,329304,1,233,328198,233,328198,233,328198]
["PF3D7_0108100","+",332708,330738,1,696,333404,696,333404,696,333404]
["PF3D7_0108300","+",343833,337168,2,490,344323,583,344416,583,344416]
["PF3D7_0108400","-",344400,346540,0,"null","null","null","null","null","null"]
["PF3D7_0108500","+",349709,349170,2,378,350087,476,350185,378,350087]
["PF3D7_0108600","-",349995,351626,0,"null","null","null","null","null","null"]
["PF3D7_0108700","-",352314,356211,2,238,352076,656,351658,656,351658]
["PF3D7_0108800","+",360339,357834,3,298,360637,446,360785,446,360785]
["PF3D7_0109000","+",363992,363318,1,987,364979,987,364979,987,364979]
["PF3D7_0109100","+",368795,365610,1,1039,369834,1039,369834,1039,369834]
["PF3D7_0109200","-",369480,370178,0,"null","null","null","null","null","null"]
["PF3D7_0109300","-",371815,373012,1,656,371159,656,371159,656,371159]
["PF3D7_0109400","-",374439,375087,4,319,374120,586,373853,586,373853]
["PF3D7_0109500","-",376294,377004,5,276,376018,694,375600,694,375600]
["PF3D7_0109600","-",377874,378599,3,230,377644,330,377544,230,377644]
["PF3D7_0109700","-",379149,379806,2,494,378655,1035,378114,1035,378114]
["PF3D7_0109800","+",382424,380697,1,318,382742,318,382742,318,382742]
["PF3D7_0109900","+",387940,383284,1,347,388287,347,388287,347,388287]
["PF3D7_0110000","+",389076,388372,2,225,389301,469,389545,469,389545]
["PF3D7_0110100","-",389261,392065,1,360,388901,360,388901,360,388901]
["PF3D7_0110200","+",393035,392604,1,1161,394196,1161,394196,1161,394196]
["PF3D7_0110400","-",393875,394835,3,557,393318,884,392991,884,392991]
["PF3D7_0110500","+",403606,396591,1,519,404125,519,404125,519,404125]
["PF3D7_0110600","+",412169,405739,2,132,412301,661,412830,661,412830]
["PF3D7_0110700","-",413760,415100,4,385,413375,693,413067,693,413067]
["PF3D7_0110800","+",419607,417921,2,620,420227,733,420340,620,420227]
["PF3D7_0110900","-",420293,420853,1,499,419794,499,419794,499,419794]
["PF3D7_0111000","-",421776,427575,1,731,421045,731,421045,731,421045]
["PF3D7_0111200","-",430152,430858,0,"null","null","null","null","null","null"]
["PF3D7_0111300","-",431539,435042,1,315,431224,315,431224,315,431224]
["PF3D7_0111400","+",438564,436408,0,"null","null","null","null","null","null"]
["PF3D7_0111500","-",439652,441418,1,369,439283,369,439283,369,439283]
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["PF3D7_0111800","+",448849,446026,2,712,449561,762,449611,762,449611]
["PF3D7_0111900","-",450043,450646,1,506,449537,506,449537,506,449537]
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["PF3D7_0112100","+",455338,454847,0,"null","null","null","null","null","null"]
["PF3D7_0112200","+",470194,464726,3,388,470582,572,470766,388,470582]
["PF3D7_0112800","-",481809,482618,0,"null","null","null","null","null","null"]
["PF3D7_0112900","+",487186,486500,1,311,487497,311,487497,311,487497]
["PF3D7_0113000","-",487892,490127,5,386,487506,1820,486072,386,487506]
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["PF3D7_0113700","+",522579,520807,2,611,523190,698,523277,611,523190]
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["PF3D7_0205800","-",232729,233476,3,241,232488,613,232116,613,232116]
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["PF3D7_0206900","-",275540,276494,3,213,275327,842,274698,213,275327]
["PF3D7_0207000","-",277494,278456,3,317,277177,985,276509,317,277177]
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