Supplementary Table 1. Approximate mapping coordinates (alignment scores ? 20) for assembled contigs in GRCz10. Each line shows cross-referenced alignment results for paired end reads where one read maps to the assembly and the second to the genome. contig name bp location of hit in contig alignment score of contig hit chromosome name bp location of hit on chromosome alignment score of chromosome hit ERR163_all_c1000007 52 0 CM002901.1 44756630 42 ERR163_all_c1000010 1 0 CM002894.1 39965602 1 ERR163_all_c100001 1 0 CM002889.1 54012054 42 ERR163_all_c1000021 39 42 CM002896.1 18526 1 ERR163_all_c1000036 64 0 CM002889.1 65971430 0 ERR163_all_c1000036 64 0 CM002909.1 17610394 1 ERR163_all_c1000036 64 0 CM002909.1 918444 1 ERR163_all_c1000036 69 0 CM002889.1 66422877 1 ERR163_all_c1000036 69 2 CM002897.1 5575395 1 ERR163_all_c1000036 70 4 CM002888.1 22769440 1 ERR163_all_c1000036 71 0 CM002885.1 28682906 1 ERR163_all_c1000036 71 0 CM002889.1 4248768 1 ERR163_all_c1000036 71 0 CM002908.1 39509677 1 ERR163_all_c100004 48 42 CM002892.1 25738938 3 ERR163_all_c1000050 31 3 CM002908.1 32928452 1 ERR163_all_c100005 124 42 CM002886.1 34691622 40 ERR163_all_c1000073 1 0 CM002903.1 35381894 1 ERR163_all_c100007 48 0 CM002890.1 29125294 14 ERR163_all_c1000085 29 3 CM002888.1 28595212 6 ERR163_all_c1000085 33 3 CM002888.1 28570351 30 ERR163_all_c1000085 35 0 CM002888.1 28582474 30 ERR163_all_c1000085 37 42 CM002892.1 32848203 1 ERR163_all_c1000085 40 2 CM002897.1 19038999 1 ERR163_all_c1000085 4 0 CM002888.1 28596747 7 ERR163_all_c1000086 63 6 CM002888.1 59876852 1 ERR163_all_c1000093 2 0 CM002902.1 49066222 40 ERR163_all_c1000099 103 26 CM002900.1 9140317 40 ERR163_all_c1000099 44 8 CM002886.1 9243014 42 ERR163_all_c100010 41 24 CM002898.1 3962659 2 ERR163_all_c1000105 10 42 CM002885.1 551298 35 ERR163_all_c100011 1 42 CM002895.1 38424657 42 ERR163_all_c1000119 18 0 CM002886.1 13022787 1 ERR163_all_c1000119 31 0 CM002888.1 55227115 1 ERR163_all_c1000122 17 2 KN149699.1 17348 1 ERR163_all_c1000134 1 0 CM002887.1 10948052 42 ERR163_all_c1000147 28 42 CM002907.1 5572251 1 ERR163_all_c1000152 12 42 CM002904.1 51415595 1 ERR163_all_c1000160 1 42 CM002899.1 6623068 1 ERR163_all_c100017 134 3 CM002886.1 7288052 8 ERR163_all_c1000197 12 42 CM002891.1 18270213 36 ERR163_all_c100019 74 5 KN150003.1 9222 0 ERR163_all_c1000202 11 42 CM002897.1 21414425 36 ERR163_all_c1000202 20 24 CM002897.1 21414416 2 ERR163_all_c1000212 1 23 CM002887.1 16093122 1 ERR163_all_c100024 27 42 KN149684.1 47223 0 ERR163_all_c100024 60 42 CM002890.1 33316632 1 ERR163_all_c1000268 53 36 CM002888.1 18797778 23 ERR163_all_c1000276 103 42 CM002900.1 23335630 1 ERR163_all_c1000276 13 42 CM002891.1 73810957 6 ERR163_all_c10002 80 42 CM002891.1 5439064 40 ERR163_all_c1000301 24 24 CM002887.1 8569174 6 ERR163_all_c1000301 7 42 CM002886.1 56406400 24 ERR163_all_c10003 154 42 CM002892.1 31295059 0 ERR163_all_c100032 4 42 CM002909.1 7063326 40 ERR163_all_c1000326 10 42 CM002904.1 16627005 1 ERR163_all_c10003 401 2 CM002889.1 71363054 1 ERR163_all_c1000353 12 42 CM002898.1 4778537 1 ERR163_all_c100035 44 42 CM002896.1 25950651 24 ERR163_all_c1000360 6 42 CM002902.1 15594093 1 ERR163_all_c100036 167 3 CM002891.1 3469860 40 ERR163_all_c100036 190 42 CM002891.1 3469920 3 ERR163_all_c1000365 1 40 CM002901.1 27476400 1 ERR163_all_c1000365 43 0 CM002901.1 50837631 1 ERR163_all_c1000365 68 17 CM002898.1 39466178 31 ERR163_all_c1000367 102 0 CM002896.1 45573484 1 ERR163_all_c1000367 68 3 CM002900.1 36514007 1 ERR163_all_c1000367 73 0 CM002891.1 11820166 6 ERR163_all_c100037 2 3 CM002889.1 62195647 40 ERR163_all_c1000378 9 42 CM002897.1 49904739 3 ERR163_all_c1000420 18 32 CM002902.1 14080348 23 ERR163_all_c10004 25 42 CM002905.1 45800279 0 ERR163_all_c1000434 8 3 CM002900.1 4977606 1 ERR163_all_c1000464 20 42 CM002898.1 1513600 23 ERR163_all_c1000464 27 42 CM002898.1 1512925 2 ERR163_all_c1000464 9 42 CM002898.1 1513611 3 ERR163_all_c1000466 44 0 CM002904.1 7757732 31 ERR163_all_c100047 71 42 CM002904.1 44669653 42 ERR163_all_c100047 71 42 CM002904.1 44669653 42 ERR163_all_c100049 55 30 CM002906.1 29408505 2 ERR163_all_c1000500 3 42 CM002888.1 43331493 1 ERR163_all_c1000504 10 1 CM002897.1 47267290 1 ERR163_all_c1000541 31 2 CM002891.1 72636913 1 ERR163_all_c10005 530 23 CM002889.1 26630157 0 ERR163_all_c10005 541 3 CM002886.1 48249203 3 ERR163_all_c1000556 49 40 CM002889.1 63818784 14 ERR163_all_c10005 571 42 CM002886.1 48249279 3 ERR163_all_c100058 2 42 CM002887.1 29030172 42 ERR163_all_c1000591 27 37 KN149692.1 1806 3 ERR163_all_c1000591 7 0 CM002901.1 45202214 1 ERR163_all_c1000591 9 2 CM002894.1 16881092 1 ERR163_all_c10006 100 42 CM002900.1 20372175 1 ERR163_all_c1000611 50 42 CM002893.1 17221859 1 ERR163_all_c1000616 2 8 CM002900.1 13495550 40 ERR163_all_c1000620 3 0 CM002908.1 29353003 1 ERR163_all_c1000620 8 42 CM002889.1 22224869 1 ERR163_all_c100063 159 40 CM002897.1 19913346 1 ERR163_all_c1000633 24 8 CM002898.1 3060204 0 ERR163_all_c100064 53 0 CM002900.1 28012665 40 ERR163_all_c1000681 38 42 CM002894.1 20430975 1 ERR163_all_c1000699 104 0 CM002885.1 38012881 1 ERR163_all_c1000699 89 2 CM002909.1 13459395 1 ERR163_all_c100070 9 8 CM002886.1 3013342 42 ERR163_all_c100072 1 0 CM002909.1 17998025 42 ERR163_all_c1000727 35 42 CM002905.1 34698787 22 ERR163_all_c1000728 36 0 CM002903.1 24046973 1 ERR163_all_c100073 286 3 CM002890.1 52495719 40 ERR163_all_c10007 462 42 CM002905.1 9714357 1 ERR163_all_c1000747 1 42 CM002897.1 33485508 42 ERR163_all_c1000765 16 42 CM002889.1 64578154 0 ERR163_all_c1000765 18 42 CM002891.1 68580979 6 ERR163_all_c1000781 16 42 CM002892.1 16265670 42 ERR163_all_c1000783 69 24 CM002897.1 48682277 30 ERR163_all_c100079 28 30 CM002901.1 10712826 2 ERR163_all_c1000793 13 23 CM002892.1 10121285 40 ERR163_all_c1000793 13 23 CM002892.1 10121285 42 ERR163_all_c1000797 19 42 CM002900.1 47120456 0 ERR163_all_c1000800 30 42 CM002887.1 34807996 1 ERR163_all_c1000803 36 0 CM002889.1 10505968 22 ERR163_all_c1000804 21 42 CM002901.1 12188745 4 ERR163_all_c1000804 60 42 CM002903.1 43783288 0 ERR163_all_c1000812 30 23 CM002891.1 27024240 3 ERR163_all_c100081 40 42 CM002898.1 49094737 0 ERR163_all_c100083 3 8 CM002903.1 31480191 1 ERR163_all_c100085 47 0 CM002905.1 17563804 42 ERR163_all_c1000867 1 0 CM002885.1 32847721 1 ERR163_all_c100087 83 24 CM002909.1 7082738 42 ERR163_all_c1000879 36 39 CM002886.1 57600591 0 ERR163_all_c1000879 9 42 CM002889.1 73838 22 ERR163_all_c100089 101 42 CM002886.1 59486802 42 ERR163_all_c100089 75 42 CM002886.1 59486813 23 ERR163_all_c10009 158 42 CM002904.1 48140887 0 ERR163_all_c1000916 2 0 CM002907.1 13404835 1 ERR163_all_c1000920 18 42 CM002892.1 8275583 40 ERR163_all_c100092 1 0 CM002896.1 1093703 23 ERR163_all_c100092 2 0 CM002896.1 1093704 23 ERR163_all_c10009 25 4 CM002902.1 26890160 31 ERR163_all_c1000939 3 0 CM002891.1 9913896 1 ERR163_all_c1000955 119 2 CM002894.1 16826454 1 ERR163_all_c1000955 149 26 CM002897.1 18979223 0 ERR163_all_c1000955 16 40 CM002900.1 26062434 1 ERR163_all_c1000955 2 3 CM002886.1 19780215 1 ERR163_all_c1000955 54 6 CM002887.1 55094291 1 ERR163_all_c1000955 66 1 CM002906.1 24495478 6 ERR163_all_c1000955 84 2 CM002901.1 45241630 2 ERR163_all_c1000961 85 3 CM002903.1 42646226 30 ERR163_all_c1000967 26 3 CM002899.1 41682863 40 ERR163_all_c1000976 54 0 CM002902.1 12411516 1 ERR163_all_c1000976 66 42 CM002885.1 1853145 1 ERR163_all_c1000979 27 42 CM002893.1 39311489 8 ERR163_all_c1000979 49 42 CM002889.1 797910 1 ERR163_all_c100098 11 42 CM002891.1 22614617 23 ERR163_all_c1000982 14 0 CM002904.1 48072402 1 ERR163_all_c1000983 72 42 CM002892.1 16464316 1 ERR163_all_c100099 5 42 CM002895.1 1579699 0 ERR163_all_c1001000 47 42 KN149696.1 254617 1 ERR163_all_c1001000 77 0 CM002887.1 49671361 1 ERR163_all_c10010 153 0 CM002889.1 17765452 1 ERR163_all_c10010 176 27 CM002909.1 27742192 1 ERR163_all_c100102 17 0 CM002900.1 31420673 0 ERR163_all_c1001023 8 42 CM002902.1 2171850 1 ERR163_all_c100103 1 0 CM002885.1 47902188 23 ERR163_all_c1001031 25 42 CM002902.1 34485885 42 ERR163_all_c1001035 8 42 CM002891.1 7048146 0 ERR163_all_c10010 37 42 CM002900.1 35197036 3 ERR163_all_c10010 38 42 CM002900.1 35197034 3 ERR163_all_c1001046 13 42 CM002902.1 14440176 42 ERR163_all_c100105 131 42 CM002896.1 35684515 1 ERR163_all_c1001056 69 0 CM002890.1 16398832 1 ERR163_all_c100105 86 42 CM002898.1 28283893 1 ERR163_all_c1001066 1 0 CM002888.1 6886182 0 ERR163_all_c1001069 18 0 CM002904.1 35346946 31 ERR163_all_c1001074 3 42 CM002894.1 22327096 3 ERR163_all_c1001090 2 5 CM002890.1 43327061 1 ERR163_all_c10011 108 42 CM002908.1 4853296 23 ERR163_all_c1001142 19 0 CM002900.1 11236388 1 ERR163_all_c1001146 121 0 CM002890.1 2776733 1 ERR163_all_c1001147 6 0 CM002891.1 1864870 1 ERR163_all_c100115 4 42 CM002897.1 26035023 40 ERR163_all_c1001177 12 3 CM002892.1 47579384 5 ERR163_all_c1001177 3 0 CM002896.1 45083526 1 ERR163_all_c1001181 91 8 CM002895.1 3161083 1 ERR163_all_c1001181 97 42 CM002902.1 7813934 1 ERR163_all_c1001185 116 42 CM002909.1 30929402 2 ERR163_all_c100118 55 0 CM002897.1 2935822 1 ERR163_all_c100119 21 3 CM002905.1 17273204 42 ERR163_all_c1001211 35 42 CM002890.1 58959449 4 ERR163_all_c100122 359 42 CM002901.1 1809709 0 ERR163_all_c100122 359 42 CM002901.1 1809709 0 ERR163_all_c100122 458 42 CM002908.1 14991330 0 ERR163_all_c100122 524 40 CM002894.1 4527271 0 ERR163_all_c1001245 11 42 CM002906.1 33584736 1 ERR163_all_c100126 632 40 CM002888.1 3776441 26 ERR163_all_c100126 637 40 CM002888.1 3776446 14 ERR163_all_c1001273 14 0 CM002889.1 68544699 31 ERR163_all_c100128 32 42 CM002889.1 62235209 7 ERR163_all_c100130 53 42 CM002894.1 1982560 1 ERR163_all_c1001322 3 5 KN150670.1 2309 1 ERR163_all_c1001322 83 42 CM002900.1 10907326 1 ERR163_all_c1001336 35 42 CM002896.1 8076545 30 ERR163_all_c1001336 90 2 CM002889.1 49776667 1 ERR163_all_c1001336 91 42 CM002902.1 34522932 30 ERR163_all_c1001338 46 30 CM002909.1 25804873 42 ERR163_all_c100134 20 42 CM002896.1 26772033 3 ERR163_all_c1001347 51 42 CM002906.1 29145849 0 ERR163_all_c1001348 54 25 CM002906.1 24496410 1 ERR163_all_c1001356 101 6 CM002887.1 55095437 1 ERR163_all_c1001356 80 0 CM002901.1 39957667 1 ERR163_all_c1001372 3 3 CM002903.1 28633178 3 ERR163_all_c1001393 6 42 CM002891.1 12203004 6 ERR163_all_c1001398 40 42 CM002893.1 1558039 6 ERR163_all_c1001401 35 2 CM002893.1 11326313 1 ERR163_all_c1001401 39 0 CM002903.1 19359986 1 ERR163_all_c1001401 39 2 CM002894.1 24977619 1 ERR163_all_c1001401 43 3 CM002901.1 42081618 6 ERR163_all_c1001401 43 3 KN150222.1 45239 1 ERR163_all_c1001401 44 0 CM002896.1 17425154 0 ERR163_all_c1001401 44 5 CM002906.1 22711816 1 ERR163_all_c1001401 45 0 CM002894.1 24956767 1 ERR163_all_c1001401 45 3 CM002898.1 12455010 6 ERR163_all_c1001401 46 0 CM002902.1 38001775 1 ERR163_all_c1001401 46 0 CM002908.1 15933632 1 ERR163_all_c1001401 46 3 CM002888.1 26663058 1 ERR163_all_c1001401 47 0 CM002898.1 14839093 1 ERR163_all_c1001401 48 0 CM002890.1 15171336 1 ERR163_all_c1001401 48 23 CM002909.1 25272912 1 ERR163_all_c1001401 49 0 CM002896.1 21505963 1 ERR163_all_c1001401 49 3 CM002885.1 55236408 1 ERR163_all_c1001401 49 3 CM002888.1 22228544 1 ERR163_all_c1001401 50 14 CM002890.1 35422155 1 ERR163_all_c1001401 50 3 CM002901.1 20721019 1 ERR163_all_c1001401 51 0 CM002897.1 13222003 1 ERR163_all_c1001401 51 0 CM002902.1 33554784 6 ERR163_all_c1001401 51 26 CM002886.1 12767508 1 ERR163_all_c1001401 51 26 CM002907.1 23380833 1 ERR163_all_c1001401 52 0 CM002887.1 60156666 1 ERR163_all_c1001401 52 3 CM002899.1 11208193 6 ERR163_all_c1001401 52 3 CM002902.1 25379899 1 ERR163_all_c1001401 53 0 CM002905.1 35750892 1 ERR163_all_c1001401 53 3 CM002900.1 50839191 1 ERR163_all_c1001401 53 3 CM002907.1 13435478 1 ERR163_all_c1001401 53 8 CM002907.1 17660364 1 ERR163_all_c1001401 54 0 CM002898.1 9513085 1 ERR163_all_c1001401 54 3 CM002900.1 53623659 1 ERR163_all_c1001401 55 3 CM002885.1 36255974 1 ERR163_all_c1001401 56 0 CM002888.1 31551815 1 ERR163_all_c1001401 56 0 CM002890.1 20490067 1 ERR163_all_c1001401 59 0 CM002891.1 16630351 1 ERR163_all_c1001401 77 6 CM002902.1 28561648 1 ERR163_all_c1001401 81 6 CM002891.1 48767253 1 ERR163_all_c1001415 19 42 CM002907.1 11706479 1 ERR163_all_c1001429 11 42 CM002891.1 50004588 1 ERR163_all_c1001440 141 2 CM002907.1 18249293 30 ERR163_all_c1001447 12 42 CM002891.1 10220883 14 ERR163_all_c1001451 57 42 CM002906.1 28418094 1 ERR163_all_c1001455 13 22 CM002903.1 45529864 40 ERR163_all_c1001455 77 40 CM002903.1 45529795 0 ERR163_all_c1001468 19 42 CM002897.1 40796631 0 ERR163_all_c1001471 40 42 CM002907.1 20752158 3 ERR163_all_c1001473 17 23 CM002903.1 33724945 42 ERR163_all_c1001473 47 40 CM002885.1 48565780 42 ERR163_all_c1001473 95 12 CM002896.1 2295578 1 ERR163_all_c1001490 47 0 CM002899.1 33028770 12 ERR163_all_c1001497 15 18 CM002892.1 34859098 1 ERR163_all_c1001510 4 42 CM002891.1 58321409 1 ERR163_all_c10015 189 24 CM002887.1 8631407 0 ERR163_all_c1001533 1 34 CM002902.1 41386710 42 ERR163_all_c1001533 44 12 CM002902.1 41386664 42 ERR163_all_c1001545 3 0 CM002904.1 3552060 1 ERR163_all_c1001577 25 42 CM002893.1 55661178 30 ERR163_all_c1001577 76 2 CM002886.1 3339490 1 ERR163_all_c100158 12 0 CM002906.1 38536297 40 ERR163_all_c100158 9 42 CM002906.1 38536294 40 ERR163_all_c1001590 18 42 CM002890.1 10384814 4 ERR163_all_c1001593 3 0 CM002900.1 443543 3 ERR163_all_c1001593 3 0 CM002900.1 443543 3 ERR163_all_c1001600 39 23 CM002909.1 13171541 0 ERR163_all_c1001600 86 0 CM002886.1 8634875 1 ERR163_all_c100161 1 0 CM002888.1 61717125 1 ERR163_all_c1001618 95 42 KN149891.1 8783 1 ERR163_all_c1001626 27 42 CM002909.1 2226467 11 ERR163_all_c1001644 5 42 CM002900.1 50971107 16 ERR163_all_c1001653 29 0 CM002898.1 16972107 1 ERR163_all_c1001654 5 42 CM002903.1 37257486 42 ERR163_all_c1001659 16 42 CM002891.1 15286816 0 ERR163_all_c1001694 1 3 CM002902.1 49501200 0 ERR163_all_c1001704 1 0 CM002904.1 41837647 0 ERR163_all_c100171 34 42 CM002908.1 13487010 26 ERR163_all_c10017 22 42 CM002885.1 5997435 1 ERR163_all_c1001734 1 0 CM002889.1 66343073 16 ERR163_all_c1001734 11 0 CM002891.1 30347086 31 ERR163_all_c100174 32 42 CM002892.1 9788723 0 ERR163_all_c1001743 58 42 CM002905.1 342312 1 ERR163_all_c1001749 12 21 CM002889.1 36642049 1 ERR163_all_c100175 16 42 CM002892.1 8194705 11 ERR163_all_c1001754 34 7 CM002886.1 46330713 24 ERR163_all_c100175 53 42 CM002892.1 8194705 11 ERR163_all_c100176 1 0 CM002896.1 20188631 23 ERR163_all_c1001763 3 42 CM002903.1 13042010 24 ERR163_all_c1001763 4 42 CM002903.1 13042012 3 ERR163_all_c1001776 115 42 CM002897.1 41674716 2 ERR163_all_c1001776 66 42 CM002897.1 41674699 0 ERR163_all_c1001805 25 8 CM002887.1 58799444 42 ERR163_all_c1001809 57 2 CM002902.1 47184283 1 ERR163_all_c1001811 34 4 CM002890.1 58794844 1 ERR163_all_c1001811 57 34 CM002900.1 21793620 2 ERR163_all_c10018 14 42 CM002898.1 8736941 0 ERR163_all_c100182 69 42 CM002904.1 9943563 24 ERR163_all_c1001828 13 42 CM002896.1 15788189 0 ERR163_all_c1001828 60 34 CM002896.1 45850816 3 ERR163_all_c100185 18 0 CM002890.1 55932533 40 ERR163_all_c100186 19 42 CM002902.1 15946525 42 ERR163_all_c1001863 3 24 CM002885.1 13715834 3 ERR163_all_c100186 4 42 CM002902.1 15946510 31 ERR163_all_c1001868 84 24 CM002903.1 18366282 1 ERR163_all_c10018 939 42 CM002900.1 49411829 0 ERR163_all_c1001907 35 2 CM002886.1 51094150 1 ERR163_all_c1001910 64 42 CM002905.1 2285725 31 ERR163_all_c1001927 8 0 CM002893.1 50126516 14 ERR163_all_c1001932 1 0 CM002889.1 51430216 1 ERR163_all_c100193 51 24 CM002901.1 35637191 42 ERR163_all_c1001947 16 6 CM002902.1 41918441 1 ERR163_all_c1001965 5 2 KN150391.1 25466 1 ERR163_all_c1001965 96 39 CM002894.1 19901520 23 ERR163_all_c1001983 23 40 CM002897.1 31106788 0 ERR163_all_c1001983 48 1 CM002891.1 5773064 1 ERR163_all_c1001985 27 3 CM002888.1 72209760 42 ERR163_all_c1001987 104 0 CM002903.1 48080314 0 ERR163_all_c1001987 49 23 CM002902.1 7667511 30 ERR163_all_c1001987 52 23 CM002902.1 7667515 30 ERR163_all_c1002009 113 0 CM002901.1 5012204 1 ERR163_all_c10020 1 42 CM002907.1 19696279 42 ERR163_all_c1002026 14 0 CM002898.1 49318781 1 ERR163_all_c1002026 21 0 CM002908.1 7953705 1 ERR163_all_c1002031 19 32 CM002897.1 6899200 1 ERR163_all_c1002032 7 42 CM002891.1 54455849 0 ERR163_all_c100207 1 0 CM002888.1 70625761 24 ERR163_all_c100208 182 0 CM002887.1 43782321 23 ERR163_all_c1002083 20 30 CM002907.1 41669837 6 ERR163_all_c1002095 13 30 CM002899.1 28870700 0 ERR163_all_c100211 58 42 CM002887.1 9377648 1 ERR163_all_c100212 1 3 CM002885.1 55659616 1 ERR163_all_c1002132 67 42 CM002904.1 10240582 40 ERR163_all_c1002141 21 36 CM002890.1 39342055 0 ERR163_all_c1002154 1 42 CM002909.1 20153857 1 ERR163_all_c1002156 9 42 CM002890.1 50171819 0 ERR163_all_c1002160 2 2 CM002904.1 53869408 1 ERR163_all_c1002167 1 42 CM002907.1 20325486 0 ERR163_all_c1002182 1 0 CM002903.1 48642459 0 ERR163_all_c1002182 11 42 CM002886.1 16156056 1 ERR163_all_c100218 57 42 CM002887.1 44655759 40 ERR163_all_c1002191 27 0 CM002887.1 17460595 6 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