Table S1: The position infromation of the SDs in the silkworm genome scaffold start-position end-position scaffold727 14 1054 scaffold935 1603 3685 nscaf3058 2792505 2797304 scaffold781 19628 20658 nscaf2674 2864264 2865941 scaffold2959 408 1477 scaffold1411 925 4304 scaffold1350 4190 6014 nscaf2953 56328 57699 scaffold1868 480 2486 nscaf497 22500 24126 nscaf3078 604590 605759 scaffold830 16238 17252 scaffold710 2376 3540 scaffold752 26375 27468 nscaf1898 8093475 8096791 scaffold2993 2 1259 nscaf3072 2606076 2607221 scaffold1850 1751 2795 nscaf2279 519861 521735 scaffold2427 2 1536 scaffold1009 2499 3925 nscaf2855 7135619 7136626 nscaf3040 3986874 3988654 nscaf2511 634584 635599 nscaf3005 116477 117479 nscaf2847 6125572 6126887 nscaf3035 1246724 1247771 nscaf3026 42999 44289 nscaf2330 1260367 1262521 nscaf2780 214596 216695 nscaf2136 766803 770151 nscaf3048 1501406 1502447 scaffold1999 1825 2946 scaffold2554 167 1726 nscaf2818 2887091 2889060 nscaf2767 2932970 2933984 nscaf2511 998092 999131 nscaf3072 1335479 1336648 nscaf2795 2259473 2260528 nscaf3079 925588 926793 scaffold2465 81 2135 scaffold914 5026 6063 scaffold841 3599 4648 nscaf2883 1698279 1699749 scaffold769 3955 5646 nscaf3079 734919 736094 scaffold2954 165 1454 scaffold1528 3433 4526 scaffold651 46820 47872 nscaf2814 476805 478005 nscaf2813 730971 732001 scaffold1313 2608 3841 nscaf2930 1742309 1743885 nscaf2916 559756 560825 scaffold1279 2825 6261 scaffold1074 292 1901 nscaf2902 2757686 2758880 nscaf2865 4984618 4985781 nscaf2822 1580588 1581628 scaffold2967 2 1303 nscaf2829 3074369 3076488 nscaf2924 280893 282075 nscaf3078 607497 608520 nscaf2986 927695 928739 nscaf1681 2614584 2615774 scaffold1420 76 1554 scaffold821 12789 15859 nscaf1169 4488 5798 nscaf2905 268094 269364 nscaf3022 850617 853253 scaffold1199 4054 6023 nscaf2686 15655 16689 nscaf2210 1928039 1929498 nscaf1681 2397937 2399265 nscaf2865 5413493 5414535 nscaf2825 598060 599138 nscaf2868 1905803 1906891 scaffold985 5185 7058 nscaf2902 4136162 4137330 scaffold1109 337 1533 nscaf2797 1293207 1294265 nscaf3098 985370 986474 nscaf3034 2668965 2670253 nscaf1898 4878174 4879228 nscaf1681 2198138 2199143 nscaf2986 5241823 5243191 nscaf3048 1504443 1505463 nscaf1898 68170 69177 nscaf2889 1357875 1359123 scaffold1888 2 1389 scaffold1086 167 4045 nscaf2853 5568288 5569294 scaffold804 18154 19257 scaffold800 10515 12821 nscaf1690 1298453 1300115 scaffold2570 259 1523 nscaf3005 1767440 1769889 nscaf2986 4188779 4189839 nscaf3075 493311 494409 nscaf2847 5184414 5185598 nscaf2795 2671455 2673065 nscaf3058 8605555 8606584 nscaf2962 535217 536324 scaffold1675 107 3529 nscaf463 467527 468687 nscaf2964 4209203 4210233 nscaf15 2233 3370 nscaf3084 15481 16889 nscaf2970 1397095 1398164 nscaf2330 1537753 1539069 nscaf2623 44254 45789 scaffold821 16388 17819 nscaf3022 301531 302828 scaffold1253 3445 5986 nscaf2847 2634813 2635824 nscaf2797 1327787 1329614 nscaf2210 4378157 4379658 nscaf3005 1219189 1220203 scaffold2184 1290 2446 scaffold1873 2014 3267 nscaf3099 4061333 4062341 nscaf2826 899738 900762 nscaf2575 4384652 4385664 scaffold710 43155 44610 scaffold1510 3232 4353 nscaf3058 4554843 4555862 nscaf2210 2841739 2843468 nscaf2943 222795 223807 scaffold1247 801 2010 nscaf1898 2138280 2139905 nscaf1681 2614644 2615773 nscaf3031 4567749 4568811 scaffold418 142965 143977 nscaf2855 154947 156480 nscaf3022 294292 295313 nscaf1690 5221220 5228078 nscaf2072 47693 49082 nscaf2511 347897 349114 nscaf3034 938401 939638 nscaf1681 3267679 3268901 nscaf2852 1205355 1206368 nscaf3063 1606592 1608258 nscaf3063 1504195 1505201 nscaf1898 7146007 7147080 nscaf2829 1030777 1032128 nscaf3099 4060982 4061993 nscaf3058 1535971 1537001 scaffold1432 1971 5084 nscaf2795 2671568 2673065 nscaf1898 12068223 12069724 scaffold1014 172 1909 nscaf2681 47761 48963 nscaf1194 3253 4344 nscaf3093 1283343 1284539 scaffold976 1525 11729 scaffold839 4309 6599 nscaf2829 1935128 1936142 nscaf3063 1630001 1631405 nscaf2930 5164214 5165483 scaffold2669 370 1752 nscaf463 466200 467356 nscaf3153 2 1276 nscaf2674 4801941 4803385 nscaf2847 4164450 4165740 nscaf3058 1743651 1744825 nscaf128 8018 9155 scaffold781 466 1539 nscaf2136 7674718 7675717 nscaf3157 19122 20313 scaffold868 4100 5136 nscaf2829 1976158 1977897 nscaf3013 888567 889778 scaffold1191 3820 5843 scaffold795 1174 2395 nscaf2674 5372593 5373833 nscaf3072 1356686 1357887 scaffold2402 2 1980 nscaf3031 1320717 1321939 scaffold1074 2325 8332 nscaf3026 6275511 6276574 nscaf2888 3837636 3838855 nscaf2889 1986377 1987854 scaffold1387 2915 4399 nscaf3079 910700 911861 nscaf2279 257956 259207 scaffold781 24317 25444 scaffold3538 2 1150 nscaf2795 464013 465371 nscaf2829 1449208 1450392 nscaf2993 1854689 1855899 nscaf2962 1001394 1002850 nscaf125 41456 43434 nscaf2842 126416 127935 nscaf3063 1664944 1666129 scaffold928 8587 9764 scaffold3153 92 1361 nscaf3048 810220 811332 nscaf2136 7696309 7697312 nscaf3075 573617 574785 nscaf2903 772163 773199 nscaf3034 1638570 1639629 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nscaf3072 2522297 2523450 nscaf98 11246 15811 scaffold1840 1994 3083 nscaf3072 2522441 2523505 nscaf3031 3750642 3751708 nscaf2874 223048 224247 nscaf2853 1925239 1928669 nscaf2674 5372998 5374316 nscaf3056 32600 34772 scaffold2436 189 1482 nscaf1690 3674514 3675551 nscaf2891 11437 13407 nscaf2846 77827 79610 nscaf3058 4554841 4555862 nscaf3127 2 1656 scaffold1848 2 3312 nscaf3072 2522327 2523445 nscaf2782 106381 107536 nscaf2795 2255590 2256689 nscaf3114 37806 39186 nscaf3033 413315 414567 scaffold868 4204 5758 scaffold923 874 1920 nscaf3075 1201958 1207277 nscaf3058 8825848 8826867 nscaf2889 1298114 1299785 nscaf2210 2556728 2557768 scaffold657 68114 69389 nscaf2993 5552528 5553696 nscaf2529 530389 540593 nscaf2210 1991202 1992311 nscaf3032 1120591 1121733 scaffold1200 5191 6344 scaffold1124 4050 5238 nscaf2925 151723 153610 nscaf2847 6472567 6473570 scaffold995 2 1058 scaffold4636 2 1023 nscaf2986 1486605 1487991 nscaf2589 4291836 4292854 nscaf2847 4556157 4559404 nscaf2811 338522 339675 scaffold891 10139 11352 nscaf2853 1573799 1575575 nscaf2902 6221542 6223253 nscaf3041 933781 934807 nscaf2813 623523 624570 scaffold3523 21 1219 scaffold1897 2 1029 nscaf3058 9014894 9016360 nscaf3031 3750641 3751682 nscaf2511 1062288 1063599 scaffold1027 3465 5880 nscaf2868 1905743 1907126 nscaf2813 650010 651046 scaffold1216 3941 5013 nscaf125 200073 201261 nscaf2882 111047 112081 nscaf2674 6786202 6788107 nscaf3017 97085 98278 scaffold1362 4118 5119 nscaf3066 222302 223326 nscaf2847 5184421 5185598 nscaf3072 548322 549938 scaffold849 8785 10842 nscaf3058 1743738 1744825 nscaf2853 617628 618682 scaffold1461 1704 2885 nscaf3074 155645 156705 scaffold1099 419 1556 nscaf2176 1064165 1065361 nscaf1690 5286078 5287107 nscaf2986 5241790 5243191 scaffold776 6878 8109 nscaf2797 1321171 1323001 scaffold1255 5576 6672 scaffold1108 629 8515 nscaf2993 5262925 5264015 nscaf3045 832252 833452 nscaf2930 1752212 1753274 nscaf3031 3750759 3751808 nscaf2855 727017 728190 nscaf2987 413523 414714 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6155930 scaffold734 37327 39067 nscaf3079 627694 628782 scaffold2936 2 1263 scaffold3564 2 1074 scaffold4520 2 1036 scaffold974 7722 8924 nscaf3027 2662743 2663861 nscaf2930 131798 133057 scaffold1192 3031 5053 nscaf1681 2988278 2989317 nscaf3076 324357 325834 nscaf2901 638067 639270 nscaf2987 36965 38190 nscaf2853 5055274 5056293 nscaf2795 2671541 2673065 nscaf2829 1976418 1977896 nscaf2865 3439786 3441295 scaffold1892 412 2783 nscaf2943 78751 79917 scaffold2903 327 1509 nscaf2204 2002593 2006702 scaffold2332 2 1263 nscaf2986 6407457 6409581 nscaf1898 8390253 8391296 nscaf2829 1934974 1936141 nscaf2853 5055295 5056505 scaffold1550 2398 4398 nscaf3040 534913 535921 nscaf2511 1050250 1051348 scaffold1318 2 2393 nscaf2674 464169 465214 nscaf3005 415830 417037 nscaf2868 1905943 1907111 nscaf2814 423693 424738 nscaf2909 24736 26107 scaffold2714 2 1534 nscaf3129 11462 13469 nscaf3058 4563927 4571776 nscaf2847 5184469 5185598 nscaf2814 532068 533419 nscaf3066 970909 972483 scaffold1636 2259 3849 scaffold718 36597 37610 nscaf2847 6181732 6183142 nscaf3058 1051433 1052571 scaffold2556 2 1703 scaffold982 1927 10401 nscaf2847 2335328 2339366 nscaf2964 861602 863317 nscaf3008 1473129 1474155 nscaf2823 1797233 1798283 nscaf3034 2110805 2112096 nscaf2964 3968986 3970124 nscaf2279 257921 261186 nscaf2176 2632299 2633382 scaffold1489 1254 2567 scaffold2684 62 1080 nscaf2903 59228 60294 nscaf2814 430208 431393 scaffold1021 6099 7101 nscaf3045 832252 833417 nscaf2847 6177967 6179386 nscaf2847 4030476 4031859 nscaf3120 86393 87716 scaffold878 9961 13655 nscaf3032 406476 407767 scaffold817 11413 13287 nscaf3026 1556580 1557883 nscaf3072 2522462 2523507 nscaf2210 2844208 2845472 nscaf2829 3074353 3076432 nscaf2575 1931403 1933300 nscaf2855 2647939 2650214 scaffold547 41543 42559 scaffold1167 2 3333 nscaf3058 2798829 2800499 nscaf2855 6699543 6700710 nscaf2511 6468612 6470140 nscaf2930 5789303 5790310 nscaf2818 1261112 1262320 nscaf2176 1064255 1065351 nscaf98 1667754 1669689 scaffold690 16630 18253 nscaf2822 1383348 1384554 nscaf2210 1928033 1929546 scaffold769 5702 7088 scaffold1427 28 1121 nscaf2851 1366997 1368532 nscaf3106 337717 339056 scaffold991 9311 10610 scaffold1490 2 3378 nscaf2894 12011 13098 nscaf2589 4592019 4593835 scaffold4208 2 1077 scaffold879 1844 3427 nscaf3031 1001923 1003001 nscaf2874 679939 681439 nscaf3026 2729978 2731162 scaffold3042 2 1419 nscaf2964 733027 736530 nscaf2279 258617 259817 nscaf2575 4018822 4019860 nscaf2529 2114235 2115702 scaffold2563 780 1961 nscaf2813 676695 677762 scaffold2526 2 1637 nscaf2986 2250458 2251495 nscaf2674 6938745 6940428 nscaf3079 148126 149150 nscaf3066 907482 908546 scaffold2917 2 1066 scaffold1479 2505 4014 nscaf2993 1854519 1856313 nscaf2931 892737 893847 nscaf1681 2345919 2346953 nscaf3045 69053 70081 nscaf2795 2671539 2673065 nscaf2827 626259 627270 nscaf2818 3044560 3046784 nscaf3058 1146512 1147903 nscaf2930 4104869 4106252 nscaf3022 398384 399605 nscaf2829 1935102 1936142 nscaf2823 951981 953062 scaffold2550 323 1807 scaffold1236 4908 5937 scaffold1014 878 1982 nscaf2827 625916 627306 scaffold1162 5786 7452 nscaf2970 2522143 2523329 nscaf1681 2265894 2267575 scaffold800 11614 12802 nscaf3026 3280833 3281862 nscaf1898 4878178 4879200 nscaf2970 1396883 1398287 nscaf2859 992826 993880 scaffold785 14070 15283 scaffold2920 2 1354 scaffold2351 2 1158 nscaf2800 1294332 1295391 nscaf2589 4597944 4599425 nscaf2818 1261158 1262335 scaffold2737 337 1642 nscaf2813 699292 701163 nscaf2330 2828221 2829227 nscaf3003 1853182 1854199 nscaf2847 5184464 5185598 nscaf2136 1887679 1889077 scaffold1094 5253 6303 nscaf2838 2460227 2461262 scaffold919 11235 13124 scaffold1268 2 1266 nscaf1898 12141254 12142267 scaffold706 439 1667 nscaf2589 5413545 5415274 nscaf2962 535218 536411 nscaf2674 4827533 4828975 scaffold1303 1006 4491 nscaf3040 2005152 2006220 nscaf2623 718901 720049 nscaf2986 4188672 4189839 nscaf2986 2987876 2989367 nscaf2136 1887692 1889014 scaffold1200 1459 2859 nscaf2511 2008114 2009152 nscaf2589 2587067 2588205 scaffold864 4792 6982 nscaf3015 2436118 2437302 scaffold3563 2 1209 nscaf3142 14247 15490 nscaf3005 1129547 1130849 nscaf2767 73909 78298 nscaf2930 9664 10664 nscaf2674 7140797 7141849 nscaf2781 120407 121415 nscaf2674 4816800 4818081 nscaf3035 776840 778093 nscaf2865 4409536 4411254 nscaf2511 1107927 1109015 nscaf2853 203955 205241 nscaf2838 2457173 2458210 scaffold1140 5616 7749 nscaf2853 5055262 5056519 scaffold2465 2 2135 nscaf2925 43821 45736 nscaf1898 8389219 8390258 scaffold651 46667 47907 nscaf2964 4703272 4704379 nscaf3017 97146 98278 nscaf1898 12475457 12476822 nscaf2511 1022059 1023816 scaffold1102 4908 6648 nscaf2948 646439 647518 nscaf2136 7010458 7012358 scaffold2730 2 1682 scaffold1369 839 1917 nscaf2838 2008297 2009478 nscaf2210 4383033 4384033 scaffold789 4163 6075 nscaf2830 206178 207354 nscaf3058 8825873 8826904 nscaf2962 1001378 1002847 nscaf2846 22183 23262 nscaf2818 776168 777259 nscaf576 11759 12766 nscaf3015 2699349 2700392 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