BASED ON: Release 6 plus ISO1 mitochondrial genome Organism: Drosophila melanogaster (fruit fly) Submitter: The FlyBase Consortium/Berkeley Drosophila Genome Project/Celera Genomicsi Date: 2014/08/01 Assembly level: ChromosomeGenome representation: full RefSeq category: reference genomeSynonyms: dm 6GenBank assembly accession: GCA_000001215.4 (latest) RefSeq assembly accession: GCF_000001215.4 (latest) # SEQUENCE TOTAL REPEAT CDS # Megabase 143.73 32.06 (22.3%) 60.43 (42.0%) # # ENZYME SPEC SITES: TOTAL REPEAT CDS # AatII GACGTC 28240 3014 (10.7%) 18497 (65.5%) Acc65I GGTACC 19631 5943 (30.3%) 12063 (61.4%) AccI GTMKAC 129495 28385 (21.9%) 59419 (45.9%) AciI CCGC 1405437 195326 (13.9%) 1176455 (83.7%) AclI AACGTT 52471 12366 (23.6%) 14608 (27.8%) AcuI CTGAAG 123354 18469 (15.0%) 88429 (71.7%) AfeI AGCGCT 42092 7667 (18.2%) 25685 (61.0%) AflII CTTAAG 61959 11867 (19.2%) 16563 (26.7%) AflIII ACRYGT 154720 32605 (21.1%) 54558 (35.3%) AgeI ACCGGT 18868 2507 (13.3%) 14909 (79.0%) AluI AGCT 1047665 191891 (18.3%) 565708 (54.0%) AlwI GGATC 354521 49144 (13.9%) 341152 (96.2%) ApaI GGGCCC 20674 3097 (15.0%) 9950 (48.1%) ApaLI GTGCAC 56098 11027 (19.7%) 28746 (51.2%) ApeKI GCWGC 800760 182930 (22.8%) 685221 (85.6%) ApoI RAATTY 704034 322449 (45.8%) 91133 (12.9%) AscI GGCGCGCC 733 122 (16.6%) 627 (85.5%) AseI ATTAAT 189580 97279 (51.3%) 12699 ( 6.7%) AsiSI GCGATCGC 1625 85 ( 5.2%) 1952 (120.1%) AvaI CYCGRG 111933 12491 (11.2%) 82673 (73.9%) AvaII GGWCC 283575 92828 (32.7%) 166992 (58.9%) AvrII CCTAGG 13487 2342 (17.4%) 3632 (26.9%) BaeGI GKGCMC 161334 23272 (14.4%) 114742 (71.1%) BamHI GGATCC 42683 4108 ( 9.6%) 47884 (112.2%) BanI GGYRCC 143540 21584 (15.0%) 148301 (103.3%) BanII GRGCYC 135846 18862 (13.9%) 97231 (71.6%) BbvI GCAGC 800760 182930 (22.8%) 685221 (85.6%) BccI CCATC 498859 71126 (14.3%) 340154 (68.2%) BceAI ACGGC 301390 45220 (15.0%) 229837 (76.3%) BciVI GTATCC 74735 12214 (16.3%) 45035 (60.3%) BclI TGATCA 59144 15408 (26.1%) 38519 (65.1%) BcoDI GTCTC 266663 43497 (16.3%) 152864 (57.3%) BfuAI ACCTGC 88493 9560 (10.8%) 75482 (85.3%) BfuCI GATC 741325 119593 (16.1%) 609262 (82.2%) BglII AGATCT 49740 8937 (18.0%) 31114 (62.6%) BlpI GCTNAGC 58161 9911 (17.0%) 32511 (55.9%) BmrI ACTGGG 98112 14548 (14.8%) 62881 (64.1%) BmtI GCTAGC 31415 6424 (20.4%) 11271 (35.9%) BpmI CTGGAG 133360 18811 (14.1%) 150256 (112.7%) BpuEI CTTGAG 101606 15177 (14.9%) 60965 (60.0%) BsaAI YACGTR 130719 29378 (22.5%) 52182 (39.9%) BsaHI GRCGYC 137850 13772 (10.0%) 131984 (95.7%) BsaI GGTCTC 59168 9174 (15.5%) 45539 (77.0%) BsaWI WCCGGW 121885 14391 (11.8%) 116708 (95.8%) BseRI GAGGAG 161065 29360 (18.2%) 186921 (116.1%) BsgI GTGCAG 138520 21713 (15.7%) 96716 (69.8%) BsiEI CGRYCG 119679 13921 (11.6%) 95045 (79.4%) BsiHKAI GWGCWC 219068 34518 (15.8%) 155519 (71.0%) BsiWI CGTACG 17316 2262 (13.1%) 11212 (64.7%) BsmAI GTCTC 266663 43497 (16.3%) 152864 (57.3%) BsmBI CGTCTC 63636 10301 (16.2%) 46354 (72.8%) BsmFI GGGAC 276784 93263 (33.7%) 147489 (53.3%) BsmI GAATGC 154966 27648 (17.8%) 67594 (43.6%) BsoBI CYCGRG 111933 12491 (11.2%) 82673 (73.9%) Bsp1286I GDGCHC 387027 52974 (13.7%) 291168 (75.2%) BspCNI CTCAG 330771 58161 (17.6%) 179972 (54.4%) BspDI ATCGAT 86639 14715 (17.0%) 44015 (50.8%) BspEI TCCGGA 41205 4407 (10.7%) 46595 (113.1%) BspHI TCATGA 41046 7862 (19.2%) 19230 (46.8%) BspMI ACCTGC 88493 9560 (10.8%) 75482 (85.3%) BspQI GCTCTTC 37936 6551 (17.3%) 30013 (79.1%) BsrBI CCGCTC 95647 14422 (15.1%) 71340 (74.6%) BsrFI RCCGGY 131068 14945 (11.4%) 123990 (94.6%) BsrGI TGTACA 79979 30170 (37.7%) 23632 (29.5%) BsrI ACTGG 486562 110793 (22.8%) 309916 (63.7%) BssHII GCGCGC 25336 3752 (14.8%) 16026 (63.3%) BssSI CACGAG 60713 8137 (13.4%) 46892 (77.2%) BstBI TTCGAA 93733 22253 (23.7%) 23375 (24.9%) BstEII GGTNACC 33099 4249 (12.8%) 31756 (95.9%) BstNI CCWGG 380908 40885 (10.7%) 351566 (92.3%) BstUI CGCG 415157 59883 (14.4%) 317351 (76.4%) BstYI RGATCY 185047 25388 (13.7%) 163349 (88.3%) BstZ17I GTATAC 44526 14874 (33.4%) 9326 (20.9%) Bsu36I CCTNAGG 20074 3683 (18.3%) 11850 (59.0%) BtgI CCRYGG 144419 17249 (11.9%) 138731 (96.1%) BtgZI GCGATG 113135 13062 (11.5%) 95463 (84.4%) BtsCI GGATG 451969 69005 (15.3%) 329425 (72.9%) ClaI ATCGAT 86639 14715 (17.0%) 44015 (50.8%) CviAII CATG 808424 138953 (17.2%) 441964 (54.7%) CviKI-1 RGCY 3412254 546277 (16.0%) 2041140 (59.8%) CviQI GTAC 620719 199473 (32.1%) 277472 (44.7%) DdeI CTNAG 626140 116548 (18.6%) 246298 (39.3%) DpnII GATC 741325 119593 (16.1%) 609262 (82.2%) DraI TTTAAA 296420 183055 (61.8%) 13932 ( 4.7%) EaeI YGGCCR 325328 47999 (14.8%) 266116 (81.8%) EagI CGGCCG 28470 2887 (10.1%) 27891 (98.0%) EarI CTCTTC 136204 26865 (19.7%) 83162 (61.1%) EciI GGCGGA 116727 12101 (10.4%) 124041 (106.3%) Eco53kI GAGCTC 52449 9554 (18.2%) 37628 (71.7%) EcoO109I RGGNCCY 92023 13975 (15.2%) 56730 (61.6%) EcoRI GAATTC 76998 15643 (20.3%) 26015 (33.8%) EcoRV GATATC 52034 8268 (15.9%) 25709 (49.4%) FatI CATG 808424 138953 (17.2%) 441964 (54.7%) FauI CCCGC 267556 34602 (12.9%) 196496 (73.4%) Fnu4HI GCNGC 1217865 237146 (19.5%) 1067983 (87.7%) FokI GGATG 451969 69005 (15.3%) 329425 (72.9%) FseI GGCCGGCC 856 66 ( 7.7%) 473 (55.3%) FspI TGCGCA 59008 10777 (18.3%) 41317 (70.0%) HaeII RGCGCY 168813 23397 (13.9%) 146282 (86.7%) HaeIII GGCC 768948 104017 (13.5%) 592612 (77.1%) HgaI GACGC 252145 29426 (11.7%) 214730 (85.2%) HhaI GCGC 621169 90966 (14.6%) 473351 (76.2%) HincII GTYRAC 183275 29374 (16.0%) 77881 (42.5%) HindIII AAGCTT 76812 17492 (22.8%) 19069 (24.8%) HinfI GANTC 759271 126051 (16.6%) 425125 (56.0%) HinP1I GCGC 621169 90966 (14.6%) 473351 (76.2%) HpaI GTTAAC 47141 8272 (17.5%) 11043 (23.4%) HpaII CCGG 499201 54572 (10.9%) 465402 (93.2%) HphI GGTGA 358689 53344 (14.9%) 264281 (73.7%) Hpy188I TCNGA 779292 151416 (19.4%) 396755 (50.9%) Hpy99I CGWCG 279926 38051 (13.6%) 248273 (88.7%) HpyAV CCTTC 420933 65503 (15.6%) 275252 (65.4%) HpyCH4III ACNGT 635805 133148 (20.9%) 291697 (45.9%) HpyCH4IV ACGT 537433 109012 (20.3%) 239212 (44.5%) HpyCH4V TGCA 1423568 336840 (23.7%) 585085 (41.1%) KasI GGCGCC 42026 4253 (10.1%) 47417 (112.8%) KpnI GGTACC 19631 5943 (30.3%) 12063 (61.4%) MboI GATC 741325 119593 (16.1%) 609262 (82.2%) MboII GAAGA 576412 127673 (22.1%) 341090 (59.2%) MfeI CAATTG 116258 25123 (21.6%) 34263 (29.5%) MluCI AATT 2533383 1080728 (42.7%) 305520 (12.1%) MluI ACGCGT 22579 3694 (16.4%) 12067 (53.4%) MlyI GAGTC 296747 43457 (14.6%) 182864 (61.6%) MmeI TCCRAC 189538 31936 (16.8%) 115857 (61.1%) MnlI CCTC 1393483 218156 (15.7%) 1096307 (78.7%) MscI TGGCCA 163362 28914 (17.7%) 110824 (67.8%) MseI TTAA 2026173 871692 (43.0%) 219442 (10.8%) MspA1I CMGCKG 267871 39807 (14.9%) 238608 (89.1%) MspI CCGG 499201 54572 (10.9%) 465402 (93.2%) NaeI GCCGGC 53941 5575 (10.3%) 51808 (96.0%) NarI GGCGCC 42026 4253 (10.1%) 47417 (112.8%) NciI CCSGG 191934 22263 (11.6%) 148509 (77.4%) NcoI CCATGG 50326 4999 ( 9.9%) 42106 (83.7%) NdeI CATATG 78527 26684 (34.0%) 15060 (19.2%) NgoMIV GCCGGC 53941 5575 (10.3%) 51808 (96.0%) NheI GCTAGC 31415 6424 (20.4%) 11271 (35.9%) NlaIII CATG 808424 138953 (17.2%) 441964 (54.7%) NmeAIII GCCGAG 99683 12509 (12.5%) 87076 (87.4%) NotI GCGGCCGC 1444 175 (12.1%) 2168 (150.1%) NruI TCGCGA 33388 5727 (17.2%) 27434 (82.2%) NsiI ATGCAT 93381 28010 (30.0%) 17480 (18.7%) NspI RCATGY 231000 43866 (19.0%) 98201 (42.5%) PacI TTAATTAA 16222 11883 (73.3%) 205 ( 1.3%) PaeR7I CTCGAG 39120 4347 (11.1%) 27206 (69.5%) PciI ACATGT 62668 13967 (22.3%) 18785 (30.0%) PleI GAGTC 296747 43457 (14.6%) 182864 (61.6%) PluTI GGCGCC 42026 4253 (10.1%) 47417 (112.8%) PmeI GTTTAAAC 2640 858 (32.5%) 212 ( 8.0%) PmlI CACGTG 31876 4779 (15.0%) 18601 (58.4%) PpuMI RGGWCCY 54611 8855 (16.2%) 35532 (65.1%) PsiI TTATAA 156765 82611 (52.7%) 9326 ( 5.9%) PspGI CCWGG 380908 40885 (10.7%) 351566 (92.3%) PspOMI GGGCCC 20674 3097 (15.0%) 9950 (48.1%) PspXI VCTCGAGB 11428 1215 (10.6%) 8611 (75.4%) PstI CTGCAG 98457 16341 (16.6%) 95873 (97.4%) PvuI CGATCG 41374 4014 ( 9.7%) 33306 (80.5%) PvuII CAGCTG 117954 18087 (15.3%) 93273 (79.1%) RsaI GTAC 620719 199473 (32.1%) 277472 (44.7%) RsrII CGGWCCG 9801 1472 (15.0%) 8142 (83.1%) SacI GAGCTC 52449 9554 (18.2%) 37628 (71.7%) SacII CCGCGG 21311 2208 (10.4%) 19369 (90.9%) SalI GTCGAC 33446 4841 (14.5%) 21840 (65.3%) SapI GCTCTTC 37936 6551 (17.3%) 30013 (79.1%) Sau3AI GATC 741325 119593 (16.1%) 609262 (82.2%) Sau96I GGNCC 540139 124951 (23.1%) 328751 (60.9%) SbfI CCTGCAGG 1975 101 ( 5.1%) 2746 (139.0%) ScaI AGTACT 42274 8217 (19.4%) 21804 (51.6%) ScrFI CCNGG 572842 63148 (11.0%) 500075 (87.3%) SexAI ACCWGGT 18648 2227 (11.9%) 16878 (90.5%) SfaNI GCATC 449733 63804 (14.2%) 347854 (77.3%) SfcI CTRYAG 197494 36150 (18.3%) 137666 (69.7%) SfoI GGCGCC 42026 4253 (10.1%) 47417 (112.8%) SgrAI CRCCGGYG 5718 431 ( 7.5%) 9226 (161.4%) SmaI CCCGGG 19140 2789 (14.6%) 10678 (55.8%) SmlI CTYRAG 202685 31391 (15.5%) 104734 (51.7%) SnaBI TACGTA 36540 11884 (32.5%) 6260 (17.1%) SpeI ACTAGT 28591 6068 (21.2%) 6201 (21.7%) SphI GCATGC 54656 8813 (16.1%) 28452 (52.1%) SrfI GCCCGGGC 814 184 (22.6%) 434 (53.3%) SspI AATATT 258956 156789 (60.5%) 21930 ( 8.5%) StuI AGGCCT 28242 3859 (13.7%) 22465 (79.5%) StyD4I CCNGG 572842 63148 (11.0%) 500075 (87.3%) StyI CCWWGG 176877 19627 (11.1%) 141794 (80.2%) SwaI ATTTAAAT 19185 14802 (77.2%) 609 ( 3.2%) TaqI TCGA 954768 168244 (17.6%) 504435 (52.8%) TfiI GAWTC 462524 82594 (17.9%) 242261 (52.4%) TseI GCWGC 800760 182930 (22.8%) 685221 (85.6%) Tsp45I GTSAC 294206 47936 (16.3%) 166011 (56.4%) TspMI CCCGGG 19140 2789 (14.6%) 10678 (55.8%) TspRI CASTG 487907 81188 (16.6%) 294082 (60.3%) XbaI TCTAGA 38108 10231 (26.8%) 8037 (21.1%) XhoI CTCGAG 39120 4347 (11.1%) 27206 (69.5%) XmaI CCCGGG 19140 2789 (14.6%) 10678 (55.8%) ZraI GACGTC 28240 3014 (10.7%) 18497 (65.5%)