* A list of 363 Fur binding clusters in Escherichia coli * detected by the 24-site M9 model * 2006 Nov 1 * * Supplementary Material for * * Discovery of Fur binding site clusters in Escherichia coli * by information theory models * * Zehua Chen, Karen A. Lewis, Ryan K. Shultzaberger, Ilya G. Lyakhov, * Ming Zheng, Bernard Doan, Gisela Storz and Thomas D. Schneider * * Contact: * * Dr. Thomas D. Schneider * toms@alum.mit.edu * permanent email: toms@alum.mit.edu (use only if first address fails) * https://alum.mit.edu/www/toms/ * * Each of these clusters contains at least one site higher than 10.0 * bits (the lowest information of a site in the model is 10.1 bits). * * Coordinates are in bases on * GenBank Accesssion number: NC_000913 * * Note: * intergene means that the Fur clusters are in intergenic regions, * insidegene means that the Fur clusters are in gene coding regions, * overlap means that the Fur clusters overlap gene coding regions. * *========================================================= * Number Coordinates Cluster Location * of sites From To Length Relative * (Ri > 0) (bp) To Genes *-------------------------------------------------------- 7 41980 42020 41 intergene 3 59147 59171 25 insidegene 2 82467 82491 25 insidegene 2 113211 113255 45 overlap 1 125901 125919 19 insidegene 2 127682 127707 26 intergene 7 130297 130345 49 insidegene 3 155390 155414 25 insidegene 3 167424 167454 31 intergene 1 179136 179154 19 overlap 1 189581 189599 19 intergene 4 238843 238892 50 insidegene 5 258298 258334 37 insidegene 5 289733 289782 50 intergene 1 292489 292507 19 insidegene 1 295856 295874 19 insidegene 1 312290 312308 19 intergene 2 313178 313202 25 intergene 1 316839 316857 19 intergene 4 331040 331100 61 intergene 4 331886 331913 28 insidegene 4 333718 333753 36 overlap 2 334497 334521 25 overlap 8 343522 343580 59 insidegene 1 376821 376839 19 insidegene 2 403652 403676 25 insidegene 1 404845 404863 19 insidegene 4 451065 451104 40 intergene 3 490048 490072 25 intergene 1 490114 490132 19 insidegene 2 505029 505073 45 insidegene 1 515647 515665 19 insidegene 11 527887 527960 74 insidegene 3 535582 535606 25 insidegene 4 558193 558238 46 overlap 3 561802 561832 31 insidegene 10 563041 563090 50 overlap 1 570115 570133 19 overlap 4 571118 571167 50 insidegene 5 578185 578224 40 intergene 4 579809 579836 28 intergene 2 582464 582488 25 intergene 8 582530 582637 108 intergene 8 582766 582862 97 intergene 2 583649 583695 47 overlap 4 611880 611916 37 intergene 2 617543 617567 25 insidegene 4 621422 621458 37 intergene 2 623942 623966 25 intergene 4 624057 624093 37 intergene 3 675759 675810 52 overlap 2 676522 676567 46 insidegene 3 678149 678179 31 insidegene 2 709931 709955 25 intergene 2 732998 733020 23 overlap 3 748899 748937 39 overlap 3 751438 751462 25 overlap 1 764577 764595 19 insidegene 5 786838 786868 31 intergene 4 840850 840886 37 intergene 3 848287 848311 25 intergene 4 872505 872532 28 insidegene 1 889959 889977 19 overlap 1 902194 902212 19 overlap 6 925265 925298 34 intergene 4 953830 953864 35 intergene 7 953936 954002 67 intergene 8 997610 997666 57 overlap 2 1014179 1014200 22 insidegene 4 1020276 1020336 61 intergene 3 1027024 1027069 46 intergene 2 1047147 1047168 22 insidegene 4 1049980 1050011 32 intergene 1 1055650 1055668 19 insidegene 2 1080504 1080538 35 intergene 1 1092113 1092131 19 insidegene 2 1092362 1092383 22 insidegene 1 1092686 1092704 19 insidegene 3 1107562 1107589 28 insidegene 5 1118343 1118382 40 intergene 5 1160843 1160895 53 intergene 3 1180642 1180669 28 insidegene 1 1194235 1194253 19 intergene 2 1198185 1198209 25 insidegene 3 1210477 1210516 40 intergene 6 1211516 1211574 59 intergene 5 1215724 1215756 33 insidegene 5 1222324 1222372 49 intergene 2 1255633 1255657 25 intergene 1 1262564 1262582 19 insidegene 1 1297702 1297720 19 intergene 2 1298958 1298982 25 intergene 3 1309044 1309072 29 intergene 1 1311289 1311307 19 insidegene 3 1314109 1314153 45 intergene 1 1321089 1321107 19 overlap 1 1325016 1325034 19 insidegene 6 1333472 1333512 41 intergene 1 1393822 1393840 19 insidegene 2 1399149 1399183 35 insidegene 3 1416245 1416272 28 overlap 3 1416754 1416784 31 insidegene 7 1431711 1431772 62 intergene 3 1432249 1432288 40 overlap 5 1435095 1435128 34 intergene 4 1463680 1463707 28 intergene 1 1481750 1481768 19 insidegene 2 1486189 1486214 26 intergene 1 1497165 1497183 19 insidegene 1 1517306 1517324 19 insidegene 2 1517699 1517723 25 insidegene 1 1520370 1520388 19 insidegene 3 1521222 1521249 28 intergene 5 1524070 1524100 31 intergene 1 1528018 1528036 19 insidegene 9 1528332 1528393 62 insidegene 2 1542048 1542072 25 insidegene 5 1542473 1542509 37 insidegene 7 1544138 1544196 59 intergene 1 1552892 1552910 19 insidegene 2 1557785 1557809 25 insidegene 4 1577247 1577274 28 insidegene 2 1577349 1577373 25 overlap 1 1577785 1577803 19 insidegene 3 1589579 1589606 28 insidegene 3 1596164 1596188 25 intergene 6 1596349 1596389 41 intergene 3 1631056 1631095 40 overlap 7 1631572 1631633 62 intergene 3 1634615 1634639 25 intergene 4 1635527 1635573 47 intergene 3 1636321 1636355 35 intergene 1 1640231 1640249 19 intergene 3 1651906 1651946 41 overlap 2 1653825 1653849 25 overlap 2 1654767 1654791 25 overlap 3 1671514 1671563 50 overlap 2 1672504 1672528 25 insidegene 3 1687857 1687884 28 overlap 2 1690656 1690680 25 insidegene 4 1732338 1732380 43 intergene 7 1752669 1752771 103 intergene 3 1762448 1762478 31 intergene 3 1762567 1762608 42 intergene 2 1762629 1762663 35 intergene 2 1776815 1776836 22 insidegene 10 1787587 1787639 53 overlap 3 1790002 1790032 31 insidegene 1 1796552 1796570 19 insidegene 1 1800285 1800303 19 insidegene 1 1827892 1827910 19 insidegene 5 1830017 1830066 50 intergene 3 1875536 1875560 25 overlap 1 1876796 1876814 19 intergene 2 1886636 1886660 25 insidegene 2 1901240 1901264 25 insidegene 1 1902980 1902998 19 insidegene 2 1903397 1903421 25 intergene 4 1906147 1906180 34 intergene 4 1914243 1914270 28 intergene 4 1976296 1976323 28 intergene 2 1977438 1977462 25 intergene 4 1984678 1984722 45 intergene 1 1986100 1986118 19 intergene 3 1993678 1993721 44 intergene 11 1994873 1994947 75 intergene 4 2000925 2000955 31 insidegene 3 2034563 2034593 31 insidegene 2 2035100 2035124 25 insidegene 3 2039669 2039693 25 insidegene 4 2042860 2042904 45 intergene 3 2055706 2055730 25 intergene 3 2055987 2056011 25 intergene 12 2066544 2066638 95 intergene 1 2071666 2071684 19 insidegene 2 2101939 2101978 40 insidegene 2 2105807 2105838 32 insidegene 2 2113107 2113131 25 insidegene 3 2135666 2135693 28 intergene 4 2166286 2166313 28 insidegene 4 2183917 2183947 31 overlap 1 2186607 2186625 19 insidegene 2 2195866 2195890 25 intergene 1 2199993 2200011 19 insidegene 2 2202363 2202387 25 intergene 3 2231880 2231904 25 intergene 2 2241782 2241806 25 intergene 3 2244965 2244995 31 intergene 1 2254032 2254050 19 overlap 2 2288485 2288509 25 intergene 5 2306693 2306723 31 overlap 4 2341621 2341670 50 insidegene 5 2362463 2362493 31 intergene 1 2367596 2367614 19 insidegene 1 2372117 2372135 19 insidegene 4 2381860 2381900 41 insidegene 10 2383796 2383911 116 overlap 2 2399560 2399584 25 overlap 1 2436379 2436397 19 insidegene 1 2449080 2449098 19 overlap 1 2451703 2451721 19 insidegene 2 2454123 2454151 29 intergene 2 2460970 2461011 42 intergene 8 2462036 2462105 70 overlap 3 2462266 2462294 29 overlap 1 2466334 2466352 19 insidegene 2 2467593 2467617 25 insidegene 1 2468122 2468140 19 insidegene 2 2488167 2488209 43 overlap 2 2510775 2510799 25 intergene 3 2584122 2584146 25 insidegene 3 2599087 2599111 25 intergene 4 2626664 2626716 53 insidegene 1 2640942 2640960 19 intergene 2 2651516 2651540 25 intergene 2 2651838 2651862 25 intergene 1 2663281 2663299 19 intergene 2 2666171 2666202 32 insidegene 2 2673795 2673817 23 intergene 2 2716472 2716496 25 insidegene 1 2717080 2717098 19 insidegene 1 2749862 2749880 19 insidegene 5 2757984 2758033 50 insidegene 5 2758380 2758433 54 overlap 3 2758901 2758938 38 insidegene 5 2771487 2771548 62 insidegene 3 2771858 2771891 34 insidegene 6 2772416 2772462 47 insidegene 1 2778196 2778214 19 insidegene 2 2781032 2781056 25 intergene 3 2782955 2782985 31 insidegene 5 2783213 2783278 66 overlap 4 2783867 2783912 46 insidegene 8 2784021 2784116 96 intergene 5 2786044 2786099 56 insidegene 2 2792186 2792214 29 intergene 4 2798729 2798769 41 overlap 4 2823740 2823788 49 intergene 4 2830332 2830406 75 intergene 10 2882370 2882450 81 intergene 2 2898757 2898781 25 insidegene 2 2902645 2902669 25 intergene 1 2903663 2903681 19 intergene 7 2922620 2922682 63 intergene 2 2967247 2967268 22 intergene 1 2975389 2975407 19 insidegene 7 2980392 2980466 75 intergene 1 2984273 2984291 19 insidegene 1 2986360 2986378 19 intergene 2 2990857 2990881 25 insidegene 6 2993455 2993497 43 insidegene 9 3013800 3013907 108 intergene 1 3064937 3064955 19 insidegene 3 3122230 3122272 43 overlap 1 3135791 3135809 19 insidegene 1 3143896 3143914 19 insidegene 3 3150067 3150097 31 insidegene 1 3156648 3156666 19 overlap 5 3180501 3180531 31 intergene 9 3183317 3183438 122 overlap 8 3184048 3184110 63 intergene 2 3202236 3202257 22 overlap 8 3214502 3214607 106 overlap 1 3214719 3214737 19 intergene 2 3217363 3217391 29 intergene 2 3225335 3225356 22 insidegene 6 3251320 3251351 32 overlap 1 3258115 3258133 19 overlap 7 3266389 3266426 38 overlap 2 3270756 3270792 37 overlap 4 3272852 3272879 28 insidegene 6 3272912 3272997 86 overlap 8 3273039 3273103 65 intergene 1 3276831 3276849 19 intergene 2 3281918 3281942 25 insidegene 5 3285252 3285328 77 intergene 5 3319658 3319692 35 intergene 2 3319776 3319800 25 intergene 1 3328778 3328796 19 insidegene 1 3332930 3332948 19 overlap 1 3357223 3357241 19 insidegene 1 3361720 3361738 19 insidegene 3 3382535 3382557 23 intergene 3 3410984 3411008 25 insidegene 2 3434536 3434557 22 overlap 6 3453656 3453717 62 insidegene 1 3460936 3460954 19 overlap 3 3465038 3465068 31 intergene 2 3502785 3502809 25 overlap 1 3537997 3538015 19 intergene 4 3538044 3538092 49 intergene 4 3579039 3579069 31 intergene 8 3582757 3582797 41 overlap 1 3600759 3600777 19 overlap 3 3602998 3603040 43 overlap 3 3607791 3607821 31 insidegene 5 3630269 3630313 45 insidegene 2 3631096 3631126 31 insidegene 3 3632555 3632579 25 intergene 1 3634161 3634179 19 intergene 1 3637907 3637925 19 intergene 6 3651729 3651784 56 intergene 4 3652617 3652644 28 intergene 2 3694713 3694734 22 insidegene 4 3694934 3694965 32 insidegene 5 3718355 3718397 43 intergene 1 3725252 3725270 19 insidegene 8 3755886 3755968 83 intergene 9 3767802 3767920 119 intergene 3 3787976 3788000 25 insidegene 1 3792277 3792295 19 insidegene 2 3795420 3795442 23 insidegene 3 3796694 3796739 46 insidegene 5 3797499 3797529 31 insidegene 3 3799380 3799407 28 insidegene 4 3806295 3806362 68 intergene 1 3833233 3833251 19 insidegene 4 3851902 3851932 31 intergene 1 3904686 3904704 19 intergene 1 3925177 3925195 19 overlap 2 4000652 4000686 35 insidegene 5 4001112 4001170 59 insidegene 1 4059000 4059018 19 insidegene 2 4067356 4067389 34 intergene 1 4077085 4077103 19 intergene 3 4098731 4098761 31 intergene 3 4212132 4212178 47 overlap 2 4221673 4221697 25 intergene 6 4233743 4233814 72 intergene 1 4249341 4249359 19 insidegene 4 4249637 4249671 35 insidegene 6 4249814 4249884 71 insidegene 6 4258162 4258197 36 intergene 2 4266706 4266730 25 intergene 2 4266745 4266769 25 intergene 4 4273318 4273356 39 intergene 5 4292219 4292296 78 intergene 2 4295131 4295155 25 overlap 1 4314143 4314161 19 insidegene 1 4331956 4331974 19 overlap 5 4338621 4338692 72 intergene 3 4347299 4347323 25 intergene 1 4349208 4349226 19 insidegene 6 4425498 4425532 35 intergene 4 4435624 4435660 37 intergene 1 4463121 4463139 19 insidegene 5 4474999 4475059 61 insidegene 1 4484127 4484145 19 intergene 2 4484234 4484258 25 overlap 1 4502173 4502191 19 insidegene 2 4514764 4514788 25 overlap 7 4516294 4516352 59 intergene 1 4520026 4520044 19 overlap 3 4533640 4533664 25 insidegene 5 4538702 4538765 64 intergene 14 4539636 4539777 142 intergene 3 4540798 4540832 35 intergene 3 4554773 4554814 42 intergene 2 4570216 4570240 25 intergene 2 4601059 4601083 25 intergene 4 4603699 4603733 35 intergene 4 4603764 4603811 48 intergene 2 4604030 4604054 25 intergene 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