!!AA_SCORING_MATRIX_RECT 1.0 This scoring matrix was generated by MEME version 2.1 (Release date: 1997/03/25 22:39:11). For further information or to get a copy of the MEME software please access http://www.sdsc.edu/MEME. MEME reference: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** TRAINING SET ******************************************************************************** DATAFILE= pfam_homeobox.seq (deleted by web version of MEME) ALPHABET= ACDEFGHIKLMNPQRSTVWY Sequence name Length Sequence name Length ------------- ------ ------------- ------ APTE_DROME 469 ATH5_ARATH 312 ATH6_ARATH 311 ATH7_ARATH 267 BOX4_NOTVI 273 BOX5_NOTVI 258 BRN1_HUMAN 125 BRN1_MOUSE 495 BRN3_MOUSE 421 BRN3_RAT 128 BRN4_HUMAN 361 BRN4_RAT 361 CAUP_DROME 693 CDP_CANFA 975 CDP_HUMAN 1505 CDP_MOUSE 1332 CDP_RAT 862 CDX1_HUMAN 265 CDX1_MOUSE 268 CDX1_RAT 123 CDX2_MOUSE 311 CDX3_MESAU 313 CDX4_MOUSE 282 CF1A_DROME 549 DBX_MOUSE 335 EGL5_CAEEL 218 EMX1_HUMAN 153 EMX1_MOUSE 66 EMX2_HUMAN 158 EMX2_MOUSE 66 EVX1_HUMAN 407 EVX1_MOUSE 416 EVX2_HUMAN 157 EVX2_MOUSE 475 EXD_DROME 376 GBX2_HUMAN 133 GBX2_MOUSE 348 GSBD_DROME 427 GSBP_DROME 449 GSCA_XENLA 243 GSCB_XENLA 243 GSC_BRARE 240 GSC_CHICK 245 GSC_DROME 419 GSC_MOUSE 256 GSH1_MOUSE 261 GSH2_MOUSE 305 GSH4_MOUSE 230 H114_BRARE 250 HAT1_ARATH 282 HAT2_ARATH 208 HAT3_ARATH 315 HAT4_ARATH 284 HAT5_ARATH 272 HAT7_ARATH 251 HAT9_ARATH 274 HB9_HUMAN 401 HBX3_ECHGR 60 HGL2_ARATH 660 HK11_MOUSE 305 HK22_MESAU 273 HK22_MOUSE 273 HK25_HUMAN 324 HK25_MOUSE 318 HK25_XENLA 299 HK26_MOUSE 92 HK51_MOUSE 458 HK52_MOUSE 156 HM01_CAEEL 132 HM05_CAEEL 60 HM06_CAEEL 159 HM07_CAEEL 60 HM10_CAEEL 344 HM12_CAEEL 27 HM13_CAEEL 86 HM14_CAEEL 348 HM16_CAEEL 240 HM16_XENLA 111 HM17_APIME 79 HM18_CAEEL 542 HM19_CAEEL 130 HM19_XENLA 105 HM1D_DROAN 606 HM1_CHICK 67 HM20_CAEEL 338 HM20_XENLA 105 HM22_CAEEL 346 HM23_CAEEL 305 HM3_CHICK 232 HM71_SHEEP 46 HM7X_CHICK 124 HM81_SHEEP 46 HM8_XENLA 271 HM90_APIME 74 HMA2_HELTR 60 HMAA_AEDAE 74 HMAA_APIME 74 HMAA_DROME 590 HMAA_SCHGR 157 HMAB_DROME 493 HMAN_DROME 378 HMB1_TRIGR 307 HMB3_TRIGR 108 HMB4_TRIGR 107 HMBC_DROME 494 HMBP_DROME 194 HMCA_DROME 472 HMCU_DROME 2175 HMD1_CHICK 248 HMD1_XENLA 250 HMD2_BRARE 270 HMD2_CHICK 60 HMD2_HUMAN 244 HMD2_MOUSE 332 HMD2_XENLA 277 HMD3_BRARE 269 HMD3_RAT 289 HMD3_XENLA 289 HMD4_BRARE 283 HMD4_XENLA 285 HMD5_CHICK 286 HMDF_DROME 590 HMDL_BRAFL 321 HMDL_DROME 327 HME1_BRARE 231 HME1_CHICK 333 HME1_HUMAN 391 HME1_MOUSE 401 HME2_BRARE 265 HME2_CHICK 288 HME2_HUMAN 332 HME2_MOUSE 324 HME3_APIME 109 HME3_BRARE 261 HME6_APIME 109 HMEA_MYXGL 60 HMEA_XENLA 60 HMEB_MYXGL 60 HMEB_XENLA 171 HMEC_XENLA 265 HMED_XENLA 265 HMEN_ARTSF 349 HMEN_BOMMO 372 HMEN_DROME 552 HMEN_DROVI 584 HMEN_HELTR 98 HMEN_LAMPL 60 HMEN_SCHAM 93 HMEN_TRIGR 154 HMES_APIME 74 HMES_DROME 497 HMEV_DROME 376 HMFT_DROHY 456 HMFT_DROME 413 HMH1_DUGTI 533 HMH2_DROME 410 HMH2_DUGTI 363 HMIN_BOMMO 476 HMIN_DROME 576 HMIX_XENLA 377 HML2_HELRO 429 HML2_HIRME 118 HMLA_DROME 635 HMMA_BRARE 61 HMMB_BRARE 61 HMMC_BRARE 273 HMMD_BRARE 226 HMN1_DROME 659 HMN2_DROME 158 HMOC_DROME 671 HMP1_BOVIN 291 HMP1_HUMAN 291 HMP1_MELGA 370 HMP1_MOUSE 291 HMP1_ONCMY 358 HMP1_PIG 129 HMP1_RAT 317 HMPB_DROME 798 HMPH_CHICK 277 HMPH_HUMAN 270 HMPH_MOUSE 271 HMPR_DROME 613 HMPR_HUMAN 331 HMRO_DROME 350 HMRO_DROVI 339 HMSA_SALSA 75 HMSH_DROME 515 HMTI_DROME 416 HMUX_DROME 389 HMX1_CHICK 249 HMX1_HUMAN 297 HMX1_MOUSE 293 HMX2_CHICK 259 HMX2_COTJA 259 HMX2_HUMAN 267 HMX2_MOUSE 267 HMXX_CHICK 288 HMZ1_DROME 353 HMZ2_DROME 252 HNK2_XENLA 196 HOX1_HALRO 741 HOX3_BRAFL 411 HPR1_CHICK 244 HT14_ARATH 165 HT22_ARATH 278 HT31_ARATH 660 HX11_HUMAN 330 HX11_MOUSE 332 HX1A_MAIZE 719 HX3_XENLA 388 HX5L_BRARE 81 HX71_XENLA 295 HX7P_XENLA 291 HXA1_HUMAN 330 HXA1_MOUSE 331 HXA2_CHICK 375 HXA2_MOUSE 372 HXA2_NOTVI 90 HXA2_RAT 372 HXA3_MOUSE 74 HXA4_CHICK 309 HXA4_HUMAN 320 HXA4_MOUSE 326 HXA4_RAT 67 HXA5_AMBME 148 HXA5_HUMAN 270 HXA5_MOUSE 270 HXA5_RAT 233 HXA5_SALSA 78 HXA6_HUMAN 66 HXA6_MOUSE 97 HXA7_COTJA 242 HXA7_HUMAN 66 HXA7_MOUSE 229 HXA7_RAT 105 HXA7_XENLA 209 HXA9_AMBME 143 HXA9_CAVPO 162 HXA9_HUMAN 129 HXA9_MOUSE 93 HXAA_HUMAN 496 HXAA_MOUSE 399 HXAB_CHICK 297 HXAB_HUMAN 66 HXAB_MOUSE 313 HXAD_AMBME 107 HXAD_HUMAN 66 HXB1_AMBME 184 HXB1_CHICK 309 HXB1_HUMAN 301 HXB1_MOUSE 297 HXB2_HUMAN 356 HXB2_SALSA 60 HXB3_CHICK 399 HXB3_HUMAN 431 HXB3_MOUSE 433 HXB3_XENLA 60 HXB4_CHICK 245 HXB4_HUMAN 251 HXB4_MOUSE 250 HXB4_XENLA 232 HXB5_BRARE 275 HXB5_CHICK 82 HXB5_HUMAN 269 HXB5_MOUSE 269 HXB5_SHEEP 46 HXB5_XENLA 230 HXB6_BRARE 228 HXB6_CHICK 84 HXB6_HUMAN 224 HXB6_MOUSE 224 HXB6_XENLA 48 HXB7_HUMAN 217 HXB7_MOUSE 217 HXB7_RAT 112 HXB7_XENLA 220 HXB8_CHICK 74 HXB8_HUMAN 70 HXB8_MOUSE 243 HXB8_PIG 93 HXB8_RAT 92 HXB9_HUMAN 78 HXB9_MOUSE 250 HXB9_XENLA 232 HXC4_HUMAN 264 HXC4_MOUSE 264 HXC4_RAT 76 HXC5_BRARE 232 HXC5_HUMAN 222 HXC5_MOUSE 222 HXC5_NOTVI 71 HXC5_XENLA 87 HXC6_BRARE 96 HXC6_HUMAN 153 HXC6_MOUSE 235 HXC6_NOTVI 234 HXC6_SHEEP 153 HXC6_XENLA 234 HXC8_HUMAN 66 HXC8_MOUSE 242 HXC8_RAT 104 HXC9_HUMAN 66 HXC9_MOUSE 260 HXCA_MOUSE 342 HXCB_MOUSE 60 HXCC_HUMAN 66 HXCC_MOUSE 60 HXCD_HUMAN 66 HXCD_MOUSE 38 HXD1_MOUSE 327 HXD3_HUMAN 416 HXD3_MOUSE 417 HXD3_RAT 114 HXD4_BRARE 86 HXD4_CHICK 235 HXD4_HUMAN 255 HXD4_MOUSE 250 HXD8_CHICK 188 HXD8_HUMAN 95 HXD8_MOUSE 289 HXD9_CHICK 60 HXD9_HUMAN 342 HXD9_MOUSE 339 HXDA_CHICK 95 HXDA_HUMAN 340 HXDA_MOUSE 340 HXDB_CHICK 280 HXDB_HUMAN 66 HXDB_MOUSE 323 HXDB_NOTVI 277 HXDC_CHICK 266 HXDC_HUMAN 66 HXDC_MOUSE 279 HXDD_CHICK 301 HXDD_HUMAN 66 IPF1_HUMAN 283 IPF1_MOUSE 284 IPF1_RAT 283 IPOU_DROME 367 IS2A_ONCTS 358 IS2B_ONCTS 340 ISL1_BRARE 349 ISL1_CHICK 349 ISL1_HUMAN 349 ISL2_BRARE 359 ISL2_CHICK 319 ISL2_RAT 360 ISL3_BRARE 358 ISL3_ONCTS 363 LBX1_HUMAN 280 LBX1_MOUSE 280 LH2_HUMAN 423 LH2_RAT 426 LI11_CAEEL 382 LI39_CAEEL 253 LIM1_CHICK 406 LIM1_HUMAN 404 LIM1_MOUSE 406 LIM1_XENLA 403 LIM2_RAT 402 LIM3_CHICK 395 LIM3_MOUSE 400 LIM3_XENLA 395 LIM5_BRARE 399 LIM5_XENLA 402 LIMB_XENLA 39 LMX1_CHICK 377 LMX1_MESAU 382 LX10_HELTR 184 MAB5_CAEEL 353 MAT2_YEAST 210 MAY1_SCHCO 891 MAY3_SCHCO 926 MAY4_SCHCO 928 MEC3_CAEBR 295 MEC3_CAEEL 321 MEC3_CAEVU 320 MOX1_HUMAN 254 MOX1_MOUSE 253 MOX2_HUMAN 303 MOX2_MOUSE 303 MOX2_RAT 303 MOX2_XENLA 298 MSX2_RAT 139 MTA0_YEAST 130 MTA1_YEAST 126 MTPI_SCHPO 159 OC11_MOUSE 403 OC3A_HUMAN 360 OC3B_HUMAN 265 OC3N_HUMAN 443 OC3N_MOUSE 445 OCT1_CHICK 739 OCT1_HUMAN 743 OCT1_MOUSE 770 OCT1_RAT 120 OCT1_XENLA 760 OCT2_HUMAN 478 OCT3_MOUSE 352 OCT6_HUMAN 448 OCT6_MOUSE 449 OCT6_RAT 451 OTX1_HUMAN 354 OTX1_MOUSE 355 OTX2_HUMAN 289 OTX2_MOUSE 289 PAL1_CAEEL 208 PAX3_HUMAN 479 PAX3_MOUSE 479 PAX6_BRARE 437 PAX6_CHICK 216 PAX6_COTJA 416 PAX6_HUMAN 422 PAX6_MOUSE 422 PAX7_HUMAN 467 PAX7_MOUSE 290 PBX1_HUMAN 430 PBX1_MOUSE 347 PBX2_HUMAN 430 PBX3_HUMAN 434 PDM1_DROME 601 PDM2_DROME 498 PHO2_YEAST 559 PMX1_HUMAN 199 PMX1_MOUSE 217 POU1_BRARE 425 POU1_DUGJA 559 POU1_XENLA 356 POU2_XENLA 218 POU3_XENLA 382 POUC_BRARE 610 PRH_PETCR 1088 SCR_APIME 86 SCR_DROME 415 SK1A_RAT 430 SK1I_RAT 348 TTF1_CANFA 371 TTF1_HUMAN 371 TTF1_MOUSE 372 TTF1_RAT 372 UN30_CAEEL 319 UN86_CAEEL 467 UNC4_CAEEL 252 YD73_SCHPO 942 YGJ6_YEAST 276 YOX1_YEAST 385 YR63_SCHPO 201 YRM6_CAEEL 416 YRN1_CAEEL 225 ZFH1_DROME 1060 ZFH2_DROME 3005 ******************************************************************************** MOTIF 1 width = 17 sites = 451.0 ******************************************************************************** Simplified A :1::::::::::3:::: motif letter- C ::::::::1:::::::: probability D 1:::::::::::::1:: matrix E 61::::::::::::2:: F :::::::9::::::::: G ::::::::::::::::: H ::::::::::::::::: I :::4:6::::::::1:: K 1:::6:::::1::9:85 L ::::::::::::::1:: M ::::::::::::4:1:: N :::::::::9::::::: P 1:::::::::::::::: Q ::7:1:::8:::1:::: R :51:1:::::89:1:24 S :1::::::::::1:::: T :2::::::::::::::: V ::26:3::::::::::: W ::::::9:::::::3:: Y ::::::::::::::1:: bits 6.7 6.0 * 5.4 * 4.7 * Information 4.0 ** content 3.4 * ** * * * (52.5 bits) 2.7 * ******* * * 2.0 ********** * ** 1.3 ***************** 0.7 ***************** 0.0 ----------------- Multilevel ERQVKIWFQNRRMKWKK consensus I V A R sequence log-odds matrix: alength= 20 w= 17 n= 133591 bayes= 8.2056 .. Width 17 Threshold 10.0 -2.833 -7.240 0.360 3.224 -4.038 -6.682 -5.271 -3.570 0.721 -4.168 0.610 -2.585 0.677 -0.258 -2.735 -2.842 -0.907 -1.521 -7.269 -6.541 0.088 -2.021 -2.113 0.442 -7.195 -6.679 -5.267 -4.438 -2.099 -2.336 -6.032 -1.153 -4.258 -2.010 3.171 0.229 1.626 -3.163 -2.580 -2.796 -4.460 -6.776 -6.396 -2.085 -4.117 -7.232 -0.923 -3.587 -2.006 -4.870 -5.397 -2.101 -6.829 4.078 0.193 -3.796 -1.301 1.266 -6.730 -6.930 -4.621 -6.447 -2.952 -3.769 -3.056 -8.291 -7.409 2.690 -2.386 -2.885 -5.370 -7.977 -8.437 -4.115 -7.943 -7.427 -5.432 3.192 -7.260 -6.933 -2.442 -9.052 -9.014 -0.564 -9.985 -8.883 -6.742 -2.078 3.473 -8.609 -7.893 -2.755 -9.138 1.383 1.258 -1.826 -1.416 -8.652 -8.791 -8.550 -6.120 -6.058 -8.561 -7.906 -1.550 -7.788 -6.874 3.383 -4.548 -3.561 -5.019 -0.476 -7.950 -7.229 -4.400 -4.719 -1.130 2.291 -2.574 -3.667 -2.699 -5.085 -5.879 -5.339 -3.123 -4.676 -2.520 -5.795 -5.758 -3.589 -4.601 -5.659 -6.361 -3.952 -4.164 -4.734 -4.749 -5.369 6.147 -2.764 -2.343 -2.840 -6.810 -6.811 4.555 -7.088 -3.363 -4.800 -6.882 -3.420 -2.250 -6.695 -6.514 -6.911 -6.889 -5.838 -5.541 -3.518 -4.263 -2.490 -4.674 2.302 -6.002 -3.126 -8.196 -2.387 -0.695 -3.645 -0.836 -7.141 -5.966 -1.655 -7.319 4.267 -5.953 -1.267 -4.469 -7.713 -7.281 -7.684 -4.567 -5.315 -3.528 -4.568 -5.840 -3.370 -2.274 -3.341 -3.217 -6.290 -5.383 4.352 -3.532 -4.789 -3.004 -4.019 -3.888 -5.833 -5.380 -5.595 -2.784 -5.337 -6.894 -4.688 -4.206 -6.660 0.574 -6.569 0.871 -6.552 -3.373 -3.304 -6.213 -1.664 3.941 -3.476 -6.294 -7.183 -5.498 -1.072 -4.546 -5.079 -6.668 -6.797 -2.945 -6.436 -4.184 -4.474 -1.891 -3.344 -5.951 -5.544 -4.258 -4.643 4.191 -3.938 -6.101 -6.998 -5.005 -6.376 1.850 0.421 -8.349 -4.647 -6.034 -7.751 -3.230 -1.557 -7.402 -4.514 4.006 -3.307 -7.905 1.236 -1.088 -0.060 -0.321 -1.901 -0.996 0.435 -3.858 -5.422 -3.935 -4.656 -7.122 -6.518 -5.424 -5.813 3.899 -5.928 -5.634 -4.048 -4.470 -4.042 0.825 -3.273 -4.399 -6.441 -5.903 -6.503 -0.565 0.119 -0.017 1.374 -0.029 -3.268 0.568 0.319 -1.439 -0.520 1.359 -2.740 -6.780 -0.355 -2.385 -1.962 -1.241 -3.673 4.363 0.626 -8.116 -8.903 -9.050 -7.596 -9.935 -8.852 -6.733 -3.640 3.766 -8.579 -3.329 -3.309 -3.727 -3.887 1.808 -4.928 -7.876 -8.623 -8.708 -8.538 -4.838 -8.761 -8.218 -7.118 -3.175 -3.352 -2.273 -4.585 3.184 -2.359 -7.594 -3.287 -8.728 -1.343 2.841 -3.383 -1.279 -4.742 -8.578 -3.824