******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.0.0 (Release date: 2008-07-12 05:23:09 +1000 (Sat, 12 Jul 2008)) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net. This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://meme.nbcr.net. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: 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= /home/t.bailey/MEME/SVNROOT/trunk/scripts/../tests/common/adh.s ALPHABET= ACDEFGHIKLMNPQRSTVWY Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 2BHD_STREX 1.0000 255 3BHD_COMTE 1.0000 253 ADH_DROME 1.0000 255 AP27_MOUSE 1.0000 244 BA72_EUBSP 1.0000 249 BDH_HUMAN 1.0000 343 BPHB_PSEPS 1.0000 275 BUDC_KLETE 1.0000 241 DHES_HUMAN 1.0000 327 DHGB_BACME 1.0000 262 DHII_HUMAN 1.0000 292 DHMA_FLAS1 1.0000 270 ENTA_ECOLI 1.0000 248 FIXR_BRAJA 1.0000 278 GUTD_ECOLI 1.0000 259 HDE_CANTR 1.0000 906 HDHA_ECOLI 1.0000 255 LIGD_PSEPA 1.0000 305 NODG_RHIME 1.0000 245 RIDH_KLEAE 1.0000 249 YINL_LISMO 1.0000 248 YRTP_BACSU 1.0000 238 CSGA_MYXXA 1.0000 166 DHB2_HUMAN 1.0000 387 DHB3_HUMAN 1.0000 310 DHCA_HUMAN 1.0000 276 FABI_ECOLI 1.0000 262 FVT1_HUMAN 1.0000 332 HMTR_LEIMA 1.0000 287 MAS1_AGRRA 1.0000 476 PCR_PEA 1.0000 399 RFBB_NEIGO 1.0000 346 YURA_MYXXA 1.0000 258 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme /home/t.bailey/MEME/SVNROOT/trunk/scripts/../tests/common/adh.s -text -mod tcm -protein -nostatus -nmotifs 2 -minw 8 model: mod= tcm nmotifs= 2 evt= inf object function= E-value of product of p-values width: minw= 8 maxw= 50 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 50 wnsites= 0.8 theta: prob= 1 spmap= pam spfuzz= 120 global: substring= yes branching= no wbranch= no em: prior= megap b= 49980 maxiter= 50 distance= 1e-05 data: n= 9996 N= 33 sample: seed= 0 seqfrac= 1 Dirichlet mixture priors file: prior30.plib Letter frequencies in dataset: A 0.111 C 0.012 D 0.050 E 0.055 F 0.036 G 0.090 H 0.018 I 0.057 K 0.052 L 0.092 M 0.027 N 0.041 P 0.041 Q 0.029 R 0.049 S 0.064 T 0.057 V 0.083 W 0.010 Y 0.027 Background letter frequencies (from dataset with add-one prior applied): A 0.111 C 0.012 D 0.050 E 0.055 F 0.036 G 0.090 H 0.018 I 0.057 K 0.052 L 0.092 M 0.027 N 0.041 P 0.041 Q 0.029 R 0.049 S 0.064 T 0.057 V 0.083 W 0.010 Y 0.027 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 21 sites = 30 llr = 866 E-value = 5.2e-122 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::531:::1517:2:422: pos.-specific C ::::1::::::::1::::::: probability D :::::1:::::::::1:::1: matrix E :::::::::::2::11::22: F ::::::::::1:::::3:::: G :::a4319:a:::::1::1:8 H ::::::::::1::::1:1::: I 25::::::6:::2:1::1::: K ::::::2:::3:::3:::21: L 5:::::::3:2:2:2161:1: M ::::::::::::1:::::::: N :::::1:::::::::::::1: P ::::::::::::::::::::: Q ::::::1:::::::::::11: R ::::::2:::2:::21::1:: S ::::133::::1:1::::11: T ::9:::::::::2::1::1:: V 25::::::1:::12:1:1::: W ::::::::::::::::::::: Y ::::::::::::1:::::::: bits 6.7 6.0 5.4 4.7 Relative 4.0 * Entropy 3.4 ** * (41.7 bits) 2.7 *** * * * * 2.0 ***** *** * * * 1.3 *************** *** * 0.7 ********************* 0.0 --------------------- Multilevel LVTGAGSGIGKAIAKxLAAEG consensus II GA L RETV F KA sequence S -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- YRTP_BACSU 10 3.13e-18 MQSLQHKTA LITGGGRGIGRATALALAKEG VNIGLIGRTS YINL_LISMO 9 2.12e-17 MTIKNKVI IITGASSGIGKATALLLAEKG AKLVLAARRV BUDC_KLETE 6 2.50e-17 MQKVA LVTGAGQGIGKAIALRLVKDG FAVAIADYND DHII_HUMAN 38 1.32e-16 RPEMLQGKKV IVTGASKGIGREMAYHLAKMG AHVVVTARSK HDE_CANTR 326 4.49e-16 PTVSLKDKVV LITGAGAGLGKEYAKWFAKYG AKVVVNDFKD PCR_PEA 90 6.60e-16 GKKTLRKGNV VITGASSGLGLATAKALAESG KWHVIMACRD FVT1_HUMAN 36 1.09e-15 KPLALPGAHV VVTGGSSGIGKCIAIECYKQG AFITLVARNE ENTA_ECOLI 9 1.98e-15 MDFSGKNV WVTGAGKGIGYATALAFVEAG AKVTGFDQAF AP27_MOUSE 11 2.80e-15 MKLNFSGLRA LVTGAGKGIGRDTVKALHASG AKVVAVTRTN HDHA_ECOLI 15 5.50e-15 DNLRLDGKCA IITGAGAGIGKEIAITFATAG ASVVVSDINA BDH_HUMAN 59 6.84e-15 AAEPVGSKAV LVTGCDSGFGFSLAKHLHSKG FLVFAGCLMK FIXR_BRAJA 40 7.62e-15 RVDRGEPKVM LLTGASRGIGHATAKLFSEAG WRIISCARQP DHB3_HUMAN 52 2.91e-14 SFLRSMGQWA VITGAGDGIGKAYSFELAKRG LNVVLISRTL DHB2_HUMAN 86 5.76e-14 ELLPVDQKAV LVTGGDCGLGHALCKYLDELG FTVFAGVLNE DHMA_FLAS1 18 6.96e-14 RPGRLAGKAA IVTGAAGGIGRATVEAYLREG ASVVAMDLAP BA72_EUBSP 10 9.22e-14 MNLVQDKVT IITGGTRGIGFAAAKIFIDNG AKVSIFGETQ HDE_CANTR 12 1.01e-13 SPVDFKDKVV IITGAGGGLGKYYSLEFAKLG AKVVVNDLGG HMTR_LEIMA 10 1.11e-13 MTAPTVPVA LVTGAAKRLGRSIAEGLHAEG YAVCLHYHRS NODG_RHIME 10 1.33e-13 MFELTGRKA LVTGASGAIGGAIARVLHAQG AIVGLHGTQI DHCA_HUMAN 8 3.24e-13 SSGIHVA LVTGGNKGIGLAIVRDLCRLF SGDVVLTARD RIDH_KLEAE 18 3.86e-13 MNTSLSGKVA AITGAASGIGLECARTLLGAG AKVVLIDREG BPHB_PSEPS 9 4.99e-13 MKLKGEAV LITGGASGLGRALVDRFVAEA KVAVLDKSAE DHES_HUMAN 6 5.43e-13 ARTVV LITGCSSGIGLHLAVRLASDP SQSFKVYATL MAS1_AGRRA 249 8.26e-13 TVEIHQSPVI LVSGSNRGVGKAIAEDLIAHG YRLSLGARKV 3BHD_COMTE 10 9.74e-13 TNRLQGKVA LVTGGASGVGLEVVKLLLGEG AKVAFSDINE DHGB_BACME 11 2.56e-12 MYKDLEGKVV VITGSSTGLGKSMAIRFATEK AKVVVNYRSK 2BHD_STREX 10 8.69e-12 MNDLSGKTV IITGGARGLGAEAARQAVAAG ARVVLADVLD LIGD_PSEPA 10 3.19e-11 MKDFQDQVA FITGGASGAGFGQAKVFGQAG AKIVVADVRA RFBB_NEIGO 10 9.53e-11 MQTEGKKNI LVTGGAGFIGSAVVRHIIQNT RDSVVNLDKL GUTD_ECOLI 6 4.49e-10 MNQVA VVIGGGQTLGAFLCHGLAAEG YRVAVVDIQS -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- YRTP_BACSU 3.1e-18 9_[1]_208 YINL_LISMO 2.1e-17 8_[1]_219 BUDC_KLETE 2.5e-17 5_[1]_215 DHII_HUMAN 1.3e-16 37_[1]_234 HDE_CANTR 1e-13 11_[1]_293_[1]_560 PCR_PEA 6.6e-16 89_[1]_289 FVT1_HUMAN 1.1e-15 35_[1]_276 ENTA_ECOLI 2e-15 8_[1]_219 AP27_MOUSE 2.8e-15 10_[1]_213 HDHA_ECOLI 5.5e-15 14_[1]_220 BDH_HUMAN 6.8e-15 58_[1]_264 FIXR_BRAJA 7.6e-15 39_[1]_218 DHB3_HUMAN 2.9e-14 51_[1]_238 DHB2_HUMAN 5.8e-14 85_[1]_281 DHMA_FLAS1 7e-14 17_[1]_232 BA72_EUBSP 9.2e-14 9_[1]_219 HMTR_LEIMA 1.1e-13 9_[1]_257 NODG_RHIME 1.3e-13 9_[1]_215 DHCA_HUMAN 3.2e-13 7_[1]_248 RIDH_KLEAE 3.9e-13 17_[1]_211 BPHB_PSEPS 5e-13 8_[1]_246 DHES_HUMAN 5.4e-13 5_[1]_301 MAS1_AGRRA 8.3e-13 248_[1]_207 3BHD_COMTE 9.7e-13 9_[1]_223 DHGB_BACME 2.6e-12 10_[1]_231 2BHD_STREX 8.7e-12 9_[1]_225 LIGD_PSEPA 3.2e-11 9_[1]_275 RFBB_NEIGO 9.5e-11 9_[1]_316 GUTD_ECOLI 4.5e-10 5_[1]_233 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=30 YRTP_BACSU ( 10) LITGGGRGIGRATALALAKEG 1 YINL_LISMO ( 9) IITGASSGIGKATALLLAEKG 1 BUDC_KLETE ( 6) LVTGAGQGIGKAIALRLVKDG 1 DHII_HUMAN ( 38) IVTGASKGIGREMAYHLAKMG 1 HDE_CANTR ( 326) LITGAGAGLGKEYAKWFAKYG 1 PCR_PEA ( 90) VITGASSGLGLATAKALAESG 1 FVT1_HUMAN ( 36) VVTGGSSGIGKCIAIECYKQG 1 ENTA_ECOLI ( 9) WVTGAGKGIGYATALAFVEAG 1 AP27_MOUSE ( 11) LVTGAGKGIGRDTVKALHASG 1 HDHA_ECOLI ( 15) IITGAGAGIGKEIAITFATAG 1 BDH_HUMAN ( 59) LVTGCDSGFGFSLAKHLHSKG 1 FIXR_BRAJA ( 40) LLTGASRGIGHATAKLFSEAG 1 DHB3_HUMAN ( 52) VITGAGDGIGKAYSFELAKRG 1 DHB2_HUMAN ( 86) LVTGGDCGLGHALCKYLDELG 1 DHMA_FLAS1 ( 18) IVTGAAGGIGRATVEAYLREG 1 BA72_EUBSP ( 10) IITGGTRGIGFAAAKIFIDNG 1 HDE_CANTR ( 12) IITGAGGGLGKYYSLEFAKLG 1 HMTR_LEIMA ( 10) LVTGAAKRLGRSIAEGLHAEG 1 NODG_RHIME ( 10) LVTGASGAIGGAIARVLHAQG 1 DHCA_HUMAN ( 8) LVTGGNKGIGLAIVRDLCRLF 1 RIDH_KLEAE ( 18) AITGAASGIGLECARTLLGAG 1 BPHB_PSEPS ( 9) LITGGASGLGRALVDRFVAEA 1 DHES_HUMAN ( 6) LITGCSSGIGLHLAVRLASDP 1 MAS1_AGRRA ( 249) LVSGSNRGVGKAIAEDLIAHG 1 3BHD_COMTE ( 10) LVTGGASGVGLEVVKLLLGEG 1 DHGB_BACME ( 11) VITGSSTGLGKSMAIRFATEK 1 2BHD_STREX ( 10) IITGGARGLGAEAARQAVAAG 1 LIGD_PSEPA ( 10) FITGGASGAGFGQAKVFGQAG 1 RFBB_NEIGO ( 10) LVTGGAGFIGSAVVRHIIQNT 1 GUTD_ECOLI ( 6) VVIGGGQTLGAFLCHGLAAEG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 21 n= 9336 bayes= 7.6579 E= 5.2e-122 -165 -274 -583 -504 -3 -558 -390 194 -473 241 -175 -469 -484 -391 -461 -415 -338 94 163 -335 -531 -359 -752 -718 -463 -782 -747 301 -713 -122 -372 -685 -697 -696 -764 -672 -462 257 -666 -595 -377 -244 -428 -457 -428 -520 -360 -99 -371 -456 -315 -253 -430 -313 -385 -18 392 -342 -401 -449 -580 -545 -561 -628 -691 346 -560 -746 -609 -754 -700 -528 -620 -606 -602 -546 -643 -734 -581 -645 215 242 -647 -642 -608 198 -566 -625 -659 -637 -561 -521 -482 -521 -605 18 -365 -499 -584 -628 119 -401 53 -344 -588 166 -290 -659 -378 -651 -610 89 -462 -333 -458 201 -68 -611 -574 -480 -65 119 -37 -130 -349 34 -142 -353 159 -340 -273 -162 -289 123 157 200 -49 -346 -324 -272 -197 -330 -310 -372 -105 327 -335 -499 -354 -543 -446 -266 -420 -369 -129 -289 -154 -485 -372 -424 -187 -332 -582 -556 -24 -637 -502 332 -521 151 -208 -515 -560 -477 -546 -495 -393 8 -420 -410 -580 -545 -561 -628 -691 346 -560 -746 -609 -754 -700 -528 -620 -606 -602 -546 -643 -734 -581 -645 -67 -306 -226 -154 122 -141 171 -330 236 64 -270 -184 -308 -100 184 -57 -217 -333 -326 18 239 98 -112 104 -76 -150 16 -311 -250 -321 -259 -273 -384 -220 -286 36 -223 -215 -309 -43 -67 137 -484 -406 -217 -448 -290 194 -373 84 126 -362 -395 10 -368 -302 188 -3 -257 172 260 215 -486 -446 -421 -324 -419 -408 -449 -425 -362 -423 -459 -398 -445 10 -295 95 -408 -457 -264 -285 -41 85 -25 -358 84 61 233 64 -251 -176 -297 -97 157 -188 -204 -119 -312 18 43 -301 37 87 -338 -57 223 -83 -112 -6 -264 -163 -287 54 128 -177 24 -45 151 17 -175 129 -615 -536 287 -603 -405 -44 -507 261 -173 -508 -510 -410 -486 -463 -386 -287 -329 22 162 134 -79 -390 -224 -149 260 83 -361 17 -164 -355 -395 -301 -361 -79 -234 68 -261 23 87 -309 -36 148 -347 -57 -140 -351 200 -338 -271 -161 -286 123 45 16 24 -343 -322 -270 66 -307 38 190 -344 -346 86 -349 57 -7 16 70 -284 123 -26 16 -198 -342 -320 17 -197 -330 -310 -371 -105 325 -335 -499 -134 -543 -445 -266 -115 -369 -358 -289 -154 -485 -371 -424 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 21 nsites= 30 E= 5.2e-122 0.033333 0.000000 0.000000 0.000000 0.033333 0.000000 0.000000 0.233333 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.166667 0.033333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.466667 0.000000 0.033333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.033333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.033333 0.933333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.066667 0.000000 0.000000 0.000000 0.366667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.066667 0.000000 0.000000 0.000000 0.000000 0.266667 0.000000 0.066667 0.000000 0.000000 0.300000 0.000000 0.000000 0.000000 0.000000 0.000000 0.066667 0.000000 0.000000 0.000000 0.266667 0.033333 0.000000 0.000000 0.000000 0.066667 0.033333 0.033333 0.000000 0.000000 0.133333 0.000000 0.000000 0.166667 0.000000 0.000000 0.000000 0.000000 0.066667 0.166667 0.300000 0.033333 0.000000 0.000000 0.000000 0.033333 0.000000 0.000000 0.000000 0.033333 0.866667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.033333 0.000000 0.033333 0.000000 0.000000 0.000000 0.033333 0.000000 0.000000 0.000000 0.033333 0.000000 0.000000 0.566667 0.000000 0.300000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.066667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.066667 0.000000 0.000000 0.000000 0.100000 0.033333 0.066667 0.000000 0.300000 0.166667 0.000000 0.000000 0.000000 0.000000 0.200000 0.033333 0.000000 0.000000 0.000000 0.033333 0.500000 0.033333 0.033333 0.200000 0.033333 0.033333 0.033333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.033333 0.066667 0.033333 0.000000 0.000000 0.000000 0.000000 0.000000 0.233333 0.000000 0.166667 0.066667 0.000000 0.000000 0.033333 0.000000 0.000000 0.233333 0.066667 0.000000 0.100000 0.666667 0.066667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.066667 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.033333 0.100000 0.033333 0.000000 0.033333 0.100000 0.300000 0.166667 0.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.000000 0.033333 0.000000 0.033333 0.166667 0.000000 0.066667 0.100000 0.000000 0.066667 0.100000 0.033333 0.000000 0.100000 0.000000 0.000000 0.000000 0.033333 0.133333 0.000000 0.066667 0.066667 0.033333 0.033333 0.033333 0.033333 0.000000 0.000000 0.300000 0.000000 0.000000 0.033333 0.000000 0.566667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.033333 0.366667 0.033333 0.033333 0.000000 0.000000 0.033333 0.133333 0.100000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.033333 0.000000 0.133333 0.000000 0.033333 0.233333 0.000000 0.033333 0.166667 0.000000 0.066667 0.000000 0.000000 0.233333 0.000000 0.000000 0.000000 0.000000 0.066667 0.066667 0.066667 0.066667 0.000000 0.000000 0.000000 0.200000 0.000000 0.066667 0.233333 0.000000 0.000000 0.033333 0.000000 0.066667 0.100000 0.033333 0.066667 0.000000 0.066667 0.033333 0.066667 0.000000 0.000000 0.000000 0.033333 0.033333 0.000000 0.000000 0.000000 0.033333 0.833333 0.000000 0.000000 0.033333 0.000000 0.000000 0.000000 0.033333 0.000000 0.000000 0.000000 0.033333 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [LI][VI]TG[AG][GAS]SG[IL]G[KR][AE][IT][AV]Kx[LF]A[AK][EA]G -------------------------------------------------------------------------------- Time 49.60 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 22 sites = 31 llr = 890 E-value = 2.3e-120 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :162:56112:1:215:::4:: pos.-specific C :1:::::::::::::::::::: probability D ::::::::1::::::::2:::: matrix E ::::::::1:::31:::5::11 F :::::31:::3:::::1::::: G :2:::12::4:::1:1::111: H :::::::::1::1::::::::1 I :::::::11:::::::::1::: K ::::a:::1:::2:::1::121 L :::::::31:6:::5:215::1 M ::1::::1:1:1::2:1:1::: N :::::::::1:::::::::::: P ::::::::::::::::::::4: Q ::::::::::::1::11:::1: R ::::::::1:::3::21::21: S :426::1:11:213:::::1:1 T :1:1::::1::4:2::::::11 V :::::::41::2:1::1:1::: W :::::1:::::::::::::::: Y a:::::::::::::::::2::2 bits 6.7 6.0 5.4 4.7 * Relative 4.0 * * Entropy 3.4 * * (41.4 bits) 2.7 * ** * 2.0 * ***** *** ** * 1.3 ******** ******* ***** 0.7 ********************** 0.0 ---------------------- Multilevel YSASKAAVxGLTRSLAxELAPx consensus A FGL F E MR D sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------------- YRTP_BACSU 155 7.44e-19 GQRGAAVTSA YSASKFAVLGLTESLMQEVRKH NIRVSALTPS FVT1_HUMAN 186 2.23e-17 GQLGLFGFTA YSASKFAIRGLAEALQMEVKPY NVYITVAYPP BUDC_KLETE 152 6.17e-17 GHVGNPELAV YSSSKFAVRGLTQTAARDLAPL GITVNGFCPG AP27_MOUSE 149 1.24e-16 AHVTFPNLIT YSSTKGAMTMLTKAMAMELGPH KIRVNSVNPT NODG_RHIME 152 4.70e-16 GAIGNPGQTN YCASKAGMIGFSKSLAQEIATR NITVNCVAPG DHES_HUMAN 155 1.29e-15 GLMGLPFNDV YCASKFALEGLCESLAVLLLPF GVHLSLIECG GUTD_ECOLI 154 2.37e-15 GKVGSKHNSG YSAAKFGGVGLTQSLALDLAEY GITVHSLMLG BPHB_PSEPS 153 2.37e-15 GFYPNGGGPL YTAAKQAIVGLVRELAFELAPY VRVNGVGPGG FIXR_BRAJA 189 7.61e-15 SRVHPFAGSA YATSKAALASLTRELAHDYAPH GIRVNAIAPG HMTR_LEIMA 193 9.54e-15 TNQPLLGYTI YTMAKGALEGLTRSAALELAPL QIRVNGVGPG DHB2_HUMAN 232 1.19e-14 GGAPMERLAS YGSSKAAVTMFSSVMRLELSKW GIKVASIQPG DHGB_BACME 160 1.49e-14 WKIPWPLFVH YAASKGGMKLMTETLALEYAPK GIRVNNIGPG 3BHD_COMTE 151 1.49e-14 SWLPIEQYAG YSASKAAVSALTRAAALSCRKQ GYAIRVNSIH YURA_MYXXA 160 1.85e-14 AGFRGLPATR YSASKAFLSTFMESLRVDLRGT GVRVTCIYPG DHB3_HUMAN 198 3.53e-14 ALFPWPLYSM YSASKAFVCAFSKALQEEYKAK EVIIQVLTPY YINL_LISMO 154 5.37e-14 GLKAYPGGAV YGATKWAVRDLMEVLRMESAQE GTNIRTATIY RIDH_KLEAE 160 5.95e-14 GVVPVIWEPV YTASKFAVQAFVHTTRRQVAQY GVRVGAVLPG HDE_CANTR 467 5.95e-14 GIYGNFGQAN YSSSKAGILGLSKTMAIEGAKN NIKVNIVAPH DHMA_FLAS1 165 8.10e-14 SFMAEPEAAA YVAAKGGVAMLTRAMAVDLARH GILVNMIAPG DHII_HUMAN 183 8.96e-14 GKVAYPMVAA YSASKFALDGFFSSIRKEYSVS RVNVSITLCV 2BHD_STREX 152 2.93e-13 GLMGLALTSS YGASKWGVRGLSKLAAVELGTD RIRVNSVHPG HDHA_ECOLI 159 3.90e-13 AENKNINMTS YASSKAAASHLVRNMAFDLGEK NIRVNGIAPG HDE_CANTR 163 6.24e-13 GLYGNFGQAN YASAKSALLGFAETLAKEGAKY NIKANAIAPL RFBB_NEIGO 165 9.88e-13 ETTPYAPSSP YSASKAAADHLVRAWQRTYRLP SIVSNCSNNY BDH_HUMAN 208 9.88e-13 GRMANPARSP YCITKFGVEAFSDCLRYEMYPL GVKVSVVEPG BA72_EUBSP 157 1.69e-12 GIFGSLSGVG YPASKASVIGLTHGLGREIIRK NIRVVGVAPG LIGD_PSEPA 157 2.63e-12 GFMGSALAGP YSAAKAASINLMEGYRQGLEKY GIGVSVCTPA CSGA_MYXXA 88 2.87e-12 AANTDGGAYA YRMSKAALNMAVRSMSTDLRPE GFVTVLLHPG ENTA_ECOLI 144 1.52e-11 AHTPRIGMSA YGASKAALKSLALSVGLELAGS GVRCNVVSPG ADH_DROME 152 9.02e-11 GFNAIYQVPV YSGTKAAVVNFTSSLAKLAPIT GVTAYTVNPG FABI_ECOLI 159 8.74e-09 AERAIPNYNV MGLAKASLEANVRYMANAMGPE GVRVNAISAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- YRTP_BACSU 7.4e-19 154_[2]_62 FVT1_HUMAN 2.2e-17 185_[2]_125 BUDC_KLETE 6.2e-17 151_[2]_68 AP27_MOUSE 1.2e-16 148_[2]_74 NODG_RHIME 4.7e-16 151_[2]_72 DHES_HUMAN 1.3e-15 154_[2]_151 GUTD_ECOLI 2.4e-15 153_[2]_84 BPHB_PSEPS 2.4e-15 152_[2]_101 FIXR_BRAJA 7.6e-15 188_[2]_68 HMTR_LEIMA 9.5e-15 192_[2]_73 DHB2_HUMAN 1.2e-14 231_[2]_134 DHGB_BACME 1.5e-14 159_[2]_81 3BHD_COMTE 1.5e-14 150_[2]_81 YURA_MYXXA 1.9e-14 159_[2]_77 DHB3_HUMAN 3.5e-14 197_[2]_91 YINL_LISMO 5.4e-14 153_[2]_73 RIDH_KLEAE 6e-14 159_[2]_68 HDE_CANTR 6.2e-13 162_[2]_282_[2]_418 DHMA_FLAS1 8.1e-14 164_[2]_84 DHII_HUMAN 9e-14 182_[2]_88 2BHD_STREX 2.9e-13 151_[2]_82 HDHA_ECOLI 3.9e-13 158_[2]_75 RFBB_NEIGO 9.9e-13 164_[2]_160 BDH_HUMAN 9.9e-13 207_[2]_114 BA72_EUBSP 1.7e-12 156_[2]_71 LIGD_PSEPA 2.6e-12 156_[2]_127 CSGA_MYXXA 2.9e-12 87_[2]_57 ENTA_ECOLI 1.5e-11 143_[2]_83 ADH_DROME 9e-11 151_[2]_82 FABI_ECOLI 8.7e-09 158_[2]_82 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=22 seqs=31 YRTP_BACSU ( 155) YSASKFAVLGLTESLMQEVRKH 1 FVT1_HUMAN ( 186) YSASKFAIRGLAEALQMEVKPY 1 BUDC_KLETE ( 152) YSSSKFAVRGLTQTAARDLAPL 1 AP27_MOUSE ( 149) YSSTKGAMTMLTKAMAMELGPH 1 NODG_RHIME ( 152) YCASKAGMIGFSKSLAQEIATR 1 DHES_HUMAN ( 155) YCASKFALEGLCESLAVLLLPF 1 GUTD_ECOLI ( 154) YSAAKFGGVGLTQSLALDLAEY 1 BPHB_PSEPS ( 153) YTAAKQAIVGLVRELAFELAPY 1 FIXR_BRAJA ( 189) YATSKAALASLTRELAHDYAPH 1 HMTR_LEIMA ( 193) YTMAKGALEGLTRSAALELAPL 1 DHB2_HUMAN ( 232) YGSSKAAVTMFSSVMRLELSKW 1 DHGB_BACME ( 160) YAASKGGMKLMTETLALEYAPK 1 3BHD_COMTE ( 151) YSASKAAVSALTRAAALSCRKQ 1 YURA_MYXXA ( 160) YSASKAFLSTFMESLRVDLRGT 1 DHB3_HUMAN ( 198) YSASKAFVCAFSKALQEEYKAK 1 YINL_LISMO ( 154) YGATKWAVRDLMEVLRMESAQE 1 RIDH_KLEAE ( 160) YTASKFAVQAFVHTTRRQVAQY 1 HDE_CANTR ( 467) YSSSKAGILGLSKTMAIEGAKN 1 DHMA_FLAS1 ( 165) YVAAKGGVAMLTRAMAVDLARH 1 DHII_HUMAN ( 183) YSASKFALDGFFSSIRKEYSVS 1 2BHD_STREX ( 152) YGASKWGVRGLSKLAAVELGTD 1 HDHA_ECOLI ( 159) YASSKAAASHLVRNMAFDLGEK 1 HDE_CANTR ( 163) YASAKSALLGFAETLAKEGAKY 1 RFBB_NEIGO ( 165) YSASKAAADHLVRAWQRTYRLP 1 BDH_HUMAN ( 208) YCITKFGVEAFSDCLRYEMYPL 1 BA72_EUBSP ( 157) YPASKASVIGLTHGLGREIIRK 1 LIGD_PSEPA ( 157) YSAAKAASINLMEGYRQGLEKY 1 CSGA_MYXXA ( 88) YRMSKAALNMAVRSMSTDLRPE 1 ENTA_ECOLI ( 144) YGASKAALKSLALSVGLELAGS 1 ADH_DROME ( 152) YSGTKAAVVNFTSSLAKLAPIT 1 FABI_ECOLI ( 159) MGLAKASLEANVRYMANAMGPE 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 22 n= 9303 bayes= 9.52617 E= 2.3e-120 -735 -508 -715 -725 -189 -735 -324 -566 -670 -508 22 -574 -668 -545 -619 -626 -645 -620 -234 512 23 286 -532 -520 -521 73 -463 -524 -491 -545 -476 -404 -41 -430 -70 274 81 -138 -507 -517 261 -61 -387 -340 -317 -156 -323 -139 -341 -189 31 -345 -432 -310 -346 91 -112 -193 -306 -355 100 -268 -596 -609 -576 -417 -529 -598 -590 -612 -535 -455 -469 -496 -558 330 118 -501 -553 -581 -572 -446 -600 -565 -643 -626 -470 -557 423 -622 -560 -486 -552 -478 -203 -565 -529 -649 -497 -576 211 -263 -571 -562 275 48 -482 -515 -559 -538 -480 -472 -480 8 -545 -70 -357 -443 265 -441 252 -242 -594 -576 73 124 -522 -551 -585 -565 -496 -494 -481 -488 -557 12 -351 -433 -528 -572 -71 -187 -492 -414 -225 -153 -298 86 -381 155 174 -370 -403 -316 -377 -87 -243 209 -266 -255 -68 114 34 117 -347 -351 -143 53 53 -11 -271 -7 -288 51 124 58 20 2 -324 -271 39 -317 -41 -167 -363 201 166 -354 -153 -144 199 68 -320 -123 -214 9 -59 -355 -346 -297 -190 -360 -647 -564 277 -659 -454 -216 -539 276 38 -56 -531 -425 -507 -523 -441 -319 -363 -375 -30 125 -474 -435 -20 -468 -326 -205 -387 -264 163 -327 -416 -323 -388 144 267 106 -310 -309 -292 -340 -44 207 -383 -380 168 -381 159 -145 -301 -192 -318 119 236 56 -232 -374 -350 -301 58 115 -262 20 -297 -69 -192 -257 -176 -130 -234 -24 -321 -145 -228 227 136 -43 -304 9 6 -200 -497 -418 -219 -470 -306 -31 -386 233 281 -381 -405 -315 -378 -324 -67 -79 151 16 227 -245 -435 -371 -483 -54 -343 -468 -259 -471 12 -364 -445 158 203 -69 -323 -393 -450 -456 -274 -257 -247 -38 66 -376 78 -65 88 89 162 -17 -316 162 123 -208 -53 50 -301 17 -164 -570 209 326 -592 -152 -333 -531 -269 -63 -459 -327 -412 34 -381 -92 -80 -499 -563 -496 -147 132 -489 -410 -220 -63 -295 39 -377 216 121 -367 -399 -311 -372 -88 -241 34 -262 237 171 -280 -208 -26 -344 27 -150 -90 49 -143 -270 -171 -42 -92 150 11 -204 -329 -322 10 -136 -311 -205 39 -350 -62 -147 -90 176 -143 -275 -168 285 118 40 -182 19 -133 -327 -276 -261 -300 -42 81 -19 -352 256 -346 125 -12 -269 -10 -41 48 -32 11 18 -341 146 261 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 22 nsites= 31 E= 2.3e-120 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.032258 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.967742 0.129032 0.096774 0.000000 0.000000 0.000000 0.161290 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.032258 0.000000 0.032258 0.419355 0.096774 0.032258 0.000000 0.000000 0.612903 0.000000 0.000000 0.000000 0.000000 0.032258 0.000000 0.032258 0.000000 0.032258 0.064516 0.000000 0.000000 0.000000 0.000000 0.193548 0.032258 0.000000 0.000000 0.000000 0.225806 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.645161 0.129032 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.483871 0.000000 0.000000 0.000000 0.258065 0.129032 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.032258 0.000000 0.032258 0.000000 0.000000 0.064516 0.000000 0.645161 0.000000 0.000000 0.000000 0.064516 0.225806 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.064516 0.000000 0.000000 0.000000 0.000000 0.064516 0.000000 0.000000 0.000000 0.000000 0.032258 0.000000 0.096774 0.000000 0.290323 0.096774 0.000000 0.000000 0.000000 0.000000 0.032258 0.000000 0.387097 0.000000 0.000000 0.064516 0.032258 0.064516 0.129032 0.000000 0.000000 0.000000 0.096774 0.064516 0.096774 0.000000 0.032258 0.000000 0.032258 0.129032 0.096774 0.064516 0.096774 0.000000 0.000000 0.161290 0.000000 0.032258 0.000000 0.000000 0.419355 0.064516 0.000000 0.000000 0.032258 0.129032 0.064516 0.000000 0.000000 0.000000 0.064516 0.032258 0.000000 0.000000 0.000000 0.032258 0.000000 0.000000 0.000000 0.290323 0.000000 0.000000 0.000000 0.000000 0.612903 0.032258 0.032258 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.096774 0.032258 0.000000 0.000000 0.032258 0.000000 0.000000 0.000000 0.000000 0.000000 0.096774 0.000000 0.000000 0.000000 0.000000 0.193548 0.354839 0.193548 0.000000 0.000000 0.000000 0.000000 0.032258 0.258065 0.000000 0.000000 0.064516 0.000000 0.161290 0.032258 0.000000 0.000000 0.000000 0.064516 0.290323 0.096774 0.000000 0.000000 0.000000 0.000000 0.193548 0.032258 0.000000 0.064516 0.000000 0.064516 0.000000 0.000000 0.000000 0.032258 0.000000 0.032258 0.000000 0.000000 0.000000 0.322581 0.161290 0.064516 0.000000 0.032258 0.129032 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.032258 0.000000 0.483871 0.225806 0.000000 0.000000 0.000000 0.000000 0.000000 0.032258 0.032258 0.032258 0.032258 0.548387 0.000000 0.000000 0.000000 0.000000 0.064516 0.000000 0.000000 0.000000 0.000000 0.032258 0.000000 0.000000 0.096774 0.225806 0.032258 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.032258 0.064516 0.000000 0.032258 0.032258 0.096774 0.193548 0.096774 0.032258 0.000000 0.096774 0.129032 0.000000 0.032258 0.129032 0.000000 0.032258 0.032258 0.000000 0.225806 0.548387 0.000000 0.032258 0.000000 0.000000 0.000000 0.064516 0.000000 0.000000 0.000000 0.032258 0.000000 0.032258 0.032258 0.000000 0.000000 0.000000 0.032258 0.032258 0.000000 0.000000 0.000000 0.064516 0.000000 0.064516 0.000000 0.451613 0.064516 0.000000 0.000000 0.000000 0.000000 0.032258 0.000000 0.096774 0.000000 0.161290 0.419355 0.000000 0.000000 0.032258 0.000000 0.129032 0.000000 0.032258 0.064516 0.032258 0.000000 0.000000 0.032258 0.000000 0.161290 0.064516 0.000000 0.000000 0.000000 0.032258 0.032258 0.000000 0.000000 0.064516 0.000000 0.064516 0.000000 0.032258 0.193548 0.032258 0.000000 0.000000 0.354839 0.064516 0.064516 0.000000 0.064516 0.032258 0.000000 0.000000 0.000000 0.000000 0.032258 0.096774 0.032258 0.000000 0.129032 0.000000 0.129032 0.096774 0.000000 0.032258 0.032258 0.032258 0.032258 0.064516 0.064516 0.000000 0.032258 0.193548 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- YSA[SA]K[AF][AG][VL]xG[LF]T[RE]S[LM][AR]x[ED]LAPx -------------------------------------------------------------------------------- Time 93.45 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 2BHD_STREX 6.22e-18 9_[1(8.69e-12)]_121_[2(2.93e-13)]_82 3BHD_COMTE 3.89e-20 9_[1(9.74e-13)]_120_[2(1.49e-14)]_81 ADH_DROME 3.06e-09 9_[1(2.60e-05)]_121_[2(9.02e-11)]_82 AP27_MOUSE 1.05e-24 10_[1(2.80e-15)]_117_[2(1.24e-16)]_74 BA72_EUBSP 3.85e-19 9_[1(9.22e-14)]_126_[2(1.69e-12)]_71 BDH_HUMAN 3.49e-20 58_[1(6.84e-15)]_128_[2(9.88e-13)]_114 BPHB_PSEPS 3.97e-21 8_[1(4.99e-13)]_123_[2(2.37e-15)]_101 BUDC_KLETE 4.93e-27 5_[1(2.50e-17)]_125_[2(6.17e-17)]_68 DHES_HUMAN 3.43e-21 5_[1(5.43e-13)]_128_[2(1.29e-15)]_151 DHGB_BACME 1.08e-19 10_[1(2.56e-12)]_128_[2(1.49e-14)]_81 DHII_HUMAN 4.91e-23 37_[1(1.32e-16)]_124_[2(8.96e-14)]_88 DHMA_FLAS1 1.77e-20 17_[1(6.96e-14)]_126_[2(8.10e-14)]_84 ENTA_ECOLI 7.63e-20 8_[1(1.98e-15)]_114_[2(1.52e-11)]_83 FIXR_BRAJA 2.11e-22 39_[1(7.62e-15)]_128_[2(7.61e-15)]_68 GUTD_ECOLI 2.74e-18 5_[1(4.49e-10)]_127_[2(2.37e-15)]_84 HDE_CANTR 1.12e-21 11_[1(1.01e-13)]_130_[2(6.24e-13)]_141_[1(4.49e-16)]_120_[2(5.95e-14)]_418 HDHA_ECOLI 6.08e-21 14_[1(5.50e-15)]_123_[2(3.90e-13)]_75 LIGD_PSEPA 2.75e-16 9_[1(3.19e-11)]_126_[2(2.63e-12)]_127 NODG_RHIME 1.74e-22 9_[1(1.33e-13)]_121_[2(4.70e-16)]_72 RIDH_KLEAE 5.89e-20 17_[1(3.86e-13)]_121_[2(5.95e-14)]_68 YINL_LISMO 3.49e-24 8_[1(2.12e-17)]_124_[2(5.37e-14)]_73 YRTP_BACSU 7.95e-30 9_[1(3.13e-18)]_124_[2(7.44e-19)]_62 CSGA_MYXXA 1.91e-09 87_[2(2.87e-12)]_57 DHB2_HUMAN 4.77e-21 85_[1(5.76e-14)]_125_[2(1.19e-14)]_134 DHB3_HUMAN 4.47e-21 51_[1(2.91e-14)]_125_[2(3.53e-14)]_91 DHCA_HUMAN 1.16e-12 7_[1(3.24e-13)]_164_[2(1.72e-06)]_62 FABI_ECOLI 1.39e-06 158_[2(8.74e-09)]_82 FVT1_HUMAN 1.46e-25 35_[1(1.09e-15)]_129_[2(2.23e-17)]_125 HMTR_LEIMA 3.90e-21 9_[1(1.11e-13)]_162_[2(9.54e-15)]_73 MAS1_AGRRA 6.26e-11 248_[1(8.26e-13)]_122_[2(1.32e-05)]_63 PCR_PEA 2.93e-12 89_[1(6.60e-16)]_289 RFBB_NEIGO 4.00e-16 9_[1(9.53e-11)]_134_[2(9.88e-13)]_160 YURA_MYXXA 5.03e-11 159_[2(1.85e-14)]_77 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 2 reached. ******************************************************************************** CPU: tlb-sayonara.imb.uq.edu.au ********************************************************************************