******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.3.0 (Release date: Sat Sep 26 01:51:56 PDT 2009) 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= temp.fasta ALPHABET= ACDEFGHIKLMNPQRSTVWY Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ PTHP_BACSU 1.0000 88 PTHP_LACSK 1.0000 88 PTHP_STREI 1.0000 87 PTHP_LISMO 1.0000 88 PTHP_STAAS 1.0000 88 PTHP_ENTFA 1.0000 88 PTHP_MYCGE 1.0000 88 PTHP_XYLFA 1.0000 89 PTHP_BUCAI 1.0000 85 PTHP_TREPA 1.0000 88 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme temp.fasta -mod zoops -nmotifs 3 -prior dirichlet -nostatus -protein -text model: mod= zoops nmotifs= 3 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= 10 wnsites= 0.8 theta: prob= 1 spmap= pam spfuzz= 120 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 877 N= 10 sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.115 C 0.002 D 0.051 E 0.087 F 0.024 G 0.079 H 0.021 I 0.078 K 0.081 L 0.083 M 0.042 N 0.038 P 0.015 Q 0.032 R 0.025 S 0.076 T 0.062 V 0.076 W 0.000 Y 0.014 Background letter frequencies (from dataset with add-one prior applied): A 0.114 C 0.003 D 0.051 E 0.086 F 0.025 G 0.078 H 0.021 I 0.077 K 0.080 L 0.082 M 0.042 N 0.038 P 0.016 Q 0.032 R 0.026 S 0.076 T 0.061 V 0.076 W 0.001 Y 0.014 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 49 sites = 9 llr = 952 E-value = 8.7e-161 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::6:1:::9:193::::29:::11:::::::::1::3:::::::1:2 pos.-specific C ::::::::::::::::::::::::::::::::::::::::::::::::: probability D ::::22::::::::::::::::::3:7:::1:1:::::::::::::::: matrix E :::::4:::::::::::::1::::::1:::6::::1::::::::::::: F 6:::::::::::::::1::::::8::::::::::::::::::1:::::: G :::::::a:::::::::::::::::::::::::9:::::::::9::::8 H :3::::1::a::::::::::::::::::::::::::::::::::::::: I :142::::7:::::::1::::::::::6:21:::1::::::9::1:::: K :2:::1:::::::::1::1::19:::1:::::4:82:::a:::1::::: L 1::1::1:2::::::68::::::::::::8::::::::7::1::::19: M :::::::::::::::1::::1:::::::1:::::::::::::9::9:1: N ::::2:::::::::::::::::::2:1:3:::3::::a::::::::::: P :::::1::::::9:::::::::::::::::::::::::::::::::::: Q :::::::::::::::1::9:::::1:::2::::::::::::::::1::: R :1:::1:::::a::::::::::1::::::::1::11::::::::::::: S ::::::1::::::::::::::9::19::1:1::::3::::a:::::7:: T :::3::6:::1::17::::7::::1::12::111:1::::::::::1:: V 2263::::1::::::1:a:::::::::3::1:::::a:::::::9:::: W ::::::::::::::::::::::::::::::::::::::::::::::::: Y 1::::::::::::::::::::::2:::::::8::::::::::::::::: bits 9.8 8.8 7.8 6.9 Relative 5.9 * Entropy 4.9 * ** * * * (152.7 bits) 3.9 * * ** ** * * ** ** * * 2.9 * * ******** ******** ** * * ** ********** ** 2.0 *********************************** ************* 1.0 ************************************************* 0.0 ------------------------------------------------- Multilevel FHVTAETGIHARPATLLVQTASKFDSDINLEYKGKSVNLKSIMGVMSLG consensus VKIVDD L A A YN VQI N K A A sequence V IN T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------------------------------- PTHP_ENTFA 6 3.20e-58 MEKKE FHIVAETGIHARPATLLVQTASKFNSDINLEYKGKSVNLKSIMGVMSLG VGQGSDVTIT PTHP_LACSK 6 1.64e-57 MEKRD FHVVADTGIHARPATLLVQTASKFNSDVNLEYKGKSVNLKSIMGVMSLG VGQGADVTIS PTHP_STAAS 6 6.28e-54 MEQNS YVIIDETGIHARPATMLVQTASKFDSDIQLEYNGKKVNLKSIMGVMSLG VGKDAEITIY PTHP_STREI 6 3.75e-53 MASKD FHIVAETGIHARPATLLVQTASKFASDITLDYKGKAVNLKSIMGVMSLG VGQGADVTIS PTHP_BACSU 6 1.36e-50 MAQKT FKVTADSGIHARPATVLVQTASKYDADVNLEYNGKTVNLKSIMGVMSLG IAKGAEITIS PTHP_LISMO 6 2.12e-50 MEQAS FVVIDETGIHARPATLLVQAASKYSSDVQIEYTGKKVNLKSIMGVMSLG IGKGADITIY PTHP_TREPA 6 8.46e-42 MVVKT VRVLNRAGVHARPAALIVQAASRFDSKIMLVRDTIRVNAKSIMGVMAMA AGCGSELELV PTHP_XYLFA 6 2.66e-41 MLEHE LIVTNKLGLHARATAKLVQTMSKFQSNTTLSTKGREVNAKSIMGVMLLA ASQGTVIRVR PTHP_BUCAI 6 7.62e-41 MFQNQ VKITAPHGLHTRPAAQFVKEAKKFTSEISIIYNGKSVNAKSLFKIQTLG LIQGSLITLS -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- PTHP_ENTFA 3.2e-58 5_[1]_34 PTHP_LACSK 1.6e-57 5_[1]_34 PTHP_STAAS 6.3e-54 5_[1]_34 PTHP_STREI 3.8e-53 5_[1]_33 PTHP_BACSU 1.4e-50 5_[1]_34 PTHP_LISMO 2.1e-50 5_[1]_34 PTHP_TREPA 8.5e-42 5_[1]_34 PTHP_XYLFA 2.7e-41 5_[1]_35 PTHP_BUCAI 7.6e-41 5_[1]_31 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=49 seqs=9 PTHP_ENTFA ( 6) FHIVAETGIHARPATLLVQTASKFNSDINLEYKGKSVNLKSIMGVMSLG 1 PTHP_LACSK ( 6) FHVVADTGIHARPATLLVQTASKFNSDVNLEYKGKSVNLKSIMGVMSLG 1 PTHP_STAAS ( 6) YVIIDETGIHARPATMLVQTASKFDSDIQLEYNGKKVNLKSIMGVMSLG 1 PTHP_STREI ( 6) FHIVAETGIHARPATLLVQTASKFASDITLDYKGKAVNLKSIMGVMSLG 1 PTHP_BACSU ( 6) FKVTADSGIHARPATVLVQTASKYDADVNLEYNGKTVNLKSIMGVMSLG 1 PTHP_LISMO ( 6) FVVIDETGIHARPATLLVQAASKYSSDVQIEYTGKKVNLKSIMGVMSLG 1 PTHP_TREPA ( 6) VRVLNRAGVHARPAALIVQAASRFDSKIMLVRDTIRVNAKSIMGVMAMA 1 PTHP_XYLFA ( 6) LIVTNKLGLHARATAKLVQTMSKFQSNTTLSTKGREVNAKSIMGVMLLA 1 PTHP_BUCAI ( 6) VKITAPHGLHTRPAAQFVKEAKKFTSEISIIYNGKSVNAKSLFKIQTLG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 49 n= 397 bayes= 6.85505 E= 8.7e-161 -982 -982 -982 -982 450 -982 -982 -982 -982 43 -982 -982 -982 -982 -982 -982 -982 155 -982 294 -982 -982 -982 -982 -982 -982 397 53 147 -982 -982 -982 -982 -982 211 -982 -982 155 -982 -982 -982 -982 -982 -982 -982 -982 -982 253 -982 -982 -982 -982 -982 -982 -982 -982 -982 287 -982 -982 -982 -982 -982 -982 -982 -982 -982 153 -982 43 -982 -982 -982 -982 -982 -982 244 214 -982 -982 229 -982 211 -982 -982 -982 -982 -982 -982 -982 -982 255 -982 -982 -982 -982 -982 -982 -982 -982 -982 -982 211 237 -982 -982 -982 -982 47 -982 -982 -982 283 -982 211 -982 -982 -982 -982 -982 -3 -982 -982 -982 -982 -982 239 -982 -982 43 -982 -982 -982 -982 -982 55 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-982 -982 332 -982 -982 -982 -982 -982 -982 -982 -982 -982 -982 -982 -982 -982 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 49 nsites= 9 E= 8.7e-161 0.000000 0.000000 0.000000 0.000000 0.555556 0.000000 0.000000 0.000000 0.000000 0.111111 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.222222 0.000000 0.111111 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.111111 0.222222 0.000000 0.000000 0.000000 0.000000 0.000000 0.111111 0.000000 0.000000 0.222222 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.444444 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.555556 0.000000 0.000000 0.000000 0.000000 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0.111111 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.222222 0.000000 0.000000 0.000000 0.000000 0.777778 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [FV][HKV][VI][TVI][ADN][ED]TG[IL]HARPA[TA]LLVQ[TA]ASK[FY][DN]SD[IV][NQT][LI]EY[KN]GK[SK]VN[LA]KSIMGVMSL[GA] -------------------------------------------------------------------------------- Time 0.29 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 29 sites = 10 llr = 479 E-value = 7.8e-042 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::5:::::6::5:1219:38::1:::::: pos.-specific C 1::::::::::::::::::::::1::::: probability D :114:::::4::a:14::::::1:::::: matrix E :::3:1:::5:2:913::2::46::2161 F ::::::::::::::::::::::::2:::2 G :8::::::::a:::::1::1::::::::6 H 1:::::::::::::1::::1::::::::: I ::::6:7:1::::::::4::6::1::::: K 3::::::1::::::21:::::1:::3611 L :::11:2::::::::::4::4:124::1: M :::::::::::::::::2::::::4:::: N :1:1::::::::::1:::2:::::::21: P :::::::::::1::::::::::::::::: Q 5:::::::::::::::::2::::::2::: R :::::1:1::::::::::::::1::::1: S ::3::::4:1:2::1:::1::3:::11:: T ::1::8:11::::::1:::::1:4:2::: V :::13:112:::::1::::::1:2::::: W ::::::::::::::::::::::::::::: Y :::::::2::::::::::::::::::::: bits 9.8 8.8 7.8 6.9 Relative 5.9 Entropy 4.9 (69.1 bits) 3.9 * * 2.9 ** ** ** ** * ** * 2.0 ************** ************** 1.0 ***************************** 0.0 ----------------------------- Multilevel QGADITISAEGADEADAIAAIEETLKKEG consensus K SEV LYVD E KE LE LS LMEN F sequence S MN VFQ Q T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------------------------- PTHP_LACSK 57 5.95e-28 IMGVMSLGVG QGADVTISAEGADEADAINAIEETMKKEG LSE PTHP_STREI 57 3.08e-25 IMGVMSLGVG QGADVTISAEGADADDALAAIEETMTKEG LA PTHP_BACSU 57 3.74e-24 IMGVMSLGIA KGAEITISASGADENDALNALEETMKSEG LGE PTHP_STAAS 57 2.86e-23 IMGVMSLGVG KDAEITIYADGSDESDAIQAISDVLSKEG LTK PTHP_ENTFA 57 3.24e-23 IMGVMSLGVG QGSDVTITVDGADEAEGMAAIVETLQKEG LAE PTHP_LISMO 57 9.59e-23 IMGVMSLGIG KGADITIYTEGSDEKEAIEGLTEVLKKEG LAE PTHP_XYLFA 57 2.34e-21 IMGVMLLAAS QGTVIRVRIDGEDEHTAMQALSELFENRF NEDT PTHP_MYCGE 58 1.10e-20 IINLMSLGIR HNDNITIKADGADEEEALAAIKACLEKNK VI PTHP_TREPA 57 2.15e-20 IMGVMAMAAG CGSELELVVEGPDEVAALSAIERLFQNKF EEE PTHP_BUCAI 57 5.34e-20 LFKIQTLGLI QGSLITLSAEGEDEKKAIEHLSLIMTELE -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- PTHP_LACSK 6e-28 56_[2]_3 PTHP_STREI 3.1e-25 56_[2]_2 PTHP_BACSU 3.7e-24 56_[2]_3 PTHP_STAAS 2.9e-23 56_[2]_3 PTHP_ENTFA 3.2e-23 56_[2]_3 PTHP_LISMO 9.6e-23 56_[2]_3 PTHP_XYLFA 2.3e-21 56_[2]_4 PTHP_MYCGE 1.1e-20 57_[2]_2 PTHP_TREPA 2.2e-20 56_[2]_3 PTHP_BUCAI 5.3e-20 56_[2] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=29 seqs=10 PTHP_LACSK ( 57) QGADVTISAEGADEADAINAIEETMKKEG 1 PTHP_STREI ( 57) QGADVTISAEGADADDALAAIEETMTKEG 1 PTHP_BACSU ( 57) KGAEITISASGADENDALNALEETMKSEG 1 PTHP_STAAS ( 57) KDAEITIYADGSDESDAIQAISDVLSKEG 1 PTHP_ENTFA ( 57) QGSDVTITVDGADEAEGMAAIVETLQKEG 1 PTHP_LISMO ( 57) KGADITIYTEGSDEKEAIEGLTEVLKKEG 1 PTHP_XYLFA ( 57) QGTVIRVRIDGEDEHTAMQALSELFENRF 1 PTHP_MYCGE ( 58) HNDNITIKADGADEEEALAAIKACLEKNK 1 PTHP_TREPA ( 57) CGSELELVVEGPDEVAALSAIERLFQNKF 1 PTHP_BUCAI ( 57) QGSLITLSAEGEDEKKAIEHLSLIMTELE 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 29 n= 597 bayes= 6.83045 E= 7.8e-042 -997 490 -997 -997 -997 -997 224 -997 190 -997 -997 -997 -997 395 -997 -997 -997 -997 -997 -997 -997 -997 96 -997 -997 336 -997 -997 -997 -997 -997 140 -997 -997 -997 -997 -997 -997 -997 -997 214 -997 96 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 198 71 -997 -997 -997 -997 -997 296 180 -997 -997 -997 -997 -997 28 -997 140 -997 -997 -997 -997 -997 40 -997 -997 -997 -997 -997 -997 -997 -997 -997 296 -997 28 -997 -997 -997 -997 -997 -997 -997 198 -997 -997 -997 -997 -997 22 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 196 -997 370 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 318 -997 128 -997 -997 -997 -997 -997 -997 -997 40 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 32 -997 -997 -997 -997 -997 196 240 71 40 -997 379 240 -997 -997 -997 -997 -997 -997 38 -997 -997 -997 -997 -997 -997 -997 -997 71 140 -997 -997 -997 -997 296 254 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 40 -997 -997 -997 -997 -997 -997 -997 -997 -997 368 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 214 -997 -997 122 -997 -997 -997 -997 -997 -997 -997 -997 268 -997 -997 140 -997 -997 -997 -997 -997 -997 428 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -19 -997 -997 339 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 81 -997 96 22 -997 -997 224 -997 132 -997 -997 140 -997 -997 -997 40 -997 40 -997 -997 -19 -997 296 180 -997 -997 -997 -997 32 -997 -997 -997 -997 -997 -997 -997 71 -997 -997 -997 298 -997 -997 -997 -997 36 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 238 -997 228 224 -997 -997 -997 -997 -997 -997 -997 -997 -997 140 -997 -997 122 -997 -997 -997 -997 -997 -997 -997 240 -997 263 -997 40 -997 -997 -997 -997 281 -997 -997 -997 -997 36 224 -997 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-------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 29 nsites= 10 E= 7.8e-042 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.300000 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 0.100000 0.000000 0.000000 0.800000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.300000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.300000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 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0.400000 0.300000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.900000 0.000000 0.000000 0.000000 0.000000 0.100000 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 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.400000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.300000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.200000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.000000 0.000000 0.000000 0.100000 0.100000 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 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.400000 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 0.400000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.300000 0.100000 0.100000 0.000000 0.000000 0.100000 0.000000 0.100000 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.400000 0.400000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.300000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.100000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.000000 0.000000 0.100000 0.100000 0.000000 0.100000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.200000 0.600000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [QK]G[AS][DE][IV]T[IL][SY][AV][ED]G[AES]DE[AK][DE]A[ILM][AENQ]A[IL][ES]E[TLV][LMF][KEQT][KN]E[GF] -------------------------------------------------------------------------------- Time 0.38 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 8 sites = 2 llr = 34 E-value = 1.8e+005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 5::::::: pos.-specific C :::::::: probability D :::::::: matrix E :::::5:: F :::::::: G :::5::5: H :::::::: I :::::::: K :::5:::: L :::::::: M 5::::::: N :::::::5 P :5:::::: Q :::::::: R ::::::5: S ::5::::: T ::::5::: V :55:55:5 W :::::::: Y :::::::: bits 9.8 8.8 7.8 6.9 Relative 5.9 Entropy 4.9 (24.3 bits) 3.9 * * 2.9 ******** 2.0 ******** 1.0 ******** 0.0 -------- Multilevel APSGTEGN consensus MVVKVVRV sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- PTHP_TREPA 1 1.20e-08 . MVVKTVRV LNRAGVHARP PTHP_MYCGE 37 1.20e-08 SKFKSELKLV APSGVEGN IKSIINLMSL -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- PTHP_TREPA 1.2e-08 [3]_80 PTHP_MYCGE 1.2e-08 36_[3]_44 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=8 seqs=2 PTHP_TREPA ( 1) MVVKTVRV 1 PTHP_MYCGE ( 37) APSGVEGN 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 8 n= 807 bayes= 8.65284 E= 1.8e+005 213 -765 -765 -765 -765 -765 -765 -765 -765 -765 355 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 499 -765 -765 -765 -765 272 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 272 -765 272 -765 -765 -765 -765 -765 -765 -765 267 -765 -765 263 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 302 272 -765 -765 -765 -765 -765 254 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 272 -765 -765 -765 -765 -765 -765 -765 267 -765 -765 -765 -765 -765 -765 -765 -765 428 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 371 -765 -765 -765 -765 -765 272 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 8 nsites= 2 E= 1.8e+005 0.500000 0.000000 0.000000 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 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 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 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 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 0.000000 0.000000 0.000000 0.500000 0.500000 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 0.000000 0.000000 0.000000 0.000000 0.500000 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 0.500000 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 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [AM][PV][SV][GK][TV][EV][GR][NV] -------------------------------------------------------------------------------- Time 0.42 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- PTHP_BACSU 4.84e-67 5_[1(1.36e-50)]_2_[2(3.74e-24)]_3 PTHP_LACSK 1.46e-77 5_[1(1.64e-57)]_2_[2(5.95e-28)]_3 PTHP_STREI 1.37e-70 5_[1(3.75e-53)]_2_[2(3.08e-25)]_2 PTHP_LISMO 3.51e-65 5_[1(2.12e-50)]_2_[2(9.59e-23)]_3 PTHP_STAAS 2.17e-69 5_[1(6.28e-54)]_2_[2(2.86e-23)]_3 PTHP_ENTFA 1.41e-73 5_[1(3.20e-58)]_2_[2(3.24e-23)]_3 PTHP_MYCGE 4.89e-26 36_[3(1.20e-08)]_13_[2(1.10e-20)]_2 PTHP_XYLFA 8.33e-55 5_[1(2.66e-41)]_2_[2(2.34e-21)]_4 PTHP_BUCAI 5.64e-53 5_[1(7.62e-41)]_2_[2(5.34e-20)] PTHP_TREPA 4.59e-60 5_[1(8.46e-42)]_2_[2(2.15e-20)]_3 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: kodomo ********************************************************************************