******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.1.1 (Release date: Tue Apr 21 15:00:06 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 ------------- ------ ------ ------------- ------ ------ LUXS_BACSU 1.0000 157 LUXS_CLOAB 1.0000 158 LUXS_DESAD 1.0000 159 LUXS_PORGI 1.0000 159 LUXS_BIFAA 1.0000 161 LUXS_PEDPA 1.0000 157 LUXS1_LACDB 1.0000 159 LUXS_SHEPA 1.0000 169 LUXS_VIBFM 1.0000 172 LUXS_CAMJR 1.0000 164 LUXS_ARCB4 1.0000 171 ******************************************************************************** ******************************************************************************** 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= 11 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= 1786 N= 11 sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.069 C 0.020 D 0.073 E 0.076 F 0.040 G 0.064 H 0.034 I 0.064 K 0.059 L 0.093 M 0.035 N 0.044 P 0.046 Q 0.020 R 0.044 S 0.057 T 0.061 V 0.064 W 0.009 Y 0.030 Background letter frequencies (from dataset with add-one prior applied): A 0.069 C 0.020 D 0.073 E 0.075 F 0.040 G 0.064 H 0.034 I 0.064 K 0.059 L 0.092 M 0.035 N 0.044 P 0.047 Q 0.020 R 0.044 S 0.056 T 0.061 V 0.064 W 0.009 Y 0.030 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 41 sites = 8 llr = 747 E-value = 6.0e-130 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::::::1::a:5:::5:::1:::::::::::::::1::: pos.-specific C :::::::::::::::::1::::::::::::::::::5:::: probability D 5::::a::::::::::::1::::::193::::a:::::::: matrix E 5::4::::::1:::::::::41::::::::::::::::::4 F ::a::::::::::::::::::::::::::::9:::6::::: G ::::::::::::::::::1:::41:91:::::::::::::: H ::::::a:::::::::1:::1:::1:::::::::::::::: I ::::::::1::::::::4::::::::::9::::1:::1::: K :::1::::5:4:::::::5::3::8::3::1:::::::::6 L ::::5:::::::::::4::::::1:::::::::9:4::::: M :::::::::5::::::::::5:::::::::::::::::::: N :::::::1::1::::::::::::1:::::14::::::::a: P ::::::::::3:a::::::::::6::::::::::::::a:: Q :::1:::::::::::::::::3:::::::::::::::5::: R :::1::::3::::::a::::::::::::::::::a:::::: S :a:::::::::::::::::1:::::::::5::::::::::: T :::3:::9::::::::::33:35:1::3:4::::::1:::: V ::::5::::51:::a:4::6::1::::31:5:::::43::: W ::::::::::::::::::::::::::::::::::::::::: Y :::::::::::::5::1::::::::::::::1::::::::: bits 6.7 6.1 5.4 4.7 * * * * * ** Relative 4.0 ** ** ** ** ** * ** Entropy 3.4 ** *** * ***** *** * ** ****** (134.6 bits) 2.7 *** ****** ***** * ** ***** ************* 2.0 ***************************************** 1.3 ***************************************** 0.7 ***************************************** 0.0 ----------------------------------------- Multilevel DSFELDHTKMKAPAVRLAKVMKTPKGDDISVFDLRFCQPNK consensus E TV RVP Y VITTEQG K TN LVV E sequence T T V -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------------------------------------- LUXS_ARCB4 5 1.79e-45 MPLL DSFRVDHTIMPAPAVRVAKVMQTPKGDDITVFDLRFCVPNK SMMSEKGTHT LUXS_CAMJR 5 5.92e-45 MPLL DSFKVDHTKMPAPAVRLAKVMKTPKGDDISVFDLRFCIPNK DIMSEKGTHT LUXS_SHEPA 5 7.81e-44 MPLL DSFTVDHTRMNAPAVRVAKSMATPKGDTITVFDLRFCVPNK EILSERGIHT LUXS_VIBFM 5 3.38e-43 MPLL DSFTVDHTRMEAPAVRVAKTMQTPKGDTITVFDLRFTAPNK DILSEKGIHT LUXS1_LACDB 5 6.28e-43 MAKV ESFELDHTKVKAPYVRLITVEEGPKGDKISNFDLRLVQPNE NAIPTGGLHT LUXS_PEDPA 5 1.28e-42 MAKV ESFELDHTKVKAPYVRLITVETGNKGDKISNFDLRLVQPNE NAIPTAGLHT LUXS_BIFAA 9 1.35e-40 MAEDKPVV ESFQLDHTKVKAPYVRYIDTETGLHGDVISNYDLRLVQPNE NAIPTGGLHT LUXS_BACSU 5 1.08e-37 MPSV ESFELDHNAVVAPYVRHCGVHKVGTDGVVNKFDIRFCQPNK QAMKPDTIHT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- LUXS_ARCB4 1.8e-45 4_[1]_126 LUXS_CAMJR 5.9e-45 4_[1]_119 LUXS_SHEPA 7.8e-44 4_[1]_124 LUXS_VIBFM 3.4e-43 4_[1]_127 LUXS1_LACDB 6.3e-43 4_[1]_114 LUXS_PEDPA 1.3e-42 4_[1]_112 LUXS_BIFAA 1.4e-40 8_[1]_112 LUXS_BACSU 1.1e-37 4_[1]_112 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=41 seqs=8 LUXS_ARCB4 ( 5) DSFRVDHTIMPAPAVRVAKVMQTPKGDDITVFDLRFCVPNK 1 LUXS_CAMJR ( 5) DSFKVDHTKMPAPAVRLAKVMKTPKGDDISVFDLRFCIPNK 1 LUXS_SHEPA ( 5) DSFTVDHTRMNAPAVRVAKSMATPKGDTITVFDLRFCVPNK 1 LUXS_VIBFM ( 5) DSFTVDHTRMEAPAVRVAKTMQTPKGDTITVFDLRFTAPNK 1 LUXS1_LACDB ( 5) ESFELDHTKVKAPYVRLITVEEGPKGDKISNFDLRLVQPNE 1 LUXS_PEDPA ( 5) ESFELDHTKVKAPYVRLITVETGNKGDKISNFDLRLVQPNE 1 LUXS_BIFAA ( 9) ESFQLDHTKVKAPYVRYIDTETGLHGDVISNYDLRLVQPNE 1 LUXS_BACSU ( 5) ESFELDHNAVVAPYVRHCGVHKVGTDGVVNKFDIRFCQPNK 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 41 n= 1346 bayes= 7.38586 E= 6.0e-130 -965 -965 278 273 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 414 -965 -965 -965 -965 -965 -965 -965 -965 463 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 231 -965 -965 -965 -965 109 -965 -965 -965 -965 265 151 -965 204 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 243 -965 -965 -965 -965 -965 -965 -965 297 -965 -965 -965 -965 378 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 486 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 151 -965 -965 -965 -965 384 -965 -965 -965 85 -965 -965 -965 -965 -965 -965 97 309 -965 -965 -965 -965 -965 251 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 384 -965 -965 -965 -965 -965 -965 297 -965 -965 -965 -965 -965 73 -965 -965 -965 -965 267 -965 -965 151 242 -965 -965 -965 -965 97 -965 -965 385 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 442 -965 -965 -965 -965 -965 -965 -965 285 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 404 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 397 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 451 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 186 -965 -965 202 -965 -965 -965 -965 -965 -965 -965 256 -965 204 285 265 -965 -965 -965 -965 -965 256 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 78 -965 -965 97 -965 -965 309 -965 -965 -965 -965 -965 -965 -965 204 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 115 204 329 -965 -965 -965 -965 -965 231 -965 -965 186 -965 -965 -965 384 -965 -965 -965 -965 -965 -965 -965 -965 -965 85 -965 -965 73 -965 -965 -965 -965 209 -965 -965 -965 -965 365 -965 -965 204 -965 -965 -965 -965 -965 -965 -965 -965 256 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 304 97 -965 -965 -965 -965 -965 -965 -965 97 -965 -965 -965 43 -965 151 375 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 186 -965 367 -965 -965 -965 -965 -965 -965 -965 104 -965 -965 -965 -965 -965 78 -965 -965 378 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 359 -965 -965 97 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 178 -965 -965 -965 -965 -965 209 -965 -965 -965 -965 -965 -965 -965 204 197 -965 -965 -965 -965 -965 -965 -965 -965 -965 378 -965 -965 -965 -965 -965 -965 -965 -965 -965 97 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 151 -965 -965 -965 314 262 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 109 -965 -965 310 -965 -965 -965 -965 -965 297 -965 -965 -965 -965 -965 -965 443 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 204 -965 -965 378 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 97 -965 324 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 451 -965 -965 -965 -965 -965 -965 -965 -965 -965 395 -965 -965 -965 -965 202 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 465 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 104 256 -965 -965 85 -965 -965 -965 -965 -965 -965 97 -965 -965 -965 -965 -965 465 -965 -965 -965 197 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 442 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 451 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 231 -965 -965 -965 -965 341 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 41 nsites= 8 E= 6.0e-130 0.000000 0.000000 0.500000 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 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 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 0.000000 0.000000 0.000000 0.000000 0.375000 0.000000 0.000000 0.000000 0.000000 0.125000 0.000000 0.000000 0.000000 0.000000 0.125000 0.125000 0.000000 0.250000 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 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 0.000000 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 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.125000 0.000000 0.000000 0.000000 0.000000 0.875000 0.000000 0.000000 0.000000 0.125000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.125000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 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 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 0.125000 0.000000 0.000000 0.000000 0.000000 0.375000 0.000000 0.000000 0.125000 0.250000 0.000000 0.000000 0.000000 0.000000 0.125000 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 0.000000 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 1.000000 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 0.500000 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 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 0.000000 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 0.125000 0.000000 0.000000 0.375000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.375000 0.000000 0.125000 0.500000 0.125000 0.000000 0.000000 0.000000 0.000000 0.000000 0.375000 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 0.125000 0.000000 0.000000 0.125000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 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 0.125000 0.250000 0.625000 0.000000 0.000000 0.000000 0.000000 0.000000 0.375000 0.000000 0.000000 0.125000 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 0.125000 0.000000 0.000000 0.125000 0.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.250000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.375000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.125000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.125000 0.000000 0.000000 0.000000 0.125000 0.000000 0.125000 0.625000 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 0.125000 0.000000 0.750000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.125000 0.000000 0.000000 0.000000 0.000000 0.000000 0.125000 0.000000 0.000000 0.875000 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 0.875000 0.000000 0.000000 0.125000 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 0.250000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.250000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.875000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.125000 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 0.125000 0.000000 0.000000 0.000000 0.500000 0.375000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.125000 0.000000 0.000000 0.375000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.875000 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 0.125000 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 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.125000 0.000000 0.875000 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.625000 0.000000 0.000000 0.000000 0.000000 0.375000 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 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.125000 0.375000 0.000000 0.000000 0.125000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.125000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 0.250000 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 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 0.000000 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 0.375000 0.000000 0.000000 0.000000 0.000000 0.625000 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 -------------------------------------------------------------------------------- [DE]SF[ET][LV]DHT[KR][MV][KP]AP[AY]VR[LV][AI][KT][VT][ME][KQT][TG]PKGD[DKTV]I[ST][VN]FDLR[FL][CV][QV]PN[KE] -------------------------------------------------------------------------------- Time 1.86 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 29 sites = 11 llr = 680 E-value = 2.3e-128 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::::::::::::::1::::1:11:6:6: pos.-specific C ::3::::a::::::::::::::::::::: probability D :7::::::::::::::::2:2::4::3:: matrix E ::::::::::::::::::4::414::::: F :12::3:::::8:1::::::::::::::: G :::3::a:::a::::::a::::::::::: H ::::::::::::3::::::2::::::::: I 8:4:::::::::::3:4:::::::3:::1 K ::::::::::::::::::1:::3:::3:: L ::::::::2::::535:::::::::1:45 M :::::7:::::::4:1::::::::::::1 N :::::::::::1::::1:::::1:::::: P ::::a::::::::::::::5::::::2:: Q ::::::::1:::::::1:::::2:::::: R ::::::::7:::::::1:::::::::1:: S :::7::::::::::4:1:::4411::1:: T :::::::::a:::::2::4:332:::::: V 2:1:::::::::::11::::1::1731:: W ::1:::::::::::::3:::::::::::4 Y :2:::::::::17::::::3::::::::: bits 6.7 6.1 5.4 * 4.7 * * Relative 4.0 **** **** * Entropy 3.4 * ********** * * * * (89.2 bits) 2.7 ************** ** * * ** ** 2.0 ***************************** 1.3 ***************************** 0.7 ***************************** 0.0 ----------------------------- Multilevel IDISPMGCRTGFYLSLIGEPSEKDVADAL consensus CG F HMI W TYTS EIVKLW sequence L T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------------------------- LUXS_ARCB4 76 2.91e-32 NHLNSPTVEI IDVSPMGCRTGFYMSLIGTPSEQEVAVAW KKAMEDVLKV LUXS_CAMJR 76 2.91e-32 DHLNSNSVEI IDISPMGCRTGFYMSLIGTPDEKSVAKAW EEAMKDVLSV LUXS_VIBFM 76 6.58e-32 NHLNGSGVEI IDISPMGCRTGFYMSLIGTPAEQAVADAW VSSMEDVLKV LUXS_SHEPA 76 8.03e-32 DHLNSDSVEI IDISPMGCRTGFYMSLIGTPSESVVADAW LAAMQDVLNV LUXS1_LACDB 72 5.31e-30 SLLRDRLDGV IDCSPFGCRTGFHLITWGEHSTTEVAKAL RDSLKAIRDD LUXS_PEDPA 72 7.21e-30 GLLRDRMDGI IDCSPFGCRTGFHLIAWGEPTTTEVAKAL KGALEEIANV LUXS_BIFAA 76 6.73e-29 VLLRERIPGY IDCSPFGCRTGFHLLTWGEHSTEDVARAL KESLEFIAYE LUXS_CLOAB 74 3.88e-27 RNHGTYAEKT VYFGPMGCRTGFYLILQGDYTSNDIVPLL REMYKFIADF LUXS_BACSU 77 2.60e-26 HAEKYDHFDI IDISPMGCQTGYYLVVSGEPTSAEIVDLL EDTMKEAVEI LUXS_DESAD 74 3.08e-26 RNHSEYGDKI IYFGPMGCLTGFYLLLNGKYDSKDVVSLI RELFKFAADF LUXS_PORGI 74 1.56e-24 RNHPLYKDRI VFWGPMGCLTGNYFLMRGDYVSKDILPLM QETFRFIRDF -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- LUXS_ARCB4 2.9e-32 75_[2]_67 LUXS_CAMJR 2.9e-32 75_[2]_60 LUXS_VIBFM 6.6e-32 75_[2]_68 LUXS_SHEPA 8e-32 75_[2]_65 LUXS1_LACDB 5.3e-30 71_[2]_59 LUXS_PEDPA 7.2e-30 71_[2]_57 LUXS_BIFAA 6.7e-29 75_[2]_57 LUXS_CLOAB 3.9e-27 73_[2]_56 LUXS_BACSU 2.6e-26 76_[2]_52 LUXS_DESAD 3.1e-26 73_[2]_57 LUXS_PORGI 1.6e-24 73_[2]_57 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=29 seqs=11 LUXS_ARCB4 ( 76) IDVSPMGCRTGFYMSLIGTPSEQEVAVAW 1 LUXS_CAMJR ( 76) IDISPMGCRTGFYMSLIGTPDEKSVAKAW 1 LUXS_VIBFM ( 76) IDISPMGCRTGFYMSLIGTPAEQAVADAW 1 LUXS_SHEPA ( 76) IDISPMGCRTGFYMSLIGTPSESVVADAW 1 LUXS1_LACDB ( 72) IDCSPFGCRTGFHLITWGEHSTTEVAKAL 1 LUXS_PEDPA ( 72) IDCSPFGCRTGFHLIAWGEPTTTEVAKAL 1 LUXS_BIFAA ( 76) IDCSPFGCRTGFHLLTWGEHSTEDVARAL 1 LUXS_CLOAB ( 74) VYFGPMGCRTGFYLILQGDYTSNDIVPLL 1 LUXS_BACSU ( 77) IDISPMGCQTGYYLVVSGEPTSAEIVDLL 1 LUXS_DESAD ( 74) IYFGPMGCLTGFYLLLNGKYDSKDVVSLI 1 LUXS_PORGI ( 74) VFWGPMGCLTGNYFLMRGDYVSKDILPLM 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 29 n= 1478 bayes= 7.41667 E= 2.3e-128 -1010 -1010 -1010 -1010 -1010 -1010 -1010 368 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 151 -1010 -1010 -1010 -1010 332 -1010 117 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 258 -1010 377 -1010 -1010 217 -1010 -1010 251 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 51 327 -1010 -1010 -1010 -1010 -1010 -1010 210 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 369 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 443 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 275 -1010 -1010 -1010 -1010 -1010 438 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 397 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 565 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 97 -1010 -1010 -1010 219 405 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 404 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 397 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 434 -1010 -1010 -1010 -1010 -1010 -1010 105 -1010 -1010 -1010 -1010 -1010 -1010 -1010 158 -1010 -1010 -1010 -1010 -1010 -1010 299 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 458 -1010 -1010 -1010 -1010 117 -1010 -1010 -1010 -1010 256 338 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 210 -1010 156 -1010 -1010 -1010 -1010 -1010 269 -1010 51 -1010 -1010 39 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 256 138 -1010 -1010 -1010 -1010 -1010 158 51 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 251 -1010 -1010 -1010 105 -1010 219 105 69 -1010 -1010 486 -1010 -1010 -1010 -1010 -1010 -1010 397 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 132 227 -1010 -1010 -1010 -1010 63 -1010 -1010 -1010 -1010 -1010 -1010 -1010 258 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 240 -1010 -1010 -1010 -1010 -1010 355 -1010 -1010 -1010 -1010 -1010 -1010 316 39 -1010 132 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 269 216 51 -1010 -1010 -1010 -1010 -1010 227 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 269 216 -1010 -1010 -1010 39 -1010 -1010 27 -1010 -1010 -1010 -1010 222 -1010 -1010 105 -1010 319 -1010 69 158 -1010 -1010 -1010 39 -1010 232 227 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 69 -1010 51 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 210 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 351 -1010 -1010 320 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -2 -1010 -1010 -1010 -1010 -1010 -1010 -1010 210 -1010 -1010 -1010 -1010 191 -1010 -1010 -1010 -1010 -1010 222 -1010 -1010 -1010 197 -1010 105 69 -1010 51 -1010 -1010 320 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 197 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 51 -1010 230 138 -1010 -1010 -1010 -1010 -1010 -1010 -1010 527 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 29 nsites= 11 E= 2.3e-128 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.818182 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.181818 0.000000 0.000000 0.000000 0.000000 0.727273 0.000000 0.090909 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 0.181818 0.000000 0.272727 0.000000 0.000000 0.181818 0.000000 0.000000 0.363636 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.090909 0.090909 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.272727 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.727273 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.272727 0.000000 0.000000 0.000000 0.000000 0.000000 0.727273 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 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 0.000000 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 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.181818 0.000000 0.000000 0.000000 0.090909 0.727273 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 1.000000 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 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.818182 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.090909 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.090909 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.272727 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.727273 0.000000 0.000000 0.000000 0.000000 0.090909 0.000000 0.000000 0.000000 0.000000 0.545455 0.363636 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 0.272727 0.000000 0.272727 0.000000 0.000000 0.000000 0.000000 0.000000 0.363636 0.000000 0.090909 0.000000 0.000000 0.090909 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.545455 0.090909 0.000000 0.000000 0.000000 0.000000 0.000000 0.181818 0.090909 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.363636 0.000000 0.000000 0.000000 0.090909 0.000000 0.090909 0.090909 0.090909 0.000000 0.000000 0.272727 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 0.000000 0.000000 0.181818 0.363636 0.000000 0.000000 0.000000 0.000000 0.090909 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.363636 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.181818 0.000000 0.000000 0.000000 0.000000 0.000000 0.545455 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.272727 0.090909 0.000000 0.181818 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.363636 0.272727 0.090909 0.000000 0.000000 0.000000 0.000000 0.000000 0.363636 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.363636 0.272727 0.000000 0.000000 0.000000 0.090909 0.000000 0.000000 0.090909 0.000000 0.000000 0.000000 0.000000 0.272727 0.000000 0.000000 0.090909 0.000000 0.181818 0.000000 0.090909 0.181818 0.000000 0.000000 0.000000 0.090909 0.000000 0.363636 0.363636 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.090909 0.000000 0.090909 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.272727 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.727273 0.000000 0.000000 0.636364 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.090909 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.272727 0.000000 0.000000 0.000000 0.000000 0.272727 0.000000 0.000000 0.000000 0.000000 0.000000 0.272727 0.000000 0.000000 0.000000 0.181818 0.000000 0.090909 0.090909 0.000000 0.090909 0.000000 0.000000 0.636364 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.363636 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 0.090909 0.000000 0.454545 0.090909 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.363636 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- ID[IC][SG]P[MF]GCRTGF[YH][LM][SIL]L[IW]G[ET][PY][ST][EST]K[DE][VI][AV][DK][AL][LW] -------------------------------------------------------------------------------- Time 3.27 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 36 sites = 11 llr = 729 E-value = 2.5e-108 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :1:::2312:::::12::::::a:1:61:::51::: pos.-specific C :::::::::::a::3:::::::::::2::::::::: probability D :15::::1::2:::::4:2:3:::1:::3::11112 matrix E 223::4:1321::::2::::23::42:1::::2::1 F ::::::::::::::::::::3:::::::11:::::: G :3:::5::::::a::::::::1::::1::::::5:1 H :::::::::::::::::8:::::::::::::::::: I 1::5::::4::::::::::::::::4:::51:::6: K 1:2::::::1:::::1:::::::7:::35::22:1: L ::::::4:1::::::23::a:1:::1::::7:212: M ::::::::::::::::42:::2::::1::::::::: N :1:::::5:::::5::::2::::1:::11::1:::2 P ::::a:::1:::::::::::2::::::::::::::: Q 4:::::::::5::1:::::::1:21::1::::11:: R :::::::::2:::::3::::::::1::3:::1:::: S :2:::::1::3:::::::6:12::::::::112::5 T :1::::42:::::4:1:::::1::1::11::::::: V :::5:::::1:::::::::::::::::::2:::2:: W 3::::::::::::::::::::::::4:::1:::::: Y :::::::::5::::6:::::::::2::::21::::: bits 6.7 6.1 5.4 * 4.7 * * Relative 4.0 * ** * * * Entropy 3.4 * * **** * * ** * (95.7 bits) 2.7 * **** ****** **** ** ** ** * 2.0 * ************* ***** ********** *** 1.3 ************************************ 0.7 ************************************ 0.0 ------------------------------------ Multilevel QGDVPGLNIYQCGNYRDHSLDEAKEIAKKILAxGIS consensus W EI ET E S TC M F W RD sequence A L -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------------------ LUXS_PEDPA 113 5.23e-36 ALEEIANVTK WEDVPGTDIYSCGNYRDHSLFSAKEWAKKILDDGIS DQPFERNVI LUXS1_LACDB 113 3.58e-35 SLKAIRDDIT WEDVPGTTIESCGNYRDHSLFSAQEWCNDILKKGIS DDPFDRHVVE LUXS_BIFAA 117 8.91e-35 SLEFIAYEAT WDDVPATTIESCGNYRDHSLFTAKEWCKDILAKGIS SDPFERRLV LUXS_CAMJR 117 1.81e-34 AMKDVLSVSD QSKIPELNIYQCGTCAMHSLDEAKQIAQKVLNLGIS IMNNKELKLE LUXS_SHEPA 117 4.71e-33 AMQDVLNVVA QADIPELNEYQCGTYEMHSLEQAQEIARNIIAAGIN VNRNDDLSLS LUXS_VIBFM 117 1.15e-32 SMEDVLKVEA QNKIPELNEYQCGTYEMHSLDEAKAIATTVLASGIS VNKNDELALS LUXS_ARCB4 117 1.79e-32 AMEDVLKVEN QSDIPELNLYQCGTCAMHSLDEAKDIARDILKSQIG VMSNKELYLS LUXS_PORGI 113 4.54e-28 QETFRFIRDF EGEVPGTEPRDCGNCLLHNLPMAKYEAEKYLREVLD VATEENLNYP LUXS_CLOAB 113 3.26e-27 REMYKFIADF KGEVPGAAARDCGNYLDMNLPMANYWGKKFSALLDN ISEDRLNYPE LUXS_DESAD 113 2.12e-26 RELFKFAADF EGDVPGASAVECGNYTLMDLSLAKTEAAKYYAEVLD GIGLDNLNYP LUXS_BACSU 115 8.38e-26 LEDTMKEAVE ITEIPAANEKQCGQAKLHDLEGAKRLMRFWLSQDKE ELLKVFG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- LUXS_PEDPA 5.2e-36 112_[3]_9 LUXS1_LACDB 3.6e-35 112_[3]_11 LUXS_BIFAA 8.9e-35 116_[3]_9 LUXS_CAMJR 1.8e-34 116_[3]_12 LUXS_SHEPA 4.7e-33 116_[3]_17 LUXS_VIBFM 1.2e-32 116_[3]_20 LUXS_ARCB4 1.8e-32 116_[3]_19 LUXS_PORGI 4.5e-28 112_[3]_11 LUXS_CLOAB 3.3e-27 112_[3]_10 LUXS_DESAD 2.1e-26 112_[3]_11 LUXS_BACSU 8.4e-26 114_[3]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=36 seqs=11 LUXS_PEDPA ( 113) WEDVPGTDIYSCGNYRDHSLFSAKEWAKKILDDGIS 1 LUXS1_LACDB ( 113) WEDVPGTTIESCGNYRDHSLFSAQEWCNDILKKGIS 1 LUXS_BIFAA ( 117) WDDVPATTIESCGNYRDHSLFTAKEWCKDILAKGIS 1 LUXS_CAMJR ( 117) QSKIPELNIYQCGTCAMHSLDEAKQIAQKVLNLGIS 1 LUXS_SHEPA ( 117) QADIPELNEYQCGTYEMHSLEQAQEIARNIIAAGIN 1 LUXS_VIBFM ( 117) QNKIPELNEYQCGTYEMHSLDEAKAIATTVLASGIS 1 LUXS_ARCB4 ( 117) QSDIPELNLYQCGTCAMHSLDEAKDIARDILKSQIG 1 LUXS_PORGI ( 113) EGEVPGTEPRDCGNCLLHNLPMAKYEAEKYLREVLD 1 LUXS_CLOAB ( 113) KGEVPGAAARDCGNYLDMNLPMANYWGKKFSALLDN 1 LUXS_DESAD ( 113) EGDVPGASAVECGNYTLMDLSLAKTEAAKYYAEVLD 1 LUXS_BACSU ( 115) ITEIPAANEKQCGQAKLHDLEGAKRLMRFWLSQDKE 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 36 n= 1401 bayes= 8.52232 E= 2.5e-108 -1010 -1010 -1010 127 -1010 -1010 -1010 51 63 -1010 -1010 -1010 -1010 419 -1010 -1010 -1010 -1010 486 -1010 39 -1010 33 127 -1010 210 -1010 -1010 -1010 -1010 -1010 105 -1010 -1010 -1010 169 58 -1010 -1010 -1010 -1010 -1010 291 186 -1010 -1010 -1010 -1010 163 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 283 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 310 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 443 -1010 -1010 -1010 -1010 -1010 -1010 -1010 139 -1010 -1010 227 -1010 283 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 198 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 197 -1010 -1010 -1010 -1010 -1010 -1010 258 -1010 -1010 -1010 39 -1010 33 27 -1010 -1010 -1010 -1010 -1010 -1010 -1010 338 -1010 -1010 -1010 69 158 -1010 -1010 -1010 139 -1010 -1010 186 -1010 -1010 -1010 251 -1010 -2 -1010 -1010 97 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 127 -1010 -1010 -1010 -1010 63 -1010 -1010 -1010 -1010 -1010 205 -1010 -1010 51 -1010 390 -1010 -1010 132 27 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 451 -1010 227 -1010 -1010 -1010 -1010 -1010 565 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 397 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 364 -1010 219 -1010 -1010 258 -1010 -1010 -1010 39 377 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 438 139 -1010 -1010 127 -1010 -1010 -1010 -1010 63 97 -1010 -1010 -1010 -1010 264 -1010 58 -1010 -1010 -1010 -1010 -1010 232 -1010 -1010 -1010 -1010 -1010 -1010 156 338 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 457 -1010 -1010 -1010 238 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 132 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 205 -1010 -1010 -1010 349 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 343 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 191 127 275 -1010 -1010 -1010 -1010 -1010 -1010 -1010 197 -1010 -1010 69 -1010 -1010 -1010 -1010 -1010 -1010 -1010 186 -1010 51 -1010 -1010 -1010 -2 238 -1010 -1010 219 -1010 169 58 -1010 -1010 -1010 385 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 363 -1010 -1010 105 -1010 319 -1010 -1010 -1010 -1010 -1010 -1010 39 -1010 33 227 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 219 105 -1010 58 -1010 -1010 258 -1010 -1010 -1010 127 -1010 -1010 -1010 251 -1010 -2 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 527 -1010 320 319 -1010 -1010 -1010 51 -1010 -1010 -1010 -1010 138 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 39 -1010 -1010 27 -1010 -1010 -1010 -1010 222 -1010 -1010 105 -1010 219 264 -1010 58 -1010 -1010 -1010 -1010 -1010 191 -1010 117 -1010 -1010 -1010 295 -1010 -1010 105 -1010 -1010 -1010 -1010 58 -1010 -1010 -1010 -1010 -1010 -1010 -1010 117 -1010 -1010 283 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 151 327 258 -1010 -1010 -1010 -1010 -1010 -1010 -1010 51 -1010 297 -1010 -1010 -1010 -1010 -1010 69 -1010 -1010 -1010 158 271 -1010 33 -1010 -1010 -1010 -1010 -1010 163 -1010 -1010 105 -1010 -1010 105 69 -1010 -1010 -1010 -1010 39 -1010 33 127 -1010 -1010 -1010 -1010 163 97 -1010 -1010 -1010 219 -1010 169 -1010 -1010 -1010 -1010 -1010 -1010 33 -1010 -1010 310 -1010 -1010 -1010 -2 -1010 -1010 -1010 219 -1010 -1010 -1010 151 -1010 -1010 -1010 -1010 33 -1010 -1010 -1010 -1010 332 63 97 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 -1010 132 27 -1010 51 -1010 -1010 -1010 -1010 -1010 205 -1010 -1010 -1010 301 -1010 -1010 -1010 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 36 nsites= 11 E= 2.5e-108 0.000000 0.000000 0.000000 0.181818 0.000000 0.000000 0.000000 0.090909 0.090909 0.000000 0.000000 0.000000 0.000000 0.363636 0.000000 0.000000 0.000000 0.000000 0.272727 0.000000 0.090909 0.000000 0.090909 0.181818 0.000000 0.272727 0.000000 0.000000 0.000000 0.000000 0.000000 0.090909 0.000000 0.000000 0.000000 0.181818 0.090909 0.000000 0.000000 0.000000 0.000000 0.000000 0.545455 0.272727 0.000000 0.000000 0.000000 0.000000 0.181818 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 0.454545 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.545455 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.181818 0.000000 0.000000 0.363636 0.000000 0.454545 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 0.272727 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.363636 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.363636 0.000000 0.000000 0.000000 0.090909 0.000000 0.090909 0.090909 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.454545 0.000000 0.000000 0.000000 0.090909 0.181818 0.000000 0.000000 0.000000 0.181818 0.000000 0.000000 0.272727 0.000000 0.000000 0.000000 0.363636 0.000000 0.090909 0.000000 0.000000 0.090909 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.181818 0.000000 0.000000 0.000000 0.000000 0.090909 0.000000 0.000000 0.000000 0.000000 0.000000 0.181818 0.000000 0.000000 0.090909 0.000000 0.454545 0.000000 0.000000 0.181818 0.090909 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.454545 0.000000 0.272727 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 0.000000 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 0.000000 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 0.545455 0.000000 0.090909 0.000000 0.000000 0.363636 0.000000 0.000000 0.000000 0.090909 0.272727 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 0.636364 0.181818 0.000000 0.000000 0.181818 0.000000 0.000000 0.000000 0.000000 0.090909 0.181818 0.000000 0.000000 0.000000 0.000000 0.272727 0.000000 0.090909 0.000000 0.000000 0.000000 0.000000 0.000000 0.363636 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.272727 0.363636 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 0.818182 0.000000 0.000000 0.000000 0.181818 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.181818 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.181818 0.000000 0.000000 0.000000 0.636364 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 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 0.272727 0.181818 0.272727 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.181818 0.000000 0.000000 0.090909 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.272727 0.000000 0.090909 0.000000 0.000000 0.000000 0.090909 0.181818 0.000000 0.000000 0.090909 0.000000 0.181818 0.090909 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 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.727273 0.000000 0.000000 0.090909 0.000000 0.181818 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.090909 0.000000 0.090909 0.363636 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.090909 0.090909 0.000000 0.090909 0.000000 0.000000 0.181818 0.000000 0.000000 0.000000 0.181818 0.000000 0.000000 0.000000 0.363636 0.000000 0.090909 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.363636 0.000000 0.636364 0.181818 0.000000 0.000000 0.000000 0.090909 0.000000 0.000000 0.000000 0.000000 0.090909 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.090909 0.000000 0.000000 0.090909 0.000000 0.000000 0.000000 0.000000 0.272727 0.000000 0.000000 0.090909 0.000000 0.090909 0.272727 0.000000 0.090909 0.000000 0.000000 0.000000 0.000000 0.000000 0.272727 0.000000 0.090909 0.000000 0.000000 0.000000 0.454545 0.000000 0.000000 0.090909 0.000000 0.000000 0.000000 0.000000 0.090909 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.090909 0.000000 0.000000 0.454545 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.181818 0.090909 0.181818 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.090909 0.000000 0.727273 0.000000 0.000000 0.000000 0.000000 0.000000 0.090909 0.000000 0.000000 0.000000 0.090909 0.454545 0.000000 0.090909 0.000000 0.000000 0.000000 0.000000 0.000000 0.181818 0.000000 0.000000 0.090909 0.000000 0.000000 0.090909 0.090909 0.000000 0.000000 0.000000 0.000000 0.090909 0.000000 0.090909 0.181818 0.000000 0.000000 0.000000 0.000000 0.181818 0.181818 0.000000 0.000000 0.000000 0.090909 0.000000 0.181818 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.090909 0.000000 0.000000 0.545455 0.000000 0.000000 0.000000 0.090909 0.000000 0.000000 0.000000 0.090909 0.000000 0.000000 0.000000 0.181818 0.000000 0.000000 0.000000 0.000000 0.090909 0.000000 0.000000 0.000000 0.000000 0.636364 0.090909 0.181818 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.181818 0.090909 0.000000 0.090909 0.000000 0.000000 0.000000 0.000000 0.000000 0.181818 0.000000 0.000000 0.000000 0.454545 0.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [QW]G[DE][VI]P[GE][LTA]N[IE]Y[QS]CG[NT][YC]R[DML]HSL[DF]EAKE[IW]A[KR][KD]ILAxGIS -------------------------------------------------------------------------------- Time 4.03 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- LUXS_BACSU 7.70e-78 4_[1(1.08e-37)]_31_[2(2.60e-26)]_9_[3(8.38e-26)]_7 LUXS_CLOAB 3.52e-47 73_[2(3.88e-27)]_10_[3(3.26e-27)]_10 LUXS_DESAD 3.26e-44 73_[2(3.08e-26)]_10_[3(2.12e-26)]_11 LUXS_PORGI 1.58e-44 73_[2(1.56e-24)]_10_[3(4.54e-28)]_11 LUXS_BIFAA 4.04e-92 8_[1(1.35e-40)]_26_[2(6.73e-29)]_12_[3(8.91e-35)]_9 LUXS_PEDPA 2.37e-96 4_[1(1.28e-42)]_26_[2(7.21e-30)]_12_[3(5.23e-36)]_9 LUXS1_LACDB 6.14e-96 4_[1(6.28e-43)]_26_[2(5.31e-30)]_12_[3(3.58e-35)]_11 LUXS_SHEPA 1.93e-96 4_[1(7.81e-44)]_30_[2(8.03e-32)]_12_[3(4.71e-33)]_17 LUXS_VIBFM 1.76e-95 4_[1(3.38e-43)]_30_[2(6.58e-32)]_12_[3(1.15e-32)]_20 LUXS_CAMJR 1.92e-99 4_[1(5.92e-45)]_30_[2(2.91e-32)]_12_[3(1.81e-34)]_12 LUXS_ARCB4 6.55e-98 4_[1(1.79e-45)]_30_[2(2.91e-32)]_12_[3(1.79e-32)]_19 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: kodomo-count ********************************************************************************