******************************************************************************** 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= memeout/meme.fasta ALPHABET= ACDEFGHIKLMNPQRSTVWY Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ Bacillus_subtilis 1.0000 222 Helicobacter_pylori 1.0000 223 Haemophilus_parainfluenz 1.0000 225 Oceanimonas 1.0000 204 Desulfovibrio_africanus 1.0000 213 Geobacter 1.0000 484 Taylorella_asinigenitali 1.0000 213 Oxalobacter_formigenes 1.0000 203 Cyanobacterium 1.0000 338 Cyanothece 1.0000 339 Dysgonomonas_gadei 1.0000 212 Pelodictyon_phaeoclathra 1.0000 207 Chloroflexus_aggregans 1.0000 221 Rubrobacter_xylanophilus 1.0000 208 Treponema 1.0000 216 Fusobacterium_mortiferum 1.0000 210 Sulfurihydrogenibium_yel 1.0000 204 Aminobacterium_colombien 1.0000 207 Akkermansia_muciniphila 1.0000 204 Fibrobacter_succinogenes 1.0000 210 Saccharomyces_cerevisiae 1.0000 540 Clavispora_lusitaniae 1.0000 505 Aspergillus_terreus 1.0000 518 Coccidioides_immitis 1.0000 587 Sordaria_macrospora 1.0000 523 Cryptococcus_gattii 1.0000 537 Cucumis_sativus 1.0000 384 Arabidopsis_thaliana 1.0000 522 Physcomitrella_patens 1.0000 510 Volvox_carteri 1.0000 1251 Thalassiosira_pseudonana 1.0000 323 Phaeodactylum_tricornutu 1.0000 580 Perkinsus_marinus 1.0000 297 Xenopus(Silurana) 1.0000 321 Trichoplax_adhaerens 1.0000 214 Naegleria_gruberi 1.0000 497 Acanthamoeba_castellanii 1.0000 463 Candida_tropicalis 1.0000 482 Lodderomyces_elongisporu 1.0000 553 Selaginella_moellendorff 1.0000 527 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme memeout/meme.fasta -mod zoops -nmotifs 3 -prior dirichlet -nostatus -protein -oc memeout/ 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= 40 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= 14897 N= 40 sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.114 C 0.016 D 0.058 E 0.054 F 0.026 G 0.085 H 0.020 I 0.067 K 0.052 L 0.095 M 0.020 N 0.035 P 0.042 Q 0.036 R 0.049 S 0.061 T 0.055 V 0.085 W 0.006 Y 0.024 Background letter frequencies (from dataset with add-one prior applied): A 0.114 C 0.016 D 0.058 E 0.054 F 0.026 G 0.085 H 0.020 I 0.067 K 0.052 L 0.095 M 0.020 N 0.035 P 0.042 Q 0.036 R 0.049 S 0.061 T 0.055 V 0.085 W 0.006 Y 0.024 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 33 sites = 35 llr = 2229 E-value = 3.0e-598 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::11:2::::::::::9:71:91:::::::::1 pos.-specific C 6:::::::::::::::1::1::::::::::::: probability D :11:1:::::1a1:8:::::4:7::::::3a:1 matrix E ::1:::::::::::1:::1:1:1::::::2::: F :::::::4::::::::::::::::::::::::: G ::::5:::::::::::::::3::a:::a::::: H :2:21::::::::::::::::::::a::::::: I :::::1::77:::2:3:::2::::2:2::::1: K :23::::::::::::::11:1::::::::1::: L 1:::::152::::2:3:811::::::4::::1: M :::::::::::::::::1:::::::::::::5: N ::::2:::::9:1:::::::1:::::::::::1 P ::1:::8:::::::::::::::::::::::::6 Q :11:::::::::::::::::::::::::91::: R :321::::::::7:::::::::::::::::::: S ::1::::::::::::::::1:::::::::2::1 T 31:1:::::::::::::::::1:::::::1::: V :::::6:1:3:::6:5:1:3::::8:5::::1: W ::::::::::::::::::::::::::::::::: Y :::5::::::::::::::::::::::::::::: bits 7.4 6.7 6.0 * 5.2 * Relative 4.5 * * * Entropy 3.7 * ** * * ** * (91.9 bits) 3.0 * * ** **** * * ***** ** * 2.2 * **************** ******** *** 1.5 ********************************* 0.7 ********************************* 0.0 --------------------------------- Multilevel CRKYGVPLIINDRVDVALAVDADGVHVGQDDMP consensus TK NA FLV I L IG L S sequence I E -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------------------- Saccharomyces_cerevisiae 65 1.73e-36 VAEALEVQKI CKKYNVPLIINDRIDVAMAIDADGVHVGQDDMP IPMVRKLLGP Volvox_carteri 1096 1.82e-35 AREAAAALKV CRQYGVPLIINDRVDVALAVGADGVHVGQSDLP TAVVRALIGP Clavispora_lusitaniae 63 1.06e-34 IDRAKDVLKI TRPRGVPLIINDRVDVALAVDADGVHVGQDDMP ARIVRQLIGP Arabidopsis_thaliana 367 4.98e-33 LEEAKACIDI CRSHGVSLLINDRIDIALACDADGVHVGQSDMP VDLVRSLLGP Cucumis_sativus 231 6.89e-33 LEVAKSCIKI CHAHGVPLLINDRIDIALACNADGVHVGQSDIP AHEVRRLLGP Chloroflexus_aggregans 63 8.10e-33 VAEAQVLREL TRRTGVPLIVNDRLDVALAVDADGVHLGQDDMP AALARRLIGP Lodderomyces_elongisporu 64 1.53e-32 IKRAQQVHAL TKPRGIPLIINDRVDVALAIDAEGVHVGQDDMP ATSVRELIGP Acanthamoeba_castellanii 25 7.01e-32 IEQASRIKSV THRHGVPLIINDRLDVALAVGADGIHVGQDDMA ATTARALLKQ Fibrobacter_succinogenes 60 1.09e-31 MELAAAAHEV TKRYNIPLIIDDRVDVALAIGAEGVHVGQTDMP VKIARQLMGA Cyanothece 191 1.09e-31 LEMAQKLCEL CHQYDALFIVNDRVDIALAVNADGVHLGQQDIP IALARRILGP Pelodictyon_phaeoclathra 56 2.59e-31 FSWAVEISKR CHQYHALCIINDRVDIALASSADGVHLGQQDMP ASTARKLLGK Oceanimonas 57 2.59e-31 IERAEAVKAV LQGTGVPLIINDRVDVALAVDADGVHLGQSDMP ATHARRLLGP Aspergillus_terreus 61 4.53e-31 IHTAKKLHQI TTKYGVPLLINDRVDVALAVGAEGVHLGQDDMT IEEAKRLLPK Selaginella_moellendorff 365 6.86e-31 IKIAEASLAI GRKYGVPVLINDRVDVAVACNADGVHLGQTDMP VRLARSILGP Naegleria_gruberi 48 1.03e-30 LEQAKSLQKI CRRHGVPFLIDDRVDLAVAIDADGVHVGQKDLP PQYVRKLIGN Treponema 67 1.54e-30 EKEALELQAL CKKYKVPFIVNDNVELAKKIDADGVHVGQEDMN ACKVRELLGP Sordaria_macrospora 64 2.29e-30 IAMGKKLHAI TKKYNVPLLINDRIDVALAVGCEGVHIGQDDME LSTARRLLGP Aminobacterium_colombien 61 5.66e-30 LETALAMKRL CYDYNVPLIINDRLDVALAAQADGVHLGQKDLP LEAVRPFLPR Haemophilus_parainfluenz 73 6.42e-30 RALAIKCRDL CRQYNVPFIVDDNVDLALEIEADGIHVGQSDTP VKTIRARTHK Dysgonomonas_gadei 60 7.29e-30 YNLAMKLKSI LKSYNVPLIINDRLDIALACDAGGLHIGQSDMP YSVARKLLGK Cyanobacterium 191 8.26e-30 IKVARKLCEL CHQYDALFIMNDRVDIALAINADGVHIGQEDIS IKIAREIIGP Fusobacterium_mortiferum 63 1.06e-29 VKEAREIREL CRKNGVIFIVNDNVDIALLVDADGVHIGQEDMH PDDVRKLIGD Coccidioides_immitis 102 2.81e-29 IETASRLHTI TKAHGVPLVINDRVDVALAVGAEGVHLGQDDMG MAPNASQHYT Physcomitrella_patens 347 4.52e-29 LQEAETSLKV ARDYGIPLLINDRIDIAIACDADGVHLGQSDLP VARARAILGP Desulfovibrio_africanus 61 1.02e-28 LERAWRIKPI CDAAGAPFIINDRVDVALAVGAAGVHLGRQDMP YADARRLLGP Helicobacter_pylori 78 2.00e-28 KQLALECQKL CQKYGAPFIVNDEVQLALELKADGVHVGQEDMA IEEVMTLCKK Cryptococcus_gattii 63 8.16e-28 IEVARRTKAI CDKYNVPVLINDRIDVHLAVGTAGIHVGQTDCP IGLARSLVGP Perkinsus_marinus 35 1.19e-26 YVKLAKETKK LMPRHVPLIIDDRVDVCMASGADGVHVGDTDMS VKDARSIIGP Oxalobacter_formigenes 55 2.27e-26 LEQARALRDL CRRYEKPFIINDYVDLCLELDTDGIHVGGMDVP VKKVRAAVGP Bacillus_subtilis 69 3.90e-26 IKFAEKAQAA CREAGVPFIVNDDVELALNLKADGIHIGQEDAN AKEVRAAIGD Akkermansia_muciniphila 60 5.08e-26 YREALPIRDF LASRGIPFIVNNRIDLALALEADGVHIGQRDLP VPSVRAMIGP Geobacter 67 8.54e-26 LELGQELKHL CTEFQVEFIVNDDVELALALDADGVHLGQDDGD PAAAREALGP Sulfurihydrogenibium_yel 57 1.10e-25 LPISKDLKKL CHKYDALFIVNDRLELTLKSDADGIHVGEEDVD ISEIRKALKD Rubrobacter_xylanophilus 60 2.18e-24 LPLARRLREV CLRHGALFTVNDDIELARLSGAHGVHLGQEDEP VARAREVLGP Trichoplax_adhaerens 61 7.41e-23 LKIAYQCKEI TSTYSIPLFINDNLAIAKKALADGVHLGQSDIL LNNAREFLGN -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Saccharomyces_cerevisiae 1.7e-36 64_[1]_443 Volvox_carteri 1.8e-35 1095_[1]_123 Clavispora_lusitaniae 1.1e-34 62_[1]_410 Arabidopsis_thaliana 5e-33 366_[1]_123 Cucumis_sativus 6.9e-33 230_[1]_121 Chloroflexus_aggregans 8.1e-33 62_[1]_126 Lodderomyces_elongisporu 1.5e-32 63_[1]_457 Acanthamoeba_castellanii 7e-32 24_[1]_406 Fibrobacter_succinogenes 1.1e-31 59_[1]_118 Cyanothece 1.1e-31 190_[1]_116 Pelodictyon_phaeoclathra 2.6e-31 55_[1]_119 Oceanimonas 2.6e-31 56_[1]_115 Aspergillus_terreus 4.5e-31 60_[1]_425 Selaginella_moellendorff 6.9e-31 364_[1]_130 Naegleria_gruberi 1e-30 47_[1]_417 Treponema 1.5e-30 66_[1]_117 Sordaria_macrospora 2.3e-30 63_[1]_427 Aminobacterium_colombien 5.7e-30 60_[1]_114 Haemophilus_parainfluenz 6.4e-30 72_[1]_120 Dysgonomonas_gadei 7.3e-30 59_[1]_120 Cyanobacterium 8.3e-30 190_[1]_115 Fusobacterium_mortiferum 1.1e-29 62_[1]_115 Coccidioides_immitis 2.8e-29 101_[1]_453 Physcomitrella_patens 4.5e-29 346_[1]_131 Desulfovibrio_africanus 1e-28 60_[1]_120 Helicobacter_pylori 2e-28 77_[1]_113 Cryptococcus_gattii 8.2e-28 62_[1]_442 Perkinsus_marinus 1.2e-26 34_[1]_230 Oxalobacter_formigenes 2.3e-26 54_[1]_116 Bacillus_subtilis 3.9e-26 68_[1]_121 Akkermansia_muciniphila 5.1e-26 59_[1]_112 Geobacter 8.5e-26 66_[1]_385 Sulfurihydrogenibium_yel 1.1e-25 56_[1]_115 Rubrobacter_xylanophilus 2.2e-24 59_[1]_116 Trichoplax_adhaerens 7.4e-23 60_[1]_121 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=33 seqs=35 Saccharomyces_cerevisiae ( 65) CKKYNVPLIINDRIDVAMAIDADGVHVGQDDMP 1 Volvox_carteri ( 1096) CRQYGVPLIINDRVDVALAVGADGVHVGQSDLP 1 Clavispora_lusitaniae ( 63) TRPRGVPLIINDRVDVALAVDADGVHVGQDDMP 1 Arabidopsis_thaliana ( 367) CRSHGVSLLINDRIDIALACDADGVHVGQSDMP 1 Cucumis_sativus ( 231) CHAHGVPLLINDRIDIALACNADGVHVGQSDIP 1 Chloroflexus_aggregans ( 63) TRRTGVPLIVNDRLDVALAVDADGVHLGQDDMP 1 Lodderomyces_elongisporu ( 64) TKPRGIPLIINDRVDVALAIDAEGVHVGQDDMP 1 Acanthamoeba_castellanii ( 25) THRHGVPLIINDRLDVALAVGADGIHVGQDDMA 1 Fibrobacter_succinogenes ( 60) TKRYNIPLIIDDRVDVALAIGAEGVHVGQTDMP 1 Cyanothece ( 191) CHQYDALFIVNDRVDIALAVNADGVHLGQQDIP 1 Pelodictyon_phaeoclathra ( 56) CHQYHALCIINDRVDIALASSADGVHLGQQDMP 1 Oceanimonas ( 57) LQGTGVPLIINDRVDVALAVDADGVHLGQSDMP 1 Aspergillus_terreus ( 61) TTKYGVPLLINDRVDVALAVGAEGVHLGQDDMT 1 Selaginella_moellendorff ( 365) GRKYGVPVLINDRVDVAVACNADGVHLGQTDMP 1 Naegleria_gruberi ( 48) CRRHGVPFLIDDRVDLAVAIDADGVHVGQKDLP 1 Treponema ( 67) CKKYKVPFIVNDNVELAKKIDADGVHVGQEDMN 1 Sordaria_macrospora ( 64) TKKYNVPLLINDRIDVALAVGCEGVHIGQDDME 1 Aminobacterium_colombien ( 61) CYDYNVPLIINDRLDVALAAQADGVHLGQKDLP 1 Haemophilus_parainfluenz ( 73) CRQYNVPFIVDDNVDLALEIEADGIHVGQSDTP 1 Dysgonomonas_gadei ( 60) LKSYNVPLIINDRLDIALACDAGGLHIGQSDMP 1 Cyanobacterium ( 191) CHQYDALFIMNDRVDIALAINADGVHIGQEDIS 1 Fusobacterium_mortiferum ( 63) CRKNGVIFIVNDNVDIALLVDADGVHIGQEDMH 1 Coccidioides_immitis ( 102) TKAHGVPLVINDRVDVALAVGAEGVHLGQDDMG 1 Physcomitrella_patens ( 347) ARDYGIPLLINDRIDIAIACDADGVHLGQSDLP 1 Desulfovibrio_africanus ( 61) CDAAGAPFIINDRVDVALAVGAAGVHLGRQDMP 1 Helicobacter_pylori ( 78) CQKYGAPFIVNDEVQLALELKADGVHVGQEDMA 1 Cryptococcus_gattii ( 63) CDKYNVPVLINDRIDVHLAVGTAGIHVGQTDCP 1 Perkinsus_marinus ( 35) LMPRHVPLIIDDRVDVCMASGADGVHVGDTDMS 1 Oxalobacter_formigenes ( 55) CRRYEKPFIINDYVDLCLELDTDGIHVGGMDVP 1 Bacillus_subtilis ( 69) CREAGVPFIVNDDVELALNLKADGIHIGQEDAN 1 Akkermansia_muciniphila ( 60) LASRGIPFIVNNRIDLALALEADGVHIGQRDLP 1 Geobacter ( 67) CTEFQVEFIVNDDVELALALDADGVHLGQDDGD 1 Sulfurihydrogenibium_yel ( 57) CHKYDALFIVNDRLELTLKSDADGIHVGEEDVD 1 Rubrobacter_xylanophilus ( 60) CLRHGALFTVNDDIELARLSGAHGVHLGQEDEP 1 Trichoplax_adhaerens ( 61) TSTYSIPLFINDNLAIAKKALADGVHLGQSDIL 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 33 n= 13617 bayes= 8.70286 E= 3.0e-598 -199 515 -1177 -1177 -1177 -158 -1177 -1177 -1177 27 -1177 -1177 -1177 -1177 -1177 -1177 222 -1177 -1177 -1177 -199 -1177 -1 -1177 -1177 -1177 307 -1177 194 -173 49 -1177 -1177 66 268 -109 5 -1177 -1177 24 -41 -1177 -1 9 -1177 -158 -1177 -1177 230 -1177 -1177 -1177 102 198 181 49 -95 -1177 -1177 -1177 -99 -1177 -1177 -1177 16 -1177 307 -1177 -1177 -1177 -1177 -28 -1177 -1177 122 -1177 5 -1177 -1177 448 -1177 -1177 58 -91 -1177 267 148 -1177 -87 -1177 -1177 252 -1177 -34 -1177 -109 -1177 -1177 -1177 -1177 81 -1177 -1177 -1177 -1177 -1177 -1177 110 -87 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 289 -1177 -1177 -1177 -1177 -1177 -91 -1177 -1177 -1177 -122 -1177 59 -1177 -1177 419 -1177 -1177 -109 -1177 -1177 -1177 -1177 -1177 83 -1177 -1177 396 -1177 -1177 -1177 -1177 244 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -57 -1177 -1177 -1177 -1177 -1177 -1177 16 -1177 -1177 336 -1177 127 -1177 -1177 -1177 -1177 -1177 -1177 -95 -157 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 330 -1177 -1177 49 -1177 -1177 -1177 -1177 -1177 -1177 189 -1177 -1177 -1177 -1177 99 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 467 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 408 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -28 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 58 -91 -1177 -1177 -1177 -1177 -1177 -1177 -1177 172 -1177 -1177 392 -1177 -1177 -1177 -1177 24 -1177 -1177 -1177 -1177 -1177 -1177 -1177 178 -1177 85 -1177 -1177 -1177 -1177 -1177 -1177 -1177 282 -1177 -1177 -199 -1177 380 141 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -34 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 195 -1177 159 -1177 -1177 -1177 -1177 -1177 -1177 -1177 243 -1177 -1177 296 183 -1177 -1177 -1177 -1177 48 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -95 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -122 13 302 149 -1177 -1177 -1177 -78 -1177 -1177 -57 -1177 -1177 271 -1177 -1177 67 -1177 -1177 -1177 -1177 71 -73 -1177 -28 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -99 315 -1177 -1177 -1177 -1177 -1177 159 -1177 59 -1177 -1177 -1177 -1177 -1177 91 -1177 202 -1177 -1177 -1177 -1177 280 9 -1177 174 -1177 -1177 13 -173 -1177 172 -1177 -34 -1177 -109 -1177 -1177 -1177 -1177 301 83 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 5 -1177 -1177 -1177 -99 -1177 369 141 -1177 -158 48 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 355 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 136 -1177 -173 -1177 -1177 -1177 -1177 -1177 -1177 -1177 324 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 561 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 136 -1177 197 -1177 -1177 -1177 -1177 -1177 -1177 -1177 243 -1177 -1177 -1177 -1177 -1177 -1177 -1177 355 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -101 -91 -1177 -158 -1177 -1177 -1177 -1177 -1177 -1177 -1177 461 -78 -1177 -1177 -1177 -1177 -1177 -1177 -1177 216 189 -1177 -1177 -1177 -1177 13 -1177 49 -1177 -1177 124 -78 191 105 -1177 -1177 -1177 -1177 -1177 412 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -1177 -199 83 -1177 -91 -1177 -158 -1177 78 -1177 59 474 -1177 -1177 -1177 -1177 -1177 -95 -57 -1177 -1177 -99 -1177 -1 -91 -1177 -158 48 -1177 -1177 -173 -1177 72 390 -1177 -1177 -9 -95 -1177 -1177 -1177 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 33 nsites= 35 E= 3.0e-598 0.028571 0.571429 0.000000 0.000000 0.000000 0.028571 0.000000 0.000000 0.000000 0.114286 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.257143 0.000000 0.000000 0.000000 0.028571 0.000000 0.057143 0.000000 0.000000 0.000000 0.171429 0.000000 0.200000 0.028571 0.028571 0.000000 0.000000 0.057143 0.314286 0.028571 0.057143 0.000000 0.000000 0.028571 0.085714 0.000000 0.057143 0.057143 0.000000 0.028571 0.000000 0.000000 0.257143 0.000000 0.000000 0.000000 0.085714 0.142857 0.171429 0.085714 0.028571 0.000000 0.000000 0.000000 0.057143 0.000000 0.000000 0.000000 0.028571 0.000000 0.171429 0.000000 0.000000 0.000000 0.000000 0.028571 0.000000 0.000000 0.114286 0.000000 0.057143 0.000000 0.000000 0.542857 0.000000 0.000000 0.085714 0.028571 0.000000 0.542857 0.057143 0.000000 0.028571 0.000000 0.000000 0.200000 0.000000 0.028571 0.000000 0.028571 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.142857 0.028571 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.628571 0.000000 0.000000 0.000000 0.000000 0.000000 0.028571 0.000000 0.000000 0.000000 0.028571 0.000000 0.142857 0.000000 0.000000 0.771429 0.000000 0.000000 0.028571 0.000000 0.000000 0.000000 0.000000 0.000000 0.028571 0.000000 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 0.514286 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.057143 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.028571 0.000000 0.000000 0.685714 0.000000 0.228571 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.028571 0.028571 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.657143 0.000000 0.000000 0.028571 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.314286 0.000000 0.000000 0.000000 0.000000 0.114286 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.885714 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.971429 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.028571 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.085714 0.028571 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.114286 0.000000 0.000000 0.742857 0.000000 0.000000 0.000000 0.000000 0.028571 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.228571 0.000000 0.171429 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.028571 0.000000 0.800000 0.142857 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.028571 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.257143 0.000000 0.285714 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.457143 0.000000 0.000000 0.885714 0.057143 0.000000 0.000000 0.000000 0.000000 0.028571 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.028571 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.028571 0.057143 0.771429 0.057143 0.000000 0.000000 0.000000 0.028571 0.000000 0.000000 0.057143 0.000000 0.000000 0.742857 0.000000 0.000000 0.085714 0.000000 0.000000 0.000000 0.000000 0.085714 0.057143 0.000000 0.028571 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.057143 0.142857 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.142857 0.000000 0.000000 0.000000 0.000000 0.000000 0.114286 0.000000 0.342857 0.000000 0.000000 0.000000 0.000000 0.400000 0.057143 0.000000 0.285714 0.000000 0.000000 0.057143 0.028571 0.000000 0.114286 0.000000 0.028571 0.000000 0.028571 0.000000 0.000000 0.000000 0.000000 0.914286 0.028571 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.057143 0.000000 0.000000 0.000000 0.057143 0.000000 0.742857 0.142857 0.000000 0.028571 0.028571 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 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 0.171429 0.000000 0.028571 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.800000 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 0.171429 0.000000 0.371429 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.457143 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 0.028571 0.028571 0.000000 0.028571 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.885714 0.028571 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.257143 0.200000 0.000000 0.000000 0.000000 0.000000 0.057143 0.000000 0.028571 0.000000 0.000000 0.085714 0.028571 0.228571 0.114286 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 0.028571 0.028571 0.000000 0.028571 0.000000 0.028571 0.000000 0.114286 0.000000 0.142857 0.542857 0.000000 0.000000 0.000000 0.000000 0.000000 0.028571 0.057143 0.000000 0.000000 0.057143 0.000000 0.057143 0.028571 0.000000 0.028571 0.028571 0.000000 0.000000 0.028571 0.000000 0.057143 0.628571 0.000000 0.000000 0.057143 0.028571 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CT][RK]KY[GN][VA]P[LF][IL][IV]NDR[VI]D[VLI]ALA[VI][DG]ADGVH[VL]GQ[DSE]DMP -------------------------------------------------------------------------------- Time 19.32 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 21 sites = 39 llr = 1311 E-value = 4.8e-290 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :11:7:::1::31:2::::1: pos.-specific C :::::::::1::::::::::: probability D 1:31:8::::::::::1::14 matrix E 221::::::::::::::::11 F :::::::1:1::15::::::: G :::6::::8:91::::1:::: H 1:::::::::::::::::::: I 11:::::4:2::3:::::::: K 1211::::::::::::::a31 L 111::::4:2::1::::::1: M ::::::::::::1:::::::: N :1::::::::::::::2:::2 P :1::1::::::3::7:3::2: Q 111:::::::::::::1:::: R :1:1::::::::::::1:::: S ::1::1::1111:::113::: T :::::::::1:2:::917:21 V 1:112::2:3::5::::::11 W 1:::::::::::::::::::: Y 1:::::a::::::5::::::: bits 7.4 6.7 6.0 5.2 * Relative 4.5 * * Entropy 3.7 * * * * (48.5 bits) 3.0 ** * *** ** 2.2 ***** * *** ** 1.5 ************* **** 0.7 ********************* 0.0 --------------------- Multilevel ExDGADYIGVGAVFPTPTKKD consensus L L PIYA S PN sequence V -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- Physcomitrella_patens 407 3.34e-21 CKTPEQAEKA WKDGADYVGSGGVYPTNTKKD NKTIGIEGLR Chloroflexus_aggregans 123 1.30e-20 ASTLAEALQA VQDGADYLGVGPIFATPTKPD AAPPIGIDGL Bacillus_subtilis 128 3.04e-20 AHTMSEVKQA EEDGADYVGLGPIYPTETKKD TRAVQGVSLI Arabidopsis_thaliana 427 4.58e-20 CKTPEQAHQA WKDGADYIGSGGVFPTNTKAN NRTIGLDGLK Cucumis_sativus 291 4.58e-20 CKTTEQAEQA WIDGADYIGCGGVYPTNTKAN NLTVGIDGLK Selaginella_moellendorff 425 1.23e-19 CKTVEQAVKA YEDGADYIGCGGVYPTTTKKK NKTIGLDGLR Rubrobacter_xylanophilus 120 1.23e-19 AGGVEEARRA VREGADYLGVGSVYPTPTKPD AEVRGLGLIR Cyanothece 251 1.51e-18 TTNPQEMEKA IAEKADYIGVGPVYATPTKPD KKAAGLDYVK Cyanobacterium 251 1.51e-18 TTNPLEMEKA IEEGADYIGVGPIYPTPNKPE KETIQSDYLD Sordaria_macrospora 124 6.41e-18 VSTIEEAMVA CKGGADYLGIGTVYATPTKTN TKNIIGAAGV Treponema 127 7.47e-18 AQTVEEAILA EKQGADYLGVGAVFPTGSKSD AIDVPHETLK Lodderomyces_elongisporu 125 8.70e-18 STPEEAQEVV DQDVADYVGLGTVYATNTKKD VTNPDGVGPI Fibrobacter_succinogenes 120 1.01e-17 TKTVPQALEA YEQGADYLGVGAIYPTTTKVV TILTSVDTLK Aspergillus_terreus 121 1.17e-17 ASSIDEAQKA IAAGADYLGIGTMFATPTKTN TKSIIGTAGT Cryptococcus_gattii 123 3.22e-17 VGNVNEAKRA IQQGADYVGIGAVWPTNSKDV TKKNMLGPDG Acanthamoeba_castellanii 91 4.88e-17 ATNEAQARAA ELAGADYLGTSAVFPTDTKKD GGAGYVIGLD Helicobacter_pylori 139 4.88e-17 NTLEQALKAR HLDGVAYLGVGPIFPTQSKKD KQVVGVELLK Pelodictyon_phaeoclathra 116 1.23e-16 ASSPDEARLA EQEGADYIGFGHIYPTASKVK EFSPVGVEAL Clavispora_lusitaniae 124 2.32e-16 GNEEETTEVC EQKVADYVGLGTLYPTQTKDV KNVCGPIGVR Taylorella_asinigenitali 123 2.32e-16 YNSIDMARDA VKNGASYIAFGAMYPSPTKPN AVKADTNLIK Perkinsus_marinus 96 2.97e-16 YGRQEDAIAA IRDGADYIATGAVYPTVTKPG AVAQGLGQID Saccharomyces_cerevisiae 128 2.97e-16 PSEVETLAKW GPDMVDYIGVGTLFPTSTKKN PKKSPMGPQG Fusobacterium_mortiferum 124 4.25e-16 HSEKQGMEAY KNPNVDYIGVGPIFPTTTKDT TPVGLGYLEY Coccidioides_immitis 179 5.39e-16 VSSVEEARIA VEKRANYLGIGTVFATPTKTN TKSIIGTAGV Geobacter 127 6.79e-16 THSLTEALEA QEAGADYVGFGALYPTDSKEV EHIQGPEKLA Desulfovibrio_africanus 121 9.56e-16 VHNMAELEEA KATDADYFGLGPAFPTRTKPD APAPWGMDEY Naegleria_gruberi 110 1.07e-15 TFDQVDEALS HNVRADYLGTNAIFPTLTKKD AGQAVGLDGL Haemophilus_parainfluenz 134 1.07e-15 NRLDEAKIGE ELSEIDYFGIGPIFPTQSKEN PKPTLGMAFI Aminobacterium_colombien 121 2.06e-15 AHTVDQARIA LKSGASYIGIGAAFPTGSKED AHVVGLSRIR Trichoplax_adhaerens 121 3.46e-15 VNNLSQLNNN QNIFADYISLGPIFYTNTKLD IEKPIGIEEI Dysgonomonas_gadei 120 4.69e-15 VESIQDAIDA NNLDVDYIGISPVFGTQTKTD TAPALGLEGI Oceanimonas 117 6.31e-15 VETEQQLFES ESLPVDYLGLSAIFATPTKTD LKRHWGIDGL Akkermansia_muciniphila 120 1.23e-14 VSNKEQLRAV DASLVDYLGMGPVFPTISKLN APPVLGVEGF Volvox_carteri 1156 1.36e-13 VKTPQQARDA AAAGADYLGAGAVLPTGTKDT DVIGLEGLGA Oxalobacter_formigenes 116 2.26e-13 YGDLELARKA TRDGASYVAFGGFYPSRVKKY PVTTPQNIVS Sulfurihydrogenibium_yel 117 4.45e-13 YGDVERAILM ERLSATYVAFGSFYFSPTKPK SKIVDKSVIT Xenopus(Silurana) 232 5.07e-13 THGYAEMLRA DIVAPSYIALGAVFPTTLKKM ATQPQGVARL Phaeodactylum_tricornutu 490 5.07e-13 THSYGELATA LGVKPSYISLGPVFATSSKTV QFDPQGLSLV Thalassiosira_pseudonana 215 6.14e-13 VESASKSYQL SPRGPDYLFVGTCYLTQSHPE KSSADQLEGP -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Physcomitrella_patens 3.3e-21 406_[2]_83 Chloroflexus_aggregans 1.3e-20 122_[2]_78 Bacillus_subtilis 3e-20 127_[2]_74 Arabidopsis_thaliana 4.6e-20 426_[2]_75 Cucumis_sativus 4.6e-20 290_[2]_73 Selaginella_moellendorff 1.2e-19 424_[2]_82 Rubrobacter_xylanophilus 1.2e-19 119_[2]_68 Cyanothece 1.5e-18 250_[2]_68 Cyanobacterium 1.5e-18 250_[2]_67 Sordaria_macrospora 6.4e-18 123_[2]_379 Treponema 7.5e-18 126_[2]_69 Lodderomyces_elongisporu 8.7e-18 124_[2]_408 Fibrobacter_succinogenes 1e-17 119_[2]_70 Aspergillus_terreus 1.2e-17 120_[2]_377 Cryptococcus_gattii 3.2e-17 122_[2]_394 Acanthamoeba_castellanii 4.9e-17 90_[2]_352 Helicobacter_pylori 4.9e-17 138_[2]_64 Pelodictyon_phaeoclathra 1.2e-16 115_[2]_71 Clavispora_lusitaniae 2.3e-16 123_[2]_361 Taylorella_asinigenitali 2.3e-16 122_[2]_70 Perkinsus_marinus 3e-16 95_[2]_181 Saccharomyces_cerevisiae 3e-16 127_[2]_392 Fusobacterium_mortiferum 4.3e-16 123_[2]_66 Coccidioides_immitis 5.4e-16 178_[2]_388 Geobacter 6.8e-16 126_[2]_337 Desulfovibrio_africanus 9.6e-16 120_[2]_72 Naegleria_gruberi 1.1e-15 109_[2]_367 Haemophilus_parainfluenz 1.1e-15 133_[2]_71 Aminobacterium_colombien 2.1e-15 120_[2]_66 Trichoplax_adhaerens 3.5e-15 120_[2]_73 Dysgonomonas_gadei 4.7e-15 119_[2]_72 Oceanimonas 6.3e-15 116_[2]_67 Akkermansia_muciniphila 1.2e-14 119_[2]_64 Volvox_carteri 1.4e-13 1155_[2]_75 Oxalobacter_formigenes 2.3e-13 115_[2]_67 Sulfurihydrogenibium_yel 4.4e-13 116_[2]_67 Xenopus(Silurana) 5.1e-13 231_[2]_69 Phaeodactylum_tricornutu 5.1e-13 489_[2]_70 Thalassiosira_pseudonana 6.1e-13 214_[2]_88 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=39 Physcomitrella_patens ( 407) WKDGADYVGSGGVYPTNTKKD 1 Chloroflexus_aggregans ( 123) VQDGADYLGVGPIFATPTKPD 1 Bacillus_subtilis ( 128) EEDGADYVGLGPIYPTETKKD 1 Arabidopsis_thaliana ( 427) WKDGADYIGSGGVFPTNTKAN 1 Cucumis_sativus ( 291) WIDGADYIGCGGVYPTNTKAN 1 Selaginella_moellendorff ( 425) YEDGADYIGCGGVYPTTTKKK 1 Rubrobacter_xylanophilus ( 120) VREGADYLGVGSVYPTPTKPD 1 Cyanothece ( 251) IAEKADYIGVGPVYATPTKPD 1 Cyanobacterium ( 251) IEEGADYIGVGPIYPTPNKPE 1 Sordaria_macrospora ( 124) CKGGADYLGIGTVYATPTKTN 1 Treponema ( 127) EKQGADYLGVGAVFPTGSKSD 1 Lodderomyces_elongisporu ( 125) DQDVADYVGLGTVYATNTKKD 1 Fibrobacter_succinogenes ( 120) YEQGADYLGVGAIYPTTTKVV 1 Aspergillus_terreus ( 121) IAAGADYLGIGTMFATPTKTN 1 Cryptococcus_gattii ( 123) IQQGADYVGIGAVWPTNSKDV 1 Acanthamoeba_castellanii ( 91) ELAGADYLGTSAVFPTDTKKD 1 Helicobacter_pylori ( 139) HLDGVAYLGVGPIFPTQSKKD 1 Pelodictyon_phaeoclathra ( 116) EQEGADYIGFGHIYPTASKVK 1 Clavispora_lusitaniae ( 124) EQKVADYVGLGTLYPTQTKDV 1 Taylorella_asinigenitali ( 123) VKNGASYIAFGAMYPSPTKPN 1 Perkinsus_marinus ( 96) IRDGADYIATGAVYPTVTKPG 1 Saccharomyces_cerevisiae ( 128) GPDMVDYIGVGTLFPTSTKKN 1 Fusobacterium_mortiferum ( 124) KNPNVDYIGVGPIFPTTTKDT 1 Coccidioides_immitis ( 179) VEKRANYLGIGTVFATPTKTN 1 Geobacter ( 127) QEAGADYVGFGALYPTDSKEV 1 Desulfovibrio_africanus ( 121) KATDADYFGLGPAFPTRTKPD 1 Naegleria_gruberi ( 110) HNVRADYLGTNAIFPTLTKKD 1 Haemophilus_parainfluenz ( 134) ELSEIDYFGIGPIFPTQSKEN 1 Aminobacterium_colombien ( 121) LKSGASYIGIGAAFPTGSKED 1 Trichoplax_adhaerens ( 121) QNIFADYISLGPIFYTNTKLD 1 Dysgonomonas_gadei ( 120) NNLDVDYIGISPVFGTQTKTD 1 Oceanimonas ( 117) ESLPVDYLGLSAIFATPTKTD 1 Akkermansia_muciniphila ( 120) DASLVDYLGMGPVFPTISKLN 1 Volvox_carteri ( 1156) AAAGADYLGAGAVLPTGTKDT 1 Oxalobacter_formigenes ( 116) TRDGASYVAFGGFYPSRVKKY 1 Sulfurihydrogenibium_yel ( 117) ERLSATYVAFGSFYFSPTKPK 1 Xenopus(Silurana) ( 232) DIVAPSYIALGAVFPTTLKKM 1 Phaeodactylum_tricornutu ( 490) LGVKPSYISLGPVFATSSKTV 1 Thalassiosira_pseudonana ( 215) SPRGPDYLFVGTCYLTQSHPE 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 21 n= 14097 bayes= 8.7179 E= 4.8e-290 -215 67 42 193 -1193 -173 133 95 -3 -89 -1193 -44 -1193 50 -1193 -125 -111 27 374 108 17 -1193 -1193 152 -1193 -173 -1193 -38 156 -30 -1193 156 28 182 107 -125 -1193 -1193 -1193 -1193 -15 -1193 229 93 -1193 -173 -1193 -138 -3 -30 -1193 -44 -72 108 -93 33 -111 -14 -1193 -1193 -215 -1193 -17 -107 0 279 -1193 -1193 -3 -189 34 -44 -72 -1193 7 -125 -1193 -73 -1193 -1193 271 -1193 -1193 -1193 -1193 -1193 -1193 -138 -1193 -1193 -1193 -1193 86 -1193 -1193 -1193 -1193 86 -1193 -1193 -215 -1193 379 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -44 -1193 -1193 -1193 107 -111 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 536 -1193 -1193 -1193 -1193 100 -1193 -1193 253 -1193 192 -1193 -1193 -1193 -1193 -1193 -1193 -1193 127 -1193 -1193 17 -1193 -1193 -1193 0 322 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -25 -1193 -1193 -1193 -1193 -215 167 -1193 -1193 232 -1193 -1193 143 -1193 111 34 -1193 -1193 -1193 -1193 -25 48 160 -1193 -1193 -1193 -1193 -1193 -1193 -1193 340 -1193 -1193 -1193 -1193 -1193 -44 -1193 -1193 -1193 33 -1193 -1193 -1193 -1193 143 -1193 -1193 -1193 -1193 59 33 -1193 -1193 -1193 -1193 -1193 286 -1193 -1193 -25 170 -1193 -1193 -1193 -115 67 -1193 -1193 100 -1193 -1193 208 -1193 -30 134 -1193 -1193 -1193 -1193 -1193 -1193 244 -1193 -1193 -1193 -1193 -1193 -1193 425 -1193 -1193 -1193 -1193 -189 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 215 425 85 -1193 -1193 -1193 0 -173 -1193 -1193 -1193 -189 -1193 -1193 403 -1193 -1193 -1193 -1193 -1193 -1193 8 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 33 406 -1193 -1193 -1193 -215 -1193 -17 -107 -1193 -15 -1193 -138 -1193 -189 -1193 214 260 182 7 -25 89 -172 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -189 -1193 -44 -1193 -1193 -1193 207 359 -172 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 33 -1193 422 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -1193 -115 -1193 83 52 -1193 -1193 -1193 -1193 229 -89 -1193 -1193 245 -1193 -1193 -125 148 -73 -1193 -1193 -1193 -1193 274 -7 -1193 -173 -1193 -1193 56 -1193 34 273 -1193 -1193 -1193 -1193 -11 60 -1193 8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 21 nsites= 39 E= 4.8e-290 0.025641 0.025641 0.076923 0.205128 0.000000 0.025641 0.051282 0.128205 0.051282 0.051282 0.000000 0.025641 0.000000 0.051282 0.000000 0.025641 0.025641 0.102564 0.076923 0.051282 0.128205 0.000000 0.000000 0.153846 0.000000 0.025641 0.000000 0.051282 0.153846 0.076923 0.000000 0.102564 0.051282 0.128205 0.102564 0.025641 0.000000 0.000000 0.000000 0.000000 0.102564 0.000000 0.282051 0.102564 0.000000 0.025641 0.000000 0.025641 0.051282 0.076923 0.000000 0.025641 0.025641 0.076923 0.025641 0.076923 0.025641 0.076923 0.000000 0.000000 0.025641 0.000000 0.051282 0.025641 0.025641 0.589744 0.000000 0.000000 0.051282 0.025641 0.025641 0.025641 0.025641 0.000000 0.051282 0.025641 0.000000 0.051282 0.000000 0.000000 0.743590 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.025641 0.000000 0.000000 0.000000 0.000000 0.076923 0.000000 0.000000 0.000000 0.000000 0.153846 0.000000 0.000000 0.025641 0.000000 0.794872 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.025641 0.000000 0.000000 0.000000 0.128205 0.025641 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 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 0.051282 0.000000 0.000000 0.384615 0.000000 0.358974 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.205128 0.000000 0.000000 0.128205 0.000000 0.000000 0.000000 0.025641 0.794872 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.051282 0.000000 0.000000 0.000000 0.000000 0.025641 0.051282 0.000000 0.000000 0.128205 0.000000 0.000000 0.179487 0.000000 0.205128 0.025641 0.000000 0.000000 0.000000 0.000000 0.051282 0.076923 0.256410 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.897436 0.000000 0.000000 0.000000 0.000000 0.000000 0.025641 0.000000 0.000000 0.000000 0.076923 0.000000 0.000000 0.000000 0.000000 0.307692 0.000000 0.000000 0.000000 0.000000 0.128205 0.025641 0.000000 0.000000 0.000000 0.000000 0.000000 0.307692 0.000000 0.000000 0.051282 0.179487 0.000000 0.000000 0.000000 0.051282 0.025641 0.000000 0.000000 0.051282 0.000000 0.000000 0.282051 0.000000 0.076923 0.051282 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.461538 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.487179 0.000000 0.000000 0.000000 0.000000 0.025641 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.025641 0.461538 0.205128 0.000000 0.000000 0.000000 0.025641 0.025641 0.000000 0.000000 0.000000 0.025641 0.000000 0.000000 0.692308 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.025641 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.076923 0.923077 0.000000 0.000000 0.000000 0.025641 0.000000 0.051282 0.025641 0.000000 0.076923 0.000000 0.025641 0.000000 0.025641 0.000000 0.153846 0.256410 0.128205 0.051282 0.051282 0.102564 0.025641 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.025641 0.000000 0.025641 0.000000 0.000000 0.000000 0.256410 0.666667 0.025641 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.025641 0.000000 0.974359 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.051282 0.000000 0.102564 0.076923 0.000000 0.000000 0.000000 0.000000 0.256410 0.051282 0.000000 0.000000 0.230769 0.000000 0.000000 0.025641 0.153846 0.051282 0.000000 0.000000 0.000000 0.000000 0.384615 0.051282 0.000000 0.025641 0.000000 0.000000 0.076923 0.000000 0.025641 0.230769 0.000000 0.000000 0.000000 0.000000 0.051282 0.128205 0.000000 0.025641 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- ExDGADY[ILV]G[VL]G[AP][VI][FY][PA]TP[TS]K[KP][DN] -------------------------------------------------------------------------------- Time 35.69 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 29 sites = 34 llr = 1404 E-value = 3.0e-276 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 2:127:1::41::::::::4:1::::1:8 pos.-specific C :::::::::::1::::::::::::::::: probability D ::::::::::::::::2:2:3112::::: matrix E ::73::2:::::::::6:1:1:14:133: F ::::::::::::1:1:::::::::4:::: G :::::::9a:::::::::11112:::::1 H ::::::::::::::::1:1:::::::::: I 11:::3:::1:42:1::::1:::::3:11 K ::11::3:::1::::::a11::::::2:: L :1:1:4:::1:21:4::::1::1113:1: M 1::::::::::1::::::::::::1::1: N :::::::1::::::::::2:::::::::: P ::::::::::::::::::::1:::::1:: Q 1:12::1:::1::a::::1::::1:::1: R ::1:::1::::::::a::11::3:1:11: S :::11:::::::::::1::13:1:::::: T 11::::1::18:::::::1::5:1:::1: V 46:::2:::4:16:1::::::::1:1:1: W ::::::::::::::::::::::::::::: Y ::::::::::::::3:::::::::11::: bits 7.4 6.7 6.0 5.2 Relative 4.5 * * Entropy 3.7 * * * * (59.6 bits) 3.0 ** * * * * 2.2 ** * ** * ****** * 1.5 ******************* ********* 0.7 ***************************** 0.0 ----------------------------- Multilevel VVEEALKGGATIVQLREKxADTREFLEEA consensus A I V LI Y D S GD IK sequence Q V -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------------------------- Coccidioides_immitis 67 1.02e-25 SAHYKGDLCT VVEQAIQGGVTIVQYRDKHADTGVLIETA SRLHTITKAH Selaginella_moellendorff 330 7.21e-25 NKRWDRSTPA AVEQAIQGGATIIQIREKEAETLEFIKIA EASLAIGRKY Dysgonomonas_gadei 25 7.21e-25 SLSLGRPLET VVEEAVRGGVTMVQLREKDASTLDFYNLA MKLKSILKSY Clavispora_lusitaniae 28 3.12e-24 MIPESSSFLS QVQQAVENGVTIVQLREKNISTRDFIDRA KDVLKITRPR Lodderomyces_elongisporu 29 3.73e-24 MIPESKTFLG QIEEAVNNGVTIVQLREKKLSTREFIKRA QQVHALTKPR Desulfovibrio_africanus 26 1.06e-23 VGCMGRDLAW VVAEALAGGVTMVQLREKQATTREFLERA WRIKPICDAA Arabidopsis_thaliana 332 1.25e-23 NKKWNRSIVD ALKAAIEGGATIIQLREKEAETREFLEEA KACIDICRSH Fibrobacter_succinogenes 25 1.76e-23 TSVPADRFLP TVEAACKGGATLIQLREKNRSTREYMELA AAAHEVTKRY Aspergillus_terreus 26 2.89e-23 PILKGRDLCA VVEEALKGGVTVVQYRDKKSDTGDQIHTA KKLHQITTKY Cryptococcus_gattii 28 8.88e-23 LLPPGKDYYE SLEESLQGGVTLVQVREKDADTGEFIEVA RRTKAICDKY Physcomitrella_patens 312 1.21e-22 NKTWGRSTSE AVRAAIEGGATIVQIRSKEADTGEFLQEA ETSLKVARDY Chloroflexus_aggregans 28 4.09e-22 GLSRGRSHVA VIEAAITGGATVVQYREKHAPTRQMVAEA QVLRELTRRT Cucumis_sativus 196 7.36e-22 NERWDRSITD AVKDAVEGGATIVQIREKDAKTRDFLEVA KSCIKICHAH Sordaria_macrospora 29 1.14e-20 AILGDRDLYE VVEASVRGGTTIVQLRDKTSDTGDMIAMG KKLHAITKKY Oceanimonas 22 2.16e-20 DRQPIDTLQT VVREAVAGGVTLVQVREKHGDVRAFIERA EAVKAVLQGT Fusobacterium_mortiferum 28 2.45e-20 NFSNGRSNYF CVEEMIKGGIKIVQYRAKTKDTREKVKEA REIRELCRKN Saccharomyces_cerevisiae 30 5.81e-20 MLPPGTTLCS QVEAGLKNGVTLVQIREKDIETKNFVAEA LEVQKICKKY Cyanobacterium 156 1.49e-19 ITSPIKNLFS VVESSLKGGLQILQYREKNISDSSYIKVA RKLCELCHQY Trichoplax_adhaerens 26 1.88e-19 KQISDIEFLD IIEKSIIGGVTSVQLREKNLEDDEFLKIA YQCKEITSTY Aminobacterium_colombien 26 2.36e-19 QIGAPRTLLE QTEEVLKGGATVIQLRDKQSGGRELLETA LAMKRLCYDY Volvox_carteri 1061 3.31e-19 NKKCNRTLLE AVTLAVRGGATIIQLREKDTDGGDFAREA AAALKVCRQY Cyanothece 156 3.31e-19 VTSSRENFLK IVESALQGGLTLLQYREKKIDDIVRLEMA QKLCELCHQY Rubrobacter_xylanophilus 25 5.72e-19 VTDPRDDLEE RVEAALRGGVDIVQLREKRASREEVLPLA RRLREVCLRH Oxalobacter_formigenes 20 1.09e-18 DWDDTAKMVE VTEKALTGGAQIVQYRHKTAGPELLLEQA RALRDLCRRY Sulfurihydrogenibium_yel 22 1.20e-18 KLTPYDKIFD MVEQALKGGAKLVQLRDKNNSDDFLLPIS KDLKKLCHKY Perkinsus_marinus 1 2.02e-18 . MVASAVAGGATCVQLRLKDVSTGDYVKLA KETKKLMPRH Treponema 32 1.38e-17 HWTGEKTLYQ QTEEAILGGTTFLQIREKELNEADFEKEA LELQALCKKY Akkermansia_muciniphila 25 4.70e-17 ASKCRLSLLE TVRKAADGGVTIVQYRSTNPDAGTCYREA LPIRDFLASR Pelodictyon_phaeoclathra 21 6.03e-17 ITDEALCPVT LAEQALKGGAAMIQLRHKTASGSQLFSWA VEISKRCHQY Bacillus_subtilis 31 6.03e-17 SNNTKADPVT VVQKALKGGATLYQFREKGGDALTGEARI KFAEKAQAAC Haemophilus_parainfluenz 33 1.98e-16 GDNLADNLLS VLRQALEGGITCFQFRDKGKFSLENSPTE QRALAIKCRD Naegleria_gruberi 9 5.16e-16 MGKRSLEE TVEQSIEGGSSIIQYREKRYPQQLTTRQM LEQAKSLQKI Geobacter 32 1.51e-14 TDQAERLVHR VREALSSGGVAVLQYRDKVRAYEERLELG QELKHLCTEF Helicobacter_pylori 39 3.65e-13 KNDRINALLD ALELALQSKITAFQFRQKGDLALQDPIEI KQLALECQKL -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Coccidioides_immitis 1e-25 66_[3]_492 Selaginella_moellendorff 7.2e-25 329_[3]_169 Dysgonomonas_gadei 7.2e-25 24_[3]_159 Clavispora_lusitaniae 3.1e-24 27_[3]_449 Lodderomyces_elongisporu 3.7e-24 28_[3]_496 Desulfovibrio_africanus 1.1e-23 25_[3]_159 Arabidopsis_thaliana 1.3e-23 331_[3]_162 Fibrobacter_succinogenes 1.8e-23 24_[3]_157 Aspergillus_terreus 2.9e-23 25_[3]_464 Cryptococcus_gattii 8.9e-23 27_[3]_481 Physcomitrella_patens 1.2e-22 311_[3]_170 Chloroflexus_aggregans 4.1e-22 27_[3]_165 Cucumis_sativus 7.4e-22 195_[3]_160 Sordaria_macrospora 1.1e-20 28_[3]_466 Oceanimonas 2.2e-20 21_[3]_154 Fusobacterium_mortiferum 2.5e-20 27_[3]_154 Saccharomyces_cerevisiae 5.8e-20 29_[3]_482 Cyanobacterium 1.5e-19 155_[3]_154 Trichoplax_adhaerens 1.9e-19 25_[3]_160 Aminobacterium_colombien 2.4e-19 25_[3]_153 Volvox_carteri 3.3e-19 1060_[3]_162 Cyanothece 3.3e-19 155_[3]_155 Rubrobacter_xylanophilus 5.7e-19 24_[3]_155 Oxalobacter_formigenes 1.1e-18 19_[3]_155 Sulfurihydrogenibium_yel 1.2e-18 21_[3]_154 Perkinsus_marinus 2e-18 [3]_268 Treponema 1.4e-17 31_[3]_156 Akkermansia_muciniphila 4.7e-17 24_[3]_151 Pelodictyon_phaeoclathra 6e-17 20_[3]_158 Bacillus_subtilis 6e-17 30_[3]_163 Haemophilus_parainfluenz 2e-16 32_[3]_164 Naegleria_gruberi 5.2e-16 8_[3]_460 Geobacter 1.5e-14 31_[3]_424 Helicobacter_pylori 3.7e-13 38_[3]_156 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=29 seqs=34 Coccidioides_immitis ( 67) VVEQAIQGGVTIVQYRDKHADTGVLIETA 1 Selaginella_moellendorff ( 330) AVEQAIQGGATIIQIREKEAETLEFIKIA 1 Dysgonomonas_gadei ( 25) VVEEAVRGGVTMVQLREKDASTLDFYNLA 1 Clavispora_lusitaniae ( 28) QVQQAVENGVTIVQLREKNISTRDFIDRA 1 Lodderomyces_elongisporu ( 29) QIEEAVNNGVTIVQLREKKLSTREFIKRA 1 Desulfovibrio_africanus ( 26) VVAEALAGGVTMVQLREKQATTREFLERA 1 Arabidopsis_thaliana ( 332) ALKAAIEGGATIIQLREKEAETREFLEEA 1 Fibrobacter_succinogenes ( 25) TVEAACKGGATLIQLREKNRSTREYMELA 1 Aspergillus_terreus ( 26) VVEEALKGGVTVVQYRDKKSDTGDQIHTA 1 Cryptococcus_gattii ( 28) SLEESLQGGVTLVQVREKDADTGEFIEVA 1 Physcomitrella_patens ( 312) AVRAAIEGGATIVQIRSKEADTGEFLQEA 1 Chloroflexus_aggregans ( 28) VIEAAITGGATVVQYREKHAPTRQMVAEA 1 Cucumis_sativus ( 196) AVKDAVEGGATIVQIREKDAKTRDFLEVA 1 Sordaria_macrospora ( 29) VVEASVRGGTTIVQLRDKTSDTGDMIAMG 1 Oceanimonas ( 22) VVREAVAGGVTLVQVREKHGDVRAFIERA 1 Fusobacterium_mortiferum ( 28) CVEEMIKGGIKIVQYRAKTKDTREKVKEA 1 Saccharomyces_cerevisiae ( 30) QVEAGLKNGVTLVQIREKDIETKNFVAEA 1 Cyanobacterium ( 156) VVESSLKGGLQILQYREKNISDSSYIKVA 1 Trichoplax_adhaerens ( 26) IIEKSIIGGVTSVQLREKNLEDDEFLKIA 1 Aminobacterium_colombien ( 26) QTEEVLKGGATVIQLRDKQSGGRELLETA 1 Volvox_carteri ( 1061) AVTLAVRGGATIIQLREKDTDGGDFAREA 1 Cyanothece ( 156) IVESALQGGLTLLQYREKKIDDIVRLEMA 1 Rubrobacter_xylanophilus ( 25) RVEAALRGGVDIVQLREKRASREEVLPLA 1 Oxalobacter_formigenes ( 20) VTEKALTGGAQIVQYRHKTAGPELLLEQA 1 Sulfurihydrogenibium_yel ( 22) MVEQALKGGAKLVQLRDKNNSDDFLLPIS 1 Perkinsus_marinus ( 1) MVASAVAGGATCVQLRLKDVSTGDYVKLA 1 Treponema ( 32) QTEEAILGGTTFLQIREKELNEADFEKEA 1 Akkermansia_muciniphila ( 25) TVRKAADGGVTIVQYRSTNPDAGTCYREA 1 Pelodictyon_phaeoclathra ( 21) LAEQALKGGAAMIQLRHKTASGSQLFSWA 1 Bacillus_subtilis ( 31) VVQKALKGGATLYQFREKGGDALTGEARI 1 Haemophilus_parainfluenz ( 33) VLRQALEGGITCFQFRDKGKFSLENSPTE 1 Naegleria_gruberi ( 9) TVEQSIEGGSSIIQYREKRYPQQLTTRQM 1 Geobacter ( 32) VREALSSGGVAVLQYRDKVRAYEERLELG 1 Helicobacter_pylori ( 39) ALELALQSKITAFQFRQKGDLALQDPIEI 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 29 n= 13777 bayes= 9.45514 E= 3.0e-276 63 87 -1173 -1173 -1173 -1173 -1173 -18 -1173 -169 153 -1173 -1173 202 -73 -105 68 206 -1173 -1173 -195 -1173 -1173 -1173 -1173 -1173 -1173 41 -1173 31 -1173 -1173 -1173 -1173 -73 -1173 68 293 -1173 -1173 -95 -1173 -1173 365 -1173 -1173 -1173 -1173 17 -1173 -1173 -1173 -1173 70 127 -1173 -91 -1173 -1173 -1173 105 -1173 -97 230 -1173 -1173 -1173 -1173 117 -69 -1173 -1173 -1173 250 -1173 53 -1173 -1173 -1173 -1173 269 -1173 -1173 -1173 -1173 -153 -1173 -1173 -1173 -169 53 -1173 -1173 -1173 -1173 127 -1173 -153 -1173 -1173 -195 87 -1173 -1173 -1173 -1173 -1173 199 -1173 212 -1173 -1173 -1173 -1173 -1173 -105 -1173 147 -1173 -1173 -37 -1173 -97 171 -1173 -1173 -1173 -118 234 -169 -1173 -24 -1173 202 127 -105 9 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -1173 337 -1173 -1173 -1173 -1173 -1173 134 -1173 -1173 -1173 -105 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -1173 351 -1173 -1173 -83 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -1173 175 -1173 -1173 -1173 -1173 -1173 -1173 41 -1173 -69 -1173 -1173 -1173 -1173 -1173 -105 9 217 -1173 -1173 -95 -1173 -97 -1173 -1173 -1173 -1173 -1173 17 -1173 -1173 -1173 -1173 70 -1173 -105 379 -1173 -1173 -1173 -195 187 -1173 -1173 20 -1173 -1173 273 -1173 112 212 -1173 -1173 -1173 -1173 -105 -1173 47 -1173 -1173 -1173 -1173 -1173 -1173 120 -1173 -1173 163 -1173 31 -1173 -1173 -1173 -1173 -1173 -1173 -1173 279 -1173 28 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -1173 478 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -1173 178 -1173 -1173 114 -1173 212 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -53 -1173 360 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -1173 435 -1173 -1173 -1173 -1173 -1173 -195 -1173 184 345 -1173 -1173 152 -1173 -1173 -169 -1173 -1173 -1173 -30 -1173 -5 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -1173 421 -1173 -1173 -1173 -1173 -1173 -1173 -1173 -91 -1173 -1173 -1173 -1173 -1173 162 113 -1173 5 211 -1173 75 -1173 -1173 234 -1173 70 27 -1173 109 -153 -1173 -1173 163 -1173 -97 -1173 -1173 -54 -1173 82 17 -11 -1173 -24 -52 -1173 27 53 -91 -153 -1173 28 -195 -1173 249 113 20 -54 -1173 -1173 -83 -169 -1173 -24 48 -1173 -1173 212 -91 -1173 -1173 -1173 -37 -1173 103 -87 -1173 5 -1173 -1173 -1173 -1173 -1173 -1173 -52 -30 -73 -105 318 -153 -1173 28 -195 -1173 3 71 -1173 146 -1173 -118 -83 63 -1173 -1173 -1173 -30 259 -5 -1173 -1173 -1173 -1173 -195 -1173 203 283 20 -1173 -1173 -1173 -1173 -69 -1173 -24 -1173 128 -1173 -105 9 -53 -1173 -1173 -1173 87 -97 -1173 401 -153 -1173 -1173 -83 63 153 -24 -1173 -30 27 -1173 -91 -153 -1173 186 -195 -1173 -1173 13 20 -1173 -1173 199 -1173 177 53 -1173 -52 -1173 -1173 -105 -91 47 -1173 128 5 -1173 -97 259 -1173 -1173 52 -118 198 -1173 -1173 -24 106 -30 85 -105 -1173 -1173 -1173 -1173 -1173 -1173 -1173 230 -1173 -1173 -1173 41 -1173 63 153 -1173 -1173 70 159 -1173 109 6 235 -1173 280 -1173 -1173 -87 -1173 -54 -1173 -18 -1173 -1173 53 -1173 -1173 -1173 -1173 -105 -1173 -1173 -1173 -1173 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 29 nsites= 34 E= 3.0e-276 0.176471 0.029412 0.000000 0.000000 0.000000 0.000000 0.000000 0.058824 0.000000 0.029412 0.058824 0.000000 0.000000 0.147059 0.029412 0.029412 0.088235 0.352941 0.000000 0.000000 0.029412 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.088235 0.000000 0.117647 0.000000 0.000000 0.000000 0.000000 0.029412 0.000000 0.088235 0.647059 0.000000 0.000000 0.058824 0.000000 0.000000 0.676471 0.000000 0.000000 0.000000 0.000000 0.058824 0.000000 0.000000 0.000000 0.000000 0.058824 0.117647 0.000000 0.029412 0.000000 0.000000 0.000000 0.235294 0.000000 0.029412 0.264706 0.000000 0.000000 0.000000 0.000000 0.117647 0.058824 0.000000 0.000000 0.000000 0.205882 0.000000 0.088235 0.000000 0.000000 0.000000 0.000000 0.735294 0.000000 0.000000 0.000000 0.000000 0.029412 0.000000 0.000000 0.000000 0.029412 0.029412 0.000000 0.000000 0.000000 0.000000 0.147059 0.000000 0.029412 0.000000 0.000000 0.029412 0.029412 0.000000 0.000000 0.000000 0.000000 0.000000 0.264706 0.000000 0.411765 0.000000 0.000000 0.000000 0.000000 0.000000 0.029412 0.000000 0.235294 0.000000 0.000000 0.088235 0.000000 0.029412 0.176471 0.000000 0.000000 0.000000 0.029412 0.264706 0.029412 0.000000 0.029412 0.000000 0.147059 0.117647 0.029412 0.058824 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.882353 0.000000 0.000000 0.000000 0.000000 0.000000 0.088235 0.000000 0.000000 0.000000 0.029412 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.970588 0.000000 0.000000 0.029412 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.382353 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.088235 0.000000 0.058824 0.000000 0.000000 0.000000 0.000000 0.000000 0.029412 0.058824 0.382353 0.000000 0.000000 0.058824 0.000000 0.029412 0.000000 0.000000 0.000000 0.000000 0.000000 0.058824 0.000000 0.000000 0.000000 0.000000 0.058824 0.000000 0.029412 0.764706 0.000000 0.000000 0.000000 0.029412 0.058824 0.000000 0.000000 0.029412 0.000000 0.000000 0.441176 0.000000 0.205882 0.088235 0.000000 0.000000 0.000000 0.000000 0.029412 0.000000 0.117647 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.058824 0.000000 0.000000 0.205882 0.000000 0.117647 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.588235 0.000000 0.029412 0.000000 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 0.088235 0.000000 0.000000 0.147059 0.000000 0.411765 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.058824 0.000000 0.294118 0.000000 0.000000 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 0.029412 0.000000 0.205882 0.588235 0.000000 0.000000 0.058824 0.000000 0.000000 0.029412 0.000000 0.000000 0.000000 0.029412 0.000000 0.058824 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.970588 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.029412 0.000000 0.000000 0.000000 0.000000 0.000000 0.176471 0.117647 0.000000 0.088235 0.088235 0.000000 0.088235 0.000000 0.000000 0.176471 0.000000 0.058824 0.058824 0.000000 0.117647 0.029412 0.000000 0.000000 0.352941 0.000000 0.029412 0.000000 0.000000 0.058824 0.000000 0.117647 0.058824 0.088235 0.000000 0.029412 0.029412 0.000000 0.058824 0.088235 0.029412 0.029412 0.000000 0.029412 0.029412 0.000000 0.323529 0.117647 0.029412 0.058824 0.000000 0.000000 0.029412 0.029412 0.000000 0.029412 0.058824 0.000000 0.000000 0.264706 0.029412 0.000000 0.000000 0.000000 0.088235 0.000000 0.117647 0.029412 0.000000 0.088235 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.029412 0.029412 0.029412 0.029412 0.500000 0.029412 0.000000 0.029412 0.029412 0.000000 0.058824 0.088235 0.000000 0.235294 0.000000 0.029412 0.029412 0.147059 0.000000 0.000000 0.000000 0.029412 0.294118 0.058824 0.000000 0.000000 0.000000 0.000000 0.029412 0.000000 0.235294 0.382353 0.029412 0.000000 0.000000 0.000000 0.000000 0.058824 0.000000 0.029412 0.000000 0.088235 0.000000 0.029412 0.058824 0.058824 0.000000 0.000000 0.000000 0.029412 0.029412 0.000000 0.411765 0.029412 0.000000 0.000000 0.029412 0.147059 0.058824 0.029412 0.000000 0.029412 0.058824 0.000000 0.029412 0.029412 0.000000 0.088235 0.029412 0.000000 0.000000 0.058824 0.029412 0.000000 0.000000 0.264706 0.000000 0.323529 0.029412 0.000000 0.029412 0.000000 0.000000 0.029412 0.029412 0.117647 0.000000 0.058824 0.117647 0.000000 0.029412 0.323529 0.000000 0.000000 0.029412 0.029412 0.205882 0.000000 0.000000 0.029412 0.088235 0.029412 0.088235 0.029412 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.264706 0.000000 0.000000 0.000000 0.088235 0.000000 0.147059 0.058824 0.000000 0.000000 0.058824 0.147059 0.000000 0.117647 0.088235 0.029412 0.000000 0.794118 0.000000 0.000000 0.029412 0.000000 0.058824 0.000000 0.058824 0.000000 0.000000 0.029412 0.000000 0.000000 0.000000 0.000000 0.029412 0.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- VVE[EAQ]A[LIV]KGG[AV]T[IL][VI]Q[LY]R[ED]KxA[DS]T[RG][ED]F[LI][EK]EA -------------------------------------------------------------------------------- Time 50.37 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- Bacillus_subtilis 4.22e-51 30_[3(6.03e-17)]_9_[1(3.90e-26)]_26_[2(3.04e-20)]_74 Helicobacter_pylori 1.79e-46 38_[3(3.65e-13)]_10_[1(2.00e-28)]_28_[2(4.88e-17)]_64 Haemophilus_parainfluenz 8.03e-50 32_[3(1.98e-16)]_11_[1(6.42e-30)]_28_[2(1.07e-15)]_71 Oceanimonas 1.76e-54 21_[3(2.16e-20)]_6_[1(2.59e-31)]_27_[2(6.31e-15)]_67 Desulfovibrio_africanus 6.27e-56 25_[3(1.06e-23)]_6_[1(1.02e-28)]_27_[2(9.56e-16)]_72 Geobacter 4.79e-43 31_[3(1.51e-14)]_6_[1(8.54e-26)]_27_[2(6.79e-16)]_337 Taylorella_asinigenitali 1.05e-24 58_[1(8.34e-16)]_31_[2(2.32e-16)]_70 Oxalobacter_formigenes 2.02e-46 19_[3(1.09e-18)]_6_[1(2.27e-26)]_28_[2(2.26e-13)]_67 Cyanobacterium 5.14e-55 155_[3(1.49e-19)]_6_[1(8.26e-30)]_27_[2(1.51e-18)]_67 Cyanothece 1.60e-56 155_[3(3.31e-19)]_6_[1(1.09e-31)]_27_[2(1.51e-18)]_68 Dysgonomonas_gadei 1.56e-57 24_[3(7.21e-25)]_6_[1(7.29e-30)]_27_[2(4.69e-15)]_72 Pelodictyon_phaeoclathra 9.50e-53 20_[3(6.03e-17)]_6_[1(2.59e-31)]_27_[2(1.23e-16)]_71 Chloroflexus_aggregans 3.74e-63 27_[3(4.09e-22)]_6_[1(8.10e-33)]_27_[2(1.30e-20)]_78 Rubrobacter_xylanophilus 7.19e-51 24_[3(5.72e-19)]_6_[1(2.18e-24)]_27_[2(1.23e-19)]_68 Treponema 9.41e-54 31_[3(1.38e-17)]_6_[1(1.54e-30)]_27_[2(7.47e-18)]_69 Fusobacterium_mortiferum 5.99e-54 27_[3(2.45e-20)]_6_[1(1.06e-29)]_28_[2(4.25e-16)]_66 Sulfurihydrogenibium_yel 2.09e-45 21_[3(1.20e-18)]_6_[1(1.10e-25)]_27_[2(4.45e-13)]_29_[3(6.13e-05)]_9 Aminobacterium_colombien 1.35e-52 25_[3(2.36e-19)]_6_[1(5.66e-30)]_27_[2(2.06e-15)]_66 Akkermansia_muciniphila 1.05e-45 24_[3(4.70e-17)]_6_[1(5.08e-26)]_27_[2(1.23e-14)]_64 Fibrobacter_succinogenes 1.31e-60 24_[3(1.76e-23)]_6_[1(1.09e-31)]_27_[2(1.01e-17)]_70 Saccharomyces_cerevisiae 4.21e-59 29_[3(5.81e-20)]_6_[1(1.73e-36)]_30_[2(2.97e-16)]_392 Clavispora_lusitaniae 9.56e-62 27_[3(3.12e-24)]_6_[1(1.06e-34)]_28_[2(2.32e-16)]_361 Aspergillus_terreus 1.87e-58 25_[3(2.89e-23)]_6_[1(4.53e-31)]_27_[2(1.17e-17)]_230_[3(2.35e-05)]_118 Coccidioides_immitis 2.69e-57 66_[3(1.02e-25)]_6_[1(2.81e-29)]_44_[2(5.39e-16)]_19_[2(6.47e-05)]_348 Sordaria_macrospora 1.90e-55 28_[3(1.14e-20)]_6_[1(2.29e-30)]_27_[2(6.41e-18)]_379 Cryptococcus_gattii 2.76e-54 27_[3(8.88e-23)]_6_[1(8.16e-28)]_27_[2(3.22e-17)]_394 Cucumis_sativus 1.20e-61 195_[3(7.36e-22)]_6_[1(6.89e-33)]_27_[2(4.58e-20)]_73 Arabidopsis_thaliana 4.13e-63 331_[3(1.25e-23)]_6_[1(4.98e-33)]_27_[2(4.58e-20)]_75 Physcomitrella_patens 2.19e-59 311_[3(1.21e-22)]_6_[1(4.52e-29)]_27_[2(3.34e-21)]_83 Volvox_carteri 1.31e-53 440_[2(4.25e-05)]_599_[3(3.31e-19)]_6_[1(1.82e-35)]_27_[2(1.36e-13)]_75 Thalassiosira_pseudonana 2.37e-12 88_[3(1.64e-05)]_20_[1(1.56e-05)]_44_[2(6.14e-13)]_88 Phaeodactylum_tricornutu 6.34e-17 374_[1(3.07e-05)]_18_[1(1.33e-12)]_31_[2(5.07e-13)]_70 Perkinsus_marinus 1.02e-48 [3(2.02e-18)]_5_[1(1.19e-26)]_28_[2(2.97e-16)]_181 Xenopus(Silurana) 8.37e-19 168_[1(2.27e-13)]_30_[2(5.07e-13)]_69 Trichoplax_adhaerens 2.01e-45 25_[3(1.88e-19)]_6_[1(7.41e-23)]_27_[2(3.46e-15)]_73 Naegleria_gruberi 4.35e-49 8_[3(5.16e-16)]_10_[1(1.03e-30)]_29_[2(1.07e-15)]_367 Acanthamoeba_castellanii 1.55e-40 24_[1(7.01e-32)]_33_[2(4.88e-17)]_352 Candida_tropicalis 5.60e-01 482 Lodderomyces_elongisporu 7.98e-61 28_[3(3.73e-24)]_6_[1(1.53e-32)]_28_[2(8.70e-18)]_408 Selaginella_moellendorff 8.68e-62 329_[3(7.21e-25)]_6_[1(6.86e-31)]_27_[2(1.23e-19)]_82 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: kodomo.fbb.msu.ru ********************************************************************************