******************************************************************************** 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 ------------- ------ ------ ------------- ------ ------ yesX_Bacsu 1.0000 612 YP_003313330.1 1.0000 1880 YP_949129.1 1.0000 696 ZP_04604892.1 1.0000 761 YP_003160192.1 1.0000 787 NP_630623.1 1.0000 631 NP_823033.1 1.0000 624 ******************************************************************************** ******************************************************************************** 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= 7 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= 5991 N= 7 sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.108 C 0.001 D 0.086 E 0.037 F 0.025 G 0.116 H 0.019 I 0.027 K 0.025 L 0.067 M 0.014 N 0.037 P 0.055 Q 0.027 R 0.056 S 0.071 T 0.092 V 0.079 W 0.021 Y 0.037 Background letter frequencies (from dataset with add-one prior applied): A 0.107 C 0.001 D 0.086 E 0.037 F 0.025 G 0.115 H 0.019 I 0.027 K 0.025 L 0.067 M 0.014 N 0.037 P 0.055 Q 0.027 R 0.056 S 0.071 T 0.092 V 0.079 W 0.021 Y 0.037 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 50 sites = 7 llr = 880 E-value = 6.2e-154 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::1:::6:::1:::::::::::7:::::1::::::::::::7:a:::::: pos.-specific C :::::::::::::::::::::::::::::::::::::::::::::::::: probability D ::3:::::a:::1::::::::a::::9:::::::6::::::::::::::: matrix E :::::::::::::::::4:::::::::::::::::::::::::::::::: F :::::::::::::::::::1:::::::::1::::::::::::::::::6: G ::::::::::::1a::a:::::3::::a::::::::a:::::a::::::: H :::::::::::1::::::::::::::::::::::::::::::::a::::: I ::::::::::::::::::::3::3:::::::::6:::::a:::::::::: K 6::::::a::::::::::::::::6:::11:::::::1:::::::::::: L :::::::::::::::::::31::::a::::a1:::9:::::::::::::1 M 3:::::::::::::::::::::::::::::::1::1::::::::::::14 N :::::a:::a:::::::6::::::::::::::::1:::a::::::::::: P :::a:::::::::::::::::::::::::::::::::1:::::::::1:: Q ::3::::::::9:::::::::::::::::::::::::::::::::::9:4 R ::::::::::::::::::::::::1::::7::9::::7::a::::::::: S ::3:7:4:::9:7:::::::::::::::::::::3::::::3::::1::: T 1:::3::::::::::a::3:::::3:1:7:::::::::::::::::9::: V ::::::::::::::::::736::::::::::::4::::::::::::::1: W :a:::::::::::::::::::::::::::::9:::::::::::::::::: Y ::::::::::::::a::::3:::7:::::::::::::::::::::a::1: bits 9.6 8.6 7.6 6.7 Relative 5.7 * * * Entropy 4.8 * * * * * * * ** ** * (181.4 bits) 3.8 ** * * *** * ** * * * * ***** * *** ** *** 2.9 ** **************** ** *************************** 1.9 ************************************************** 1.0 ************************************************** 0.0 -------------------------------------------------- Multilevel KWDPSNAKDNSQSGYTGNVLVDAYKLDGTRLWRIDLGRNIRAGAHYTQFM consensus M Q T S ETVI GIT VS S Q sequence S Y -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------------------------------------- NP_823033.1 173 1.49e-57 DGDGQLDFVL KWQPTNAKDNSQSGYTGNTVVDGIKLDGTRLWRVDLGRNIRSGAHYTQFQ VYDYDGDGKA yesX_Bacsu 137 8.83e-57 DGDGEYEMIL KWDPSNSKDNAHDGYTGEVLIDAYKLDGTFLWRINLGRNIRAGAHYTQFM VYDLDGDGKA ZP_04604892.1 313 1.26e-56 DGDGDYEIVL KWDPSNSKDNSQSGYTGNVYVDAYTLTGARLWRVDLGRNIRAGAHYTQFQ VYDYDGDGDA YP_003313330.1 1180 1.77e-56 DGDGEYELVV MWSPSNSKDNSQGGYTGEVLIDAYRLDGTRLWRISMGPNIRAGAHYTQMM LFDLDSDGRA NP_630623.1 180 6.40e-56 DGDGALDLVL KWQPTNAKDNSQSGYTGNTVVDGIKLDGTRLLMVDLGRNIRSGAHYTQFQ VYDYDGDGRA YP_003160192.1 320 7.08e-56 DGDGTYEMIV MWSPSNAKDNSQSGYTGEVFLDAYKLDGKRLWRISLGKNIRAGAHYSPYM VYDLNGDGRS YP_949129.1 224 6.35e-55 DGDGKYEVIQ TWAPSNAKDNSQSGYTGNVYVDAYTLDGTKLWRIDLGRNIRAGAHYTQVL AYDFDGDGKA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- NP_823033.1 1.5e-57 172_[1]_402 yesX_Bacsu 8.8e-57 136_[1]_426 ZP_04604892.1 1.3e-56 312_[1]_399 YP_003313330.1 1.8e-56 1179_[1]_651 NP_630623.1 6.4e-56 179_[1]_402 YP_003160192.1 7.1e-56 319_[1]_418 YP_949129.1 6.4e-55 223_[1]_423 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=50 seqs=7 NP_823033.1 ( 173) KWQPTNAKDNSQSGYTGNTVVDGIKLDGTRLWRVDLGRNIRSGAHYTQFQ 1 yesX_Bacsu ( 137) KWDPSNSKDNAHDGYTGEVLIDAYKLDGTFLWRINLGRNIRAGAHYTQFM 1 ZP_04604892.1 ( 313) KWDPSNSKDNSQSGYTGNVYVDAYTLTGARLWRVDLGRNIRAGAHYTQFQ 1 YP_003313330.1 ( 1180) MWSPSNSKDNSQGGYTGEVLIDAYRLDGTRLWRISMGPNIRAGAHYTQMM 1 NP_630623.1 ( 180) KWQPTNAKDNSQSGYTGNTVVDGIKLDGTRLLMVDLGRNIRSGAHYTQFQ 1 YP_003160192.1 ( 320) MWSPSNAKDNSQSGYTGEVFLDAYKLDGKRLWRISLGKNIRAGAHYSPYM 1 YP_949129.1 ( 224) TWAPSNAKDNSQSGYTGNVYVDAYTLDGTKLWRIDLGRNIRAGAHYTQVL 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 50 n= 5648 bayes= 10.8778 E= 6.2e-154 -945 -945 -945 -945 -945 -945 -945 -945 452 -945 433 -945 -945 -945 -945 -945 64 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 555 -945 41 -945 174 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 340 -945 200 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 418 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 332 164 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 474 -945 -945 -945 -945 -945 -945 -945 -945 241 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 259 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 533 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 355 -945 -945 -945 -945 -945 -945 -945 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0.000000 0.142857 0.857143 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.571429 0.000000 0.000000 0.000000 0.000000 0.000000 0.142857 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.142857 0.000000 0.142857 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.142857 0.428571 0.000000 0.000000 0.428571 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [KM]W[DQS]P[ST]N[AS]KDNSQSGYTG[NE][VT][LVY][VI]D[AG][YI][KT]LDGTRLWR[IV][DS]LGRNIR[AS]GAHYTQF[MQ] -------------------------------------------------------------------------------- Time 6.40 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 49 sites = 7 llr = 847 E-value = 1.9e-146 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 7::::::11::::::::::::::::17:a::::7::::::::::::::: pos.-specific C :::::::::::::1::::::::::::::::::::::::::::::::::: probability D ::::::::11:1::::::::a:::::::::::::::::::::::::11: matrix E 3::::::::1:3::::::::::::::::::1:::::::::::::::4:: F ::::1:::::::::3:::::::::::::::::::::::::::a9::::: G :::::::::::1::::::::::::::3::::::1:::::::1:::a:9: H ::::::::1:::4::1:::9:::::::::::::::::::a::::::::: I :::9::::1:::::4::::::::::::3::::::::::::::::3:::: K :::::::::::::1::::::::::::::::::::::::::::::::::: L :a:::::::1::::3::a3::::::3:3::::::::::::::::7:::: M ::::::::::::::::::7:::::::::::::::::::::::::::::a N :::::::::::::::::::::::::::::::a:::a::::::::::1:: P :::::::4:3:::::::::::6:::::::::::::::aa:7:::::::: Q :::::::::1:::::::::1::4:::::::9:::::a:::::::::::: R ::a::::::::1:7:3::::::::a::::1::::::::::::::::::: S :::::4:::::3::::::::::::::::::::11:::::::9::::1:: T :::::6a41:a:4::3a::::41::4::::::6:::::::3:::::1:: V :::1:::::1::1::1::::::4::1:4::::3:::::::::::::::: W :::::::::::::::::::::::::::::9::::::::::::::::::: Y ::::9:::3::::::1:::::::a::::::::::a::::::::1::::: bits 9.6 8.6 7.6 6.7 Relative 5.7 * * * Entropy 4.8 * ** * *** *** * ** * (174.6 bits) 3.8 **** * * * ***** ** *** ****** *** * 2.9 ******* * *** ********* ***** ************ ** 1.9 ************************************************* 1.0 ************************************************* 0.0 ------------------------------------------------- Multilevel ALRIYTTPYPTEHRIRTLMHDPQYRTAVAWQNTAYNQPPHPSFFLGEGM consensus E S T ST FT L TV LGI V T I sequence L L -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------------------------------- yesX_Bacsu 545 1.44e-55 EVIWRTEDSS ALRIYTTTHLTRHCFYTLMHDPVYRLGIAWQNTAYNQPPHTSFYLGTGM KKPPKPALYI ZP_04604892.1 702 6.33e-55 EVIWRTGDSR ALRIYSTPTQTGTRIHTLMHDPQYRAAIAWQNTAYNQPPHPGFFIGDGM GIPPTPNIYL NP_823033.1 565 1.05e-54 EVVWPTTDNT ALRIYSTPYETSTKITTLLHDTQYRTALAWQNTAYNQPPHPSFFLGNDM ATAPRPTVYT NP_630623.1 572 1.05e-54 TVVWRTSNNT ALRIYSTPYDTDTRITTLLHDTQYRTALAWQNTAYNQPPHPSFFLGSGM PTAPRPSVHT YP_003313330.1 1591 1.17e-53 ELVYRTDDST ALRVFTTTDVTEHRLRTLMHDPVYRLGVAWQNVSYNQPPHPSFFLGEGM ETPAAPSITY YP_949129.1 635 2.18e-53 EIAWPSTDST ELRIYTTTAPTEVRLRTLMHDTVYRTAVARENVAYNQPPHPSFFIGEGM QAPAIPAVVY YP_003160192.1 723 3.25e-53 EVVYRSDDSA ELRIYTTAIPTSHRFVTLMQDPTYRVAVAWQNSGYNQPPHTSFFLGEGM NTPPAPQVSF -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- yesX_Bacsu 1.4e-55 544_[2]_19 ZP_04604892.1 6.3e-55 701_[2]_11 NP_823033.1 1.1e-54 564_[2]_11 NP_630623.1 1.1e-54 571_[2]_11 YP_003313330.1 1.2e-53 1590_[2]_241 YP_949129.1 2.2e-53 634_[2]_13 YP_003160192.1 3.2e-53 722_[2]_16 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=49 seqs=7 yesX_Bacsu ( 545) ALRIYTTTHLTRHCFYTLMHDPVYRLGIAWQNTAYNQPPHTSFYLGTGM 1 ZP_04604892.1 ( 702) ALRIYSTPTQTGTRIHTLMHDPQYRAAIAWQNTAYNQPPHPGFFIGDGM 1 NP_823033.1 ( 565) ALRIYSTPYETSTKITTLLHDTQYRTALAWQNTAYNQPPHPSFFLGNDM 1 NP_630623.1 ( 572) ALRIYSTPYDTDTRITTLLHDTQYRTALAWQNTAYNQPPHPSFFLGSGM 1 YP_003313330.1 ( 1591) ALRVFTTTDVTEHRLRTLMHDPVYRLGVAWQNVSYNQPPHPSFFLGEGM 1 YP_949129.1 ( 635) ELRIYTTTAPTEVRLRTLMHDTVYRTAVARENVAYNQPPHPSFFIGEGM 1 YP_003160192.1 ( 723) ELRIYTTAIPTSHRFVTLMQDPTYRVAVAWQNSGYNQPPHTSFFLGEGM 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 49 n= 5655 bayes= 10.8796 E= 1.9e-146 273 -945 -945 295 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 389 -945 -945 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0.000000 0.000000 0.000000 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 0.142857 0.428571 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.142857 0.000000 0.000000 0.000000 0.142857 0.142857 0.000000 0.000000 0.000000 0.000000 0.000000 0.142857 0.000000 0.000000 0.857143 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AE]LRIY[TS]T[PT]YPT[ES][HT]R[IFL][RT]TL[ML]HD[PT][QV]YR[TL][AG][VIL]AWQN[TV]AYNQPPH[PT]SFF[LI]GEGM -------------------------------------------------------------------------------- Time 12.30 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 50 sites = 7 llr = 848 E-value = 6.1e-139 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::::::::a1:a::::::::1::6::::::1::79::::::1::::::: pos.-specific C :::::::::::::::::::::::::::::::::::::::::::::::::: probability D :::::a:::::::::a:::::::::::::::::::::a:11::::::::: matrix E :::::::::::::::::4:::::::::::::::::::::::::::::::: F :::::::a:::::::::::::::4::::::::::::1:4::::3:::::a G :a::::::::7:::::a:::::::::a:::::::::::::49:::::::: H ::::::::::::::::::3::::::::::::::::::::::::::::::: I :::::::::::1::::::::::4::::::::::4:::::::::1:::::: K :::::::::::::::::1:::::::::::::::::::::1::3:14:::: L ::::::::a:::::a::::::4:::::::::::4::::1::::6:::::: M ::::1::::::::::::::::116:::::::::::::::::::::::::: N ::a:::::::::::::::::::::::::::::::::::::4::::::::: P :::::::::::::::::::a:::::::::::::::::::::::::::::: Q :::::::::::::::::1::::::1:::::::::::::::::::13:::: R :::a::a:::::::::::6::::::a::::a::::::::6::3::3a::: S ::::::::::1::::::3::a:::3:::::::::::::::::1:1::::: T :::::::::::6::::::1::::::::::a:9:::1:::::11:4:::6: V ::::9::::::3:::::::::34:::::::::a13::::1::::1:::4: W ::::::::::::::::::::::::::::::::::::4:3::::::::a:: Y a::::::::::::a:::::::::::::aa:::::::4:1::::::::::: bits 9.6 8.6 7.6 6.7 Relative 5.7 * * * Entropy 4.8 * * * * * ** * * (174.8 bits) 3.8 * ******* *** ** * * **** * ** *** * 2.9 ********** ********* ** ***************** * ***** 1.9 ************************************************** 1.0 ************************************************** 0.0 -------------------------------------------------- Multilevel YGNRVDRFLAGTAYLDGERPSLIMARGYYTRTVIAAWDFRGGKLTKRWTF consensus V SH VVFS LV Y W N RF Q V sequence R -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------------------------------------- yesX_Bacsu 265 8.86e-57 RGKLEDWGDG YGNRMDRFLAGTAYLDGERPSLVMARGYYTRTVLVAYDFRNGRLKKRWVF DSNQPGHEAY NP_630623.1 308 7.20e-56 RGSVSSWGDS YGNRVDRFLAGTAYLDGSRPSVIMARGYYTRTVIAAWDWRDGRFTRRWTF DTNSSTNSGK NP_823033.1 301 2.45e-55 RGTVSSWGDS YGNRVDRFLAGTAYLDGSRPSLIMARGYYTRTVLAAWDWRGGAFTRRWTF FTTSSTNSGK ZP_04604892.1 441 2.45e-55 RGNVSSWGDS YGNRVDRFLAATAYLDGQRPSLIMARGYYTRAVIAAWDFRNGTLTKRWTF ACNASGNSAA YP_949129.1 352 1.77e-53 RGSVTGWGDN YGNRVDRFLAGVAYLDGEHPSMMFSRGYYTRTVLVTYDLVNGKLVKRWTF DSNLAGDEYK YP_003313330.1 1308 9.65e-53 RGDVGAWGDG YGNRVDRFLAGIAYLDGEHPSAVFSRGYYTRTVIAAYDFDGTSISQRWVF DSDVAGRQYE YP_003160192.1 448 2.55e-52 RGKVSSWGDS YGNRVDRFLASVAYLDGKTPSVVFQRGYYTRTVVAAFDYKGGKLQQRWVF DSNNHSGTAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- yesX_Bacsu 8.9e-57 264_[3]_298 NP_630623.1 7.2e-56 307_[3]_274 NP_823033.1 2.4e-55 300_[3]_274 ZP_04604892.1 2.4e-55 440_[3]_271 YP_949129.1 1.8e-53 351_[3]_295 YP_003313330.1 9.7e-53 1307_[3]_523 YP_003160192.1 2.6e-52 447_[3]_290 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=50 seqs=7 yesX_Bacsu ( 265) YGNRMDRFLAGTAYLDGERPSLVMARGYYTRTVLVAYDFRNGRLKKRWVF 1 NP_630623.1 ( 308) YGNRVDRFLAGTAYLDGSRPSVIMARGYYTRTVIAAWDWRDGRFTRRWTF 1 NP_823033.1 ( 301) YGNRVDRFLAGTAYLDGSRPSLIMARGYYTRTVLAAWDWRGGAFTRRWTF 1 ZP_04604892.1 ( 441) YGNRVDRFLAATAYLDGQRPSLIMARGYYTRAVIAAWDFRNGTLTKRWTF 1 YP_949129.1 ( 352) YGNRVDRFLAGVAYLDGEHPSMMFSRGYYTRTVLVTYDLVNGKLVKRWTF 1 YP_003313330.1 ( 1308) YGNRVDRFLAGIAYLDGEHPSAVFSRGYYTRTVIAAYDFDGTSISQRWVF 1 YP_003160192.1 ( 448) YGNRVDRFLASVAYLDGKTPSVVFQRGYYTRTVVAAFDYKGGKLQQRWVF 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 50 n= 5648 bayes= 10.2607 E= 6.1e-139 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 474 -945 -945 -945 -945 -945 311 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 474 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 416 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 333 -945 -945 -945 -945 -945 -945 343 -945 -945 -945 -945 355 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 416 -945 -945 -945 -945 -945 -945 -945 -945 -945 534 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 389 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 322 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 41 -945 -945 -945 -945 263 -945 -945 -945 -945 -945 -945 -945 -945 -945 100 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 240 -945 -945 -945 -945 -945 -945 -945 -945 264 185 -945 -945 322 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 474 -945 -945 -945 -945 -945 -945 -945 -945 -945 389 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 355 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 311 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 353 -945 -945 -945 -945 253 -945 -945 -945 -945 240 -945 200 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 390 -945 -945 -945 -945 -945 -945 -945 336 -945 64 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 418 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 381 -945 -945 -945 -945 41 -945 -945 -945 -945 -945 -945 -945 -945 267 333 -945 -945 -945 -945 -945 -945 185 -945 -945 -945 -945 -945 -945 -945 -945 -945 398 -945 -945 333 -945 -945 -945 -945 -945 -945 243 -945 -945 -945 -945 -945 -945 412 -945 -945 -945 -945 -945 533 -945 -945 -945 -945 -945 -945 -945 -945 -945 241 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 240 -945 200 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 416 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 311 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 474 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 474 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 344 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 416 -945 -945 -945 -945 -945 41 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 322 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 366 -945 -945 -945 -945 -945 -945 -945 -945 -945 398 -945 267 -945 -945 -945 -945 -945 -945 -945 85 -945 -945 273 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 185 -945 -945 299 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 64 -945 -945 -945 -945 -945 -945 -945 253 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 433 352 -945 -945 355 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 -945 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0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.142857 0.000000 0.000000 0.000000 0.142857 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.285714 0.000000 0.000000 0.000000 0.000000 0.000000 0.285714 0.142857 0.142857 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.285714 0.000000 0.000000 0.142857 0.000000 0.571429 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.142857 0.000000 0.000000 0.000000 0.000000 0.142857 0.000000 0.142857 0.428571 0.142857 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.428571 0.000000 0.000000 0.000000 0.000000 0.285714 0.285714 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 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 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 0.571429 0.428571 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- YGNRVDRFLAG[TV]AYLDG[ES][RH]PS[LV][IV][MF][AS]RGYYTRTV[IL][AV]A[WY]D[FW]R[GN]G[KR][LF]T[KQR]RW[TV]F -------------------------------------------------------------------------------- Time 17.81 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- yesX_Bacsu 1.35e-154 136_[1(8.83e-57)]_78_[3(8.86e-57)]_230_[2(1.44e-55)]_19 YP_003313330.1 7.48e-147 754_[2(1.89e-05)]_376_[1(1.77e-56)]_78_[3(9.65e-53)]_233_[2(1.17e-53)]_178_[3(5.97e-06)]_13 YP_949129.1 4.05e-147 223_[1(6.35e-55)]_78_[3(1.77e-53)]_233_[2(2.18e-53)]_13 ZP_04604892.1 4.58e-152 312_[1(1.26e-56)]_78_[3(2.45e-55)]_211_[2(6.33e-55)]_11 YP_003160192.1 1.43e-146 319_[1(7.08e-56)]_78_[3(2.55e-52)]_225_[2(3.25e-53)]_16 NP_630623.1 6.20e-152 179_[1(6.40e-56)]_78_[3(7.20e-56)]_214_[2(1.05e-54)]_11 NP_823033.1 4.82e-153 172_[1(1.49e-57)]_78_[3(2.45e-55)]_214_[2(1.05e-54)]_11 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: kodomo-count ********************************************************************************