******************************************************************************** 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 ------------- ------ ------ ------------- ------ ------ HUTP_BACSU 1.0000 148 HUTP_BACA2 1.0000 148 HUTP_BACHD 1.0000 147 HUTP_BACCZ 1.0000 146 HUTP_BACC0 1.0000 146 HUTP_BACWK 1.0000 146 HUTP_GEOSW 1.0000 149 HUTP_GEOTN 1.0000 149 HUTP_BACCE 1.0000 132 HUTP_BACAN 1.0000 146 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme temp.fasta -mod zoops -nmotifs 3 -prior dirichlet -nostatus -protein -text model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 8 maxw= 50 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 10 wnsites= 0.8 theta: prob= 1 spmap= pam spfuzz= 120 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 1457 N= 10 sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.103 C 0.007 D 0.025 E 0.084 F 0.010 G 0.111 H 0.038 I 0.068 K 0.051 L 0.097 M 0.033 N 0.026 P 0.023 Q 0.032 R 0.058 S 0.045 T 0.053 V 0.086 W 0.013 Y 0.036 Background letter frequencies (from dataset with add-one prior applied): A 0.102 C 0.007 D 0.025 E 0.084 F 0.011 G 0.110 H 0.039 I 0.068 K 0.051 L 0.096 M 0.033 N 0.026 P 0.023 Q 0.032 R 0.058 S 0.045 T 0.053 V 0.086 W 0.014 Y 0.037 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 50 sites = 10 llr = 1228 E-value = 1.6e-273 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::::::::5:::::1::::a::::::::::3:::::a:8::::::a::: pos.-specific C :::::::::::::::::::::::::::::::::::::::::::::::::: probability D ::::::::::7:::::::::::::::::5:::::2::::::::::::::: matrix E :::::2:2::::::::::::::::::::413:a:8::::::::::::::: F :::::::::::1:::::::a:::::::::::::::::::::::::::::: G a:::a::::5::::::a:::::::a::::5:::a::::::::a::a:::: H :::::::::::::::::::::::::::::::::::::::::::::::::: I ::::::5::::::::::::::6::::::::::::::5:::::::a:::4: K ::::::::::::::::::1::::::1::1:57:::::::::::::::::8 L :::::::2a::48::::a::::2:::::::::::::::::a::::::::: M ::::::2:::::1::::::::::::::::::::::::::::::::::::: N :::::::::::::::::::::::::3:::1:::::::::::::::::::: P ::::::::::::::::::::::::::a:::1::::::::::::::::a:: Q :::::8:6::::1::::::::::::::::1:::::::::::::::::::: R :::a:::::::::a::::9::::a:::::::::::::::::::::::::2 S ::::::::::3::::::::::::::::::21::::::::2:::::::::: T ::a:::::::::::a::::::::::6:::::::::::::::::a:::::: V :a::::3::::5:::9:::::48:::::::::::::5:a:::::::::6: W :::::::::::::::::::::::::::::::::::a:::::::::::::: Y :::::::::::::::::::::::::::a:::::::::::::a:::::::: bits 7.1 6.4 * * 5.7 * * * * 4.9 * ** * * * Relative 4.2 ** * * ** * * ** * * * * Entropy 3.5 *** * * * ** **** * *** * ** ** ** ** ** * (177.2 bits) 2.8 ********* * ***************** ******************** 2.1 ************************************************** 1.4 ************************************************** 0.7 ************************************************** 0.0 -------------------------------------------------- Multilevel GVTRGQIQLADVLRTVGLRFAIVRGTPYDGKKEGEWIAVALYGTIGAPVK consensus EVE GSL VL N ESEA D V S IR sequence ML -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------------------------------------- HUTP_BACAN 83 2.51e-59 LYHAIMEALY GVTRGQIQLADVLRTVGLRFAIVRGTPYDGKKEGEWVAVALYGTIGAPVK GSEHEAIGLG HUTP_BACCE 83 2.51e-59 LYHAIMEALY GVTRGQIQLADVLRTVGLRFAIVRGTPYDGKKEGEWVAVALYGTIGAPVK HUTP_BACWK 83 2.51e-59 LYHAIMEALY GVTRGQIQLADVLRTVGLRFAIVRGTPYDGKKEGEWVAVALYGTIGAPVK GSEHEAIGLG HUTP_BACC0 83 2.51e-59 LYHAIMEALY GVTRGQIQLADVLRTVGLRFAIVRGTPYDGKKEGEWVAVALYGTIGAPVK GSEHEAIGLG HUTP_BACCZ 83 2.51e-59 LYHAIMEALY GVTRGQIQLADVLRTVGLRFAIVRGTPYDGKKEGEWVAVALYGTIGAPVK GSEHEAIGLG HUTP_GEOSW 86 1.34e-53 LYHAVVEAVQ GVTRGQVELGDLMRTVGLRFAVVRGNPYENSKEGEWIAVALYGTIGAPIR GLEHETIGLG HUTP_GEOTN 86 2.21e-53 LYHAILEAVH GVTRGQVELGDLLRTAGLRFAVVRGTPYEQPKEGEWIAVALYGTIGAPVR GLEHEAVGLG HUTP_BACHD 84 2.87e-53 LYHAIIEALH GVTRGQVQLGSFQRTVGLRFAIVRGKPYKEEAEGEWIAVALYGTIGAPIK GQEHETIGLG HUTP_BACSU 85 1.06e-52 LYHATMEALH GVTRGEMLLGSLLRTVGLRFAVLRGNPYESEAEGDWIAVSLYGTIGAPIK GLEHETFGVG HUTP_BACA2 85 4.58e-52 LYHATMEALH GVTRGEMLLGSLLRTVGLKFAVLRGNPYESEAEGDWIAVSLYGTIGAPIK GLEHETFGVG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- HUTP_BACAN 2.5e-59 82_[1]_14 HUTP_BACCE 2.5e-59 82_[1] HUTP_BACWK 2.5e-59 82_[1]_14 HUTP_BACC0 2.5e-59 82_[1]_14 HUTP_BACCZ 2.5e-59 82_[1]_14 HUTP_GEOSW 1.3e-53 85_[1]_14 HUTP_GEOTN 2.2e-53 85_[1]_14 HUTP_BACHD 2.9e-53 83_[1]_14 HUTP_BACSU 1.1e-52 84_[1]_14 HUTP_BACA2 4.6e-52 84_[1]_14 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=50 seqs=10 HUTP_BACAN ( 83) GVTRGQIQLADVLRTVGLRFAIVRGTPYDGKKEGEWVAVALYGTIGAPVK 1 HUTP_BACCE ( 83) GVTRGQIQLADVLRTVGLRFAIVRGTPYDGKKEGEWVAVALYGTIGAPVK 1 HUTP_BACWK ( 83) GVTRGQIQLADVLRTVGLRFAIVRGTPYDGKKEGEWVAVALYGTIGAPVK 1 HUTP_BACC0 ( 83) GVTRGQIQLADVLRTVGLRFAIVRGTPYDGKKEGEWVAVALYGTIGAPVK 1 HUTP_BACCZ ( 83) GVTRGQIQLADVLRTVGLRFAIVRGTPYDGKKEGEWVAVALYGTIGAPVK 1 HUTP_GEOSW ( 86) GVTRGQVELGDLMRTVGLRFAVVRGNPYENSKEGEWIAVALYGTIGAPIR 1 HUTP_GEOTN ( 86) GVTRGQVELGDLLRTAGLRFAVVRGTPYEQPKEGEWIAVALYGTIGAPVR 1 HUTP_BACHD ( 84) GVTRGQVQLGSFQRTVGLRFAIVRGKPYKEEAEGEWIAVALYGTIGAPIK 1 HUTP_BACSU ( 85) GVTRGEMLLGSLLRTVGLRFAVLRGNPYESEAEGDWIAVSLYGTIGAPIK 1 HUTP_BACA2 ( 85) GVTRGEMLLGSLLRTVGLKFAVLRGNPYESEAEGDWIAVSLYGTIGAPIK 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 50 n= 967 bayes= 6.58045 E= 1.6e-273 -997 -997 -997 -997 -997 318 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 354 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 424 -997 -997 -997 -997 -997 -997 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-------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- GVTRG[QE][IVM][QEL]L[AG][DS][VL]LRTVGLRFA[IV][VL]RG[TN]PY[DE][GS][KE][KA]EG[ED]W[IV]AV[AS]LYGTIGAP[VI][KR] -------------------------------------------------------------------------------- Time 1.46 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 50 sites = 10 llr = 1204 E-value = 3.0e-260 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::::::::1::2::::a9:::a8:::::::::::::1:a:::a:::a:: pos.-specific C :::a:::::::::::::::::::::::::::::::::::::::::::::: probability D :::::::::::2::::::::::::::::::1:5:::1::::::::::::: matrix E :::::::::::3::::::::a::::::1::513:::9:::::::::a::: F ::::::::::::::::::::::::::::1::::::::::::::::::::: G :::::a::a::::::::::::::::::3:::212:::::::::::::::: H :::::::::::::2::::::::::::1:::::::::::a:::a::::::4 I ::::1::::::::::3:::4:::::::::8::::::::::::::71:::: K :7::1:7:::::::a:::::::::a3:::::::::::::::::::::::: L ::::2:::::::1::::::::::::::::::::2::::::a::::1::8: M ::::::::::a::::::::5:::::::::::::::::2:::::::7:::: N :::::::::::5:1::::::::::::71::1::::::::::::::::::: P ::::::::::::1::::::::::::::::::::::::::::::::::::: Q :1::1::::::::7:::::::::::::4::2::::::::::::::::::1 R :2::::3::::::::::::::::::2:1::1::::a:::::::::::::: S ::1::::::9::6:::::1::::2:52::::21::::2:::::::::::: T ::::5::::::::::::::::a:::::::::5:::::5::::::2::::: V ::2::::a:::::::7a::1::::::::92:::6::::::::::11::2: W 9::::::::::::::::::::::::::::::::::::::::::::::::: Y 1:7:::::::::::::::::::::::::::::::a::::::a:::::::5 bits 7.1 * 6.4 * 5.7 * * 4.9 * * * * * ** Relative 4.2 * * ** * * * ** * ** Entropy 3.5 * ** ** *** ** ** *** * * * *** ****** ** * (173.6 bits) 2.8 **** ********************** ** * **************** 2.1 ************************************************** 1.4 ************************************************** 0.7 ************************************************** 0.0 -------------------------------------------------- Multilevel WKYCTGKVGSMNSQKVVAAMETAAKSNQVIETDVYRETHALYHAIMEALY consensus RV L R EAH I I S KSG VQGEG M T VH sequence D R S L S -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------------------------------------- HUTP_BACAN 33 9.40e-64 ESPVLSIPKG WKYCTGKVGSMNSQKVVAAMETAAKSNQVIETDVYRETHALYHAIMEALY GVTRGQIQLA HUTP_BACCE 33 9.40e-64 ESPVLSIPKG WKYCTGKVGSMNSQKVVAAMETAAKSNQVIETDVYRETHALYHAIMEALY GVTRGQIQLA HUTP_BACC0 33 9.40e-64 ESPVLSIPKG WKYCTGKVGSMNSQKVVAAMETAAKSNQVIETDVYRETHALYHAIMEALY GVTRGQIQLA HUTP_BACCZ 33 9.40e-64 ESPVLSIPKD WKYCTGKVGSMNSQKVVAAMETAAKSNQVIETDVYRETHALYHAIMEALY GVTRGQIQLA HUTP_BACWK 33 2.57e-61 ESPVLSIPKG WKYCTGKVGSMNSQKVVAAMETAAKSNRVIETDVYRETHALYHAIMEALY GVTRGQIQLA HUTP_BACSU 35 1.45e-51 TQVEELERDG WKVCLGKVGSMDAHKVVAAIETASKKSGVIQSEGYRESHALYHATMEALH GVTRGEMLLG HUTP_BACA2 35 3.06e-51 QQISRLERDG WKVCLGRVGSMDAHKVVAAIETASKKSGVIQSEGYRESHALYHATMEALH GVTRGEMLLG HUTP_GEOSW 36 8.55e-49 KITAHLDNLQ WRYCKGKVGSMELQKIVASVETAAKRNNVVNGELYREMHALYHAVVEAVQ GVTRGQVELG HUTP_BACHD 34 8.55e-49 IVEASILSSD YQSCIGRVGSMESNKIVAAIETAAKKNGFIREGVYREAHALYHAIIEALH GVTRGQVQLG HUTP_GEOTN 36 1.55e-48 AILDELRASN WRYCQGRVGAMEPQKIVAAIETAAKRHEVVDGSLYRDMHALYHAILEAVH GVTRGQVELG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- HUTP_BACAN 9.4e-64 32_[2]_64 HUTP_BACCE 9.4e-64 32_[2]_50 HUTP_BACC0 9.4e-64 32_[2]_64 HUTP_BACCZ 9.4e-64 32_[2]_64 HUTP_BACWK 2.6e-61 32_[2]_64 HUTP_BACSU 1.4e-51 34_[2]_64 HUTP_BACA2 3.1e-51 34_[2]_64 HUTP_GEOSW 8.5e-49 35_[2]_64 HUTP_BACHD 8.5e-49 33_[2]_64 HUTP_GEOTN 1.6e-48 35_[2]_64 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=50 seqs=10 HUTP_BACAN ( 33) WKYCTGKVGSMNSQKVVAAMETAAKSNQVIETDVYRETHALYHAIMEALY 1 HUTP_BACCE ( 33) WKYCTGKVGSMNSQKVVAAMETAAKSNQVIETDVYRETHALYHAIMEALY 1 HUTP_BACC0 ( 33) WKYCTGKVGSMNSQKVVAAMETAAKSNQVIETDVYRETHALYHAIMEALY 1 HUTP_BACCZ ( 33) WKYCTGKVGSMNSQKVVAAMETAAKSNQVIETDVYRETHALYHAIMEALY 1 HUTP_BACWK ( 33) WKYCTGKVGSMNSQKVVAAMETAAKSNRVIETDVYRETHALYHAIMEALY 1 HUTP_BACSU ( 35) WKVCLGKVGSMDAHKVVAAIETASKKSGVIQSEGYRESHALYHATMEALH 1 HUTP_BACA2 ( 35) WKVCLGRVGSMDAHKVVAAIETASKKSGVIQSEGYRESHALYHATMEALH 1 HUTP_GEOSW ( 36) WRYCKGKVGSMELQKIVASVETAAKRNNVVNGELYREMHALYHAVVEAVQ 1 HUTP_BACHD ( 34) YQSCIGRVGSMESNKIVAAIETAAKKNGFIREGVYREAHALYHAIIEALH 1 HUTP_GEOTN ( 36) WRYCQGRVGAMEPQKIVAAIETAAKRHEVVDGSLYRDMHALYHAILEAVH 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 50 n= 967 bayes= 6.8344 E= 3.0e-260 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 605 145 -997 -997 -997 -997 -997 -997 -997 -997 376 -997 -997 -997 -997 165 178 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 116 -997 122 -997 426 -997 707 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 56 96 106 -997 -997 -997 165 -997 -997 324 -997 -997 -997 -997 -997 -997 -997 -997 318 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 376 -997 -997 -997 -997 -997 236 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 354 -997 -997 -997 -997 -997 -997 -997 318 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -3 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 433 -997 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-------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 50 nsites= 10 E= 3.0e-260 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.900000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.700000 0.000000 0.000000 0.000000 0.000000 0.100000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.200000 0.000000 0.700000 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 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0.000000 0.800000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- W[KR][YV]C[TL]G[KR]VGSM[NED][SA][QH]K[VI]VAA[MI]ETA[AS]K[SKR][NS][QG]V[IV][EQ][TGS][DE][VGL]YRE[TMS]HALYHA[IT]MEA[LV][YH] -------------------------------------------------------------------------------- Time 2.19 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 29 sites = 10 llr = 581 E-value = 7.8e-084 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::::1:::::::8:::8:5:1::::11:1 pos.-specific C ::::::::::::::::::::::::::::: probability D :::::1:::::::::::::6::::::::1 matrix E :::1:1:::::::::::::47392:1:11 F ::::::::::::::::::1:::::::::: G :1::5:1::a:::::::::::11:2:::: H :::3::6:::::::::::1:::::::::: I ::::::::a::::1:::::::::1::3:6 K ::3:41:::::::::::::::::::1::: L :67::::::::3:1aa281:::::::51: M a::::::::::5:5:::1::::::::::: N :::::::::::1::::::1::5:1::::: P :::::::::::::::::::::1::5:::: Q :::6::::::11::::::::1:::12::: R ::::::2a::9:::::::::::::::::1 S :1:::2::::::2:::::1::::6:::7: T :2:::5::::::::::::::1:::1::1: V ::::::1::::::3:::1::::::151:: W ::::::::::::::::::::::::::::: Y ::::::::::::::::::::::::::::: bits 7.1 6.4 5.7 4.9 * Relative 4.2 * * Entropy 3.5 * * ** * ** * (83.8 bits) 2.8 * ** ************ * **** * 2.1 ***************************** 1.4 ***************************** 0.7 ***************************** 0.0 ----------------------------- Multilevel MLLQGTHRIGRMAMLLALADENESPVLSI consensus TKHKSR LSV L E E EGQI sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------------------------- HUTP_BACAN 1 4.33e-35 . MLLQGTHRIGRMAMLLALADENESPVLSI PKGWKYCTGK HUTP_BACCE 1 4.33e-35 . MLLQGTHRIGRMAMLLALADENESPVLSI PKGWKYCTGK HUTP_BACWK 1 4.33e-35 . MLLQGTHRIGRMAMLLALADENESPVLSI PKGWKYCTGK HUTP_BACCZ 1 4.33e-35 . MLLQGTHRIGRMAMLLALADENESPVLSI PKDWKYCTGK HUTP_BACC0 1 6.16e-34 . MLLQGTHRIGRMAMLLALADQNESPVLSI PKGWKYCTGK HUTP_BACA2 1 2.04e-24 . MTLHKDRRIGRLSVLLLLHETEENQQISR LERDGWKVCL HUTP_GEOSW 1 1.32e-23 . MLKQAKGRIGRNAVLLALFEEEEEGKITA HLDNLQWRYC HUTP_BACSU 1 3.95e-23 . MTLHKERRIGRLSVLLLLNEAEESTQVEE LERDGWKVCL HUTP_BACHD 1 7.24e-23 . MSKHKSHRIGQLAILLAVSEEPGIVEASI LSSDYQSCIG HUTP_GEOTN 1 3.88e-22 . MGKEKSVRIGRQALLLAMLDEGEEGAILD ELRASNWRYC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- HUTP_BACAN 4.3e-35 [3]_117 HUTP_BACCE 4.3e-35 [3]_103 HUTP_BACWK 4.3e-35 [3]_117 HUTP_BACCZ 4.3e-35 [3]_117 HUTP_BACC0 6.2e-34 [3]_117 HUTP_BACA2 2e-24 [3]_119 HUTP_GEOSW 1.3e-23 [3]_120 HUTP_BACSU 4e-23 [3]_119 HUTP_BACHD 7.2e-23 [3]_118 HUTP_GEOTN 3.9e-22 [3]_120 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=29 seqs=10 HUTP_BACAN ( 1) MLLQGTHRIGRMAMLLALADENESPVLSI 1 HUTP_BACCE ( 1) MLLQGTHRIGRMAMLLALADENESPVLSI 1 HUTP_BACWK ( 1) MLLQGTHRIGRMAMLLALADENESPVLSI 1 HUTP_BACCZ ( 1) MLLQGTHRIGRMAMLLALADENESPVLSI 1 HUTP_BACC0 ( 1) MLLQGTHRIGRMAMLLALADQNESPVLSI 1 HUTP_BACA2 ( 1) MTLHKDRRIGRLSVLLLLHETEENQQISR 1 HUTP_GEOSW ( 1) MLKQAKGRIGRNAVLLALFEEEEEGKITA 1 HUTP_BACSU ( 1) MTLHKERRIGRLSVLLLLNEAEESTQVEE 1 HUTP_BACHD ( 1) MSKHKSHRIGQLAILLAVSEEPGIVEASI 1 HUTP_GEOTN ( 1) MGKEKSVRIGRQALLLAMLDEGEEGAILD 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 29 n= 1177 bayes= 7.12018 E= 7.8e-084 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 491 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -14 -997 -997 -997 264 -997 -997 -997 -997 -997 116 192 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 254 286 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 25 -997 -997 296 -997 -997 -997 -997 -997 -997 424 -997 -997 -997 -997 -997 -997 -3 -997 -997 -997 -997 218 -997 -997 296 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 200 25 -997 -997 -997 -997 96 -997 -997 -997 -997 -997 -997 216 324 -997 -997 -997 -997 -997 -997 -997 -997 -14 396 -997 -997 -997 -997 -997 -997 -997 178 -997 -997 22 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 410 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 388 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 318 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 165 395 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 164 391 192 -997 165 -997 -997 -997 -997 -997 -997 297 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 216 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 56 -997 6 391 -997 -997 -997 -997 -997 -997 180 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 338 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 338 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 297 -997 -997 -997 -997 -997 -997 -997 -997 106 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 306 159 -997 -997 -997 -997 -997 -997 22 -997 -997 229 -997 -997 -997 321 -997 137 -997 -997 6 -997 192 -997 -997 -997 116 -997 -997 -997 -997 -997 -997 458 225 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -3 -997 -997 306 -997 -997 -997 -997 -997 -997 -997 -997 -997 165 -997 -997 92 -997 -997 -997 -997 -997 -997 184 -997 -14 -997 -997 -997 -997 -997 424 212 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 342 -997 -14 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 -997 125 -997 -997 -997 56 -997 -997 -997 192 -997 -997 -997 375 -997 -997 -997 -997 -997 -997 -997 -997 -997 86 -997 -997 -997 -997 -997 -997 444 165 -997 -997 92 22 -997 -997 -3 -997 -997 25 -997 -997 -997 -997 96 -997 -997 -997 -997 265 -997 -997 -997 254 -997 -997 -3 -997 -997 -997 -997 -997 -997 215 -997 238 -997 -997 -997 -997 -997 -997 -997 22 -997 -997 -997 -997 -997 25 -997 -997 -997 -997 -997 6 -997 -997 -997 -997 -997 397 92 -997 -997 -997 -3 -997 200 25 -997 -997 -997 315 -997 -997 -997 -997 -997 -997 78 -997 -997 -997 -997 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 29 nsites= 10 E= 7.8e-084 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 0.100000 0.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.300000 0.700000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.300000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.100000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 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0.000000 0.000000 0.000000 0.300000 0.500000 0.100000 0.000000 0.100000 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 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.100000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.300000 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 1.000000 0.000000 0.000000 0.000000 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 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 0.100000 0.000000 0.100000 0.000000 0.000000 0.100000 0.000000 0.100000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.400000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.700000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.300000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.900000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.100000 0.000000 0.000000 0.100000 0.100000 0.000000 0.000000 0.100000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.300000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 0.700000 0.100000 0.000000 0.000000 0.000000 0.100000 0.000000 0.100000 0.100000 0.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- M[LT][LK][QH][GK][TS][HR]RIGR[ML][AS][MV]LL[AL]LA[DE]E[NE]E[SE][PG][VQ][LI]SI -------------------------------------------------------------------------------- Time 2.40 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- HUTP_BACSU 2.71e-115 [3(3.95e-23)]_5_[2(1.45e-51)]_[1(1.06e-52)]_14 HUTP_BACA2 1.28e-115 [3(2.04e-24)]_5_[2(3.06e-51)]_[1(4.58e-52)]_14 HUTP_BACHD 7.37e-113 [3(7.24e-23)]_4_[2(8.55e-49)]_[1(2.87e-53)]_14 HUTP_BACCZ 6.78e-146 [3(4.33e-35)]_3_[2(9.40e-64)]_[1(2.51e-59)]_14 HUTP_BACC0 9.51e-145 [3(6.16e-34)]_3_[2(9.40e-64)]_[1(2.51e-59)]_14 HUTP_BACWK 1.80e-143 [3(4.33e-35)]_3_[2(2.57e-61)]_[1(2.51e-59)]_14 HUTP_GEOSW 6.81e-114 [3(1.32e-23)]_6_[2(8.55e-49)]_[1(1.34e-53)]_14 HUTP_GEOTN 5.77e-112 [3(3.88e-22)]_6_[2(1.55e-48)]_[1(2.21e-53)]_14 HUTP_BACCE 4.39e-146 [3(4.33e-35)]_3_[2(9.40e-64)]_[1(2.51e-59)] HUTP_BACAN 6.78e-146 [3(4.33e-35)]_3_[2(9.40e-64)]_[1(2.51e-59)]_14 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: kodomo-count ********************************************************************************