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********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.0 (Release date: 2004/08/18 09:07:01)
For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.sdsc.edu.
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.sdsc.edu.
********************************************************************************
********************************************************************************
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= farntrans5.s
ALPHABET= ACDEFGHIKLMNPQRSTVWY
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
RAM1_YEAST 1.0000 431 PFTB_RAT 1.0000 437
BET2_YEAST 1.0000 325 RATRABGERB 1.0000 331
CAL1_YEAST 1.0000 376
********************************************************************************
********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.
command: meme farntrans5.s -mod tcm -protein -nmotifs 2
model: mod= tcm nmotifs= 2 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= 25 wnsites= 0.8
theta: prob= 1 spmap= pam spfuzz= 120
em: prior= megap b= 9500 maxiter= 50
distance= 1e-05
data: n= 1900 N= 5
sample: seed= 0 seqfrac= 1
Dirichlet mixture priors file: prior30.plib
Letter frequencies in dataset:
A 0.061 C 0.037 D 0.062 E 0.061 F 0.044 G 0.075 H 0.030 I 0.053 K 0.051
L 0.114 M 0.021 N 0.034 P 0.041 Q 0.038 R 0.041 S 0.078 T 0.046 V 0.057
W 0.018 Y 0.041
Background letter frequencies (from dataset with add-one prior applied):
A 0.061 C 0.037 D 0.061 E 0.060 F 0.044 G 0.075 H 0.030 I 0.053 K 0.051
L 0.113 M 0.021 N 0.034 P 0.041 Q 0.039 R 0.041 S 0.078 T 0.046 V 0.057
W 0.018 Y 0.041
********************************************************************************
********************************************************************************
MOTIF 1 width = 30 sites = 24 llr = 854 E-value = 2.2e-094
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A :::2::::1:2:11:1:1413314:1:1::
pos.-specific C ::::1::::::::2::132::::1::::::
probability D ::::21::11:6::::::::::::::2:13
matrix E ::::::1114::::::::::::::::1111
F :16:::::::::111:31::::::::::1:
G 861241:42:::221:::2:22::::3::1
H ::::::::11:4::2::::::::::::::1
I ::1:::1::::::::1:::1:1::42:11:
K :::::1::3::::::::::::::::::2::
L ::21:::::2::31::1::5::9:55::4:
M ::::::::::::::::::::::::::::::
N :1:1:::21:::::::::::1:::::1:::
P ::::::5:::2:::::::::::::::::::
Q :::1::::1:::::1:::::1:::::::::
R :::::3:::::::2:::::::::::::1::
S :1:2::::::2:::13:1::32:3::12::
T ::::::::::::2::5:1:1:1:1:1:::1
V :::::::1::3:2:::::12::::1:::::
W ::::::::::::::::13::::::::::::
Y :::::::::::::14:31:::::::1::::
bits 5.8
5.2
4.6
4.0
Information 3.5 *
content 2.9 * * *
(51.4 bits) 2.3 *** * * ** * *
1.7 *** ** *** ***** * ****
1.2 ******************************
0.6 ******************************
0.0 ------------------------------
Multilevel GGFGGRPGKEVDLCYTFCALAALALLGSLD
consensus LAH HSYWCVSS SI
sequence P G
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Start P-value Site
------------- ----- --------- ------------------------------
BET2_YEAST 223 7.28e-22 WWLCERQLPE GGLNGRPSKLPDVCYSWWVLSSLAIIGRLD WINYEKLTEF
RATRABGERB 227 6.18e-21 WWLCERQLPS GGLNGRPEKLPDVCYSWWVLASLKIIGRLH WIDREKLRSF
CAL1_YEAST 275 9.17e-20 LNASYDQSDD GGFQGRENKFADTCYAFWCLNSLHLLTKDW KMLCQTELVT
PFTB_RAT 237 1.15e-19 EWIARCQNWE GGIGGVPGMEAHGGYTFCGLAALVILKKER SLNLKSLLQW
PFTB_RAT 138 4.30e-19 QFLELCQSPD GGFGGGPGQYPHLAPTYAAVNALCIIGTEE AYNVINREKL
RATRABGERB 179 7.36e-19 EFVLSCMNFD GGFGCRPGSESHAGQIYCCTGFLAITSQLH QVNSDLLGWW
RATRABGERB 131 8.19e-19 AYVQSLQKED GSFAGDIWGEIDTRFSFCAVATLALLGKLD AINVEKAIEF
BET2_YEAST 172 2.10e-18 DFVLKCYNFD GGFGLCPNAESHAAQAFTCLGALAIANKLD MLSDDQLEEI
RATRABGERB 276 1.43e-17 FILACQDEET GGFADRPGDMVDPFHTLFGIAGLSLLGEEQ IKPVSPVFCM
BET2_YEAST 124 3.41e-17 SFIRGNQLED GSFQGDRFGEVDTRFVYTALSALSILGELT SEVVDPAVDF
RAM1_YEAST 247 5.00e-17 YLKNCQNYEG GFGSCPHVDEAHGGYTFCATASLAILRSMD QINVEKLLEW
BET2_YEAST 272 6.64e-17 FILKCQDEKK GGISDRPENEVDVFHTVFGVAGLSLMGYDN LVPIDPIYCM
RAM1_YEAST 145 1.27e-16 VKLFTISPSG GPFGGGPGQLSHLASTYAAINALSLCDNID GCWDRIDRKG
PFTB_RAT 286 3.17e-16 WVTSRQMRFE GGFQGRCNKLVDGCYSFWQAGLLPLLHRAL HAQGDPALSM
RAM1_YEAST 296 3.47e-16 WSSARQLQEE RGFCGRSNKLVDGCYSFWVGGSAAILEAFG YGQCFNKHAL
PFTB_RAT 348 4.30e-15 YILMCCQCPA GGLLDKPGKSRDFYHTCYCLSGLSIAQHFG SGAMLHDVVM
RATRABGERB 83 2.40e-14 VFIKSCQHEC GGVSASIGHDPHLLYTLSAVQILTLYDSIH VINVDKVVAY
PFTB_RAT 189 2.81e-14 QYLYSLKQPD GSFLMHVGGEVDVRSAYCAASVASLTNIIT PDLFEGTAEW
BET2_YEAST 73 7.78e-14 FVLSCWDDKY GAFAPFPRHDAHLLTTLSAVQILATYDALD VLGKDRKVRL
CAL1_YEAST 205 1.14e-13 LLGYIMSQQC YNGAFGAHNEPHSGYTSCALSTLALLSSLE KLSDKFKEDT
RAM1_YEAST 198 1.33e-13 WLISLKEPNG GFKTCLEVGEVDTRGIYCALSIATLLNILT EELTEGVLNY
RAM1_YEAST 349 3.52e-13 ILYCCQEKEQ PGLRDKPGAHSDFYHTNYCLLGLAVAESSY SCTPNDSPHN
CAL1_YEAST 327 5.47e-13 LLDRTQKTLT GGFSKNDEEDADLYHSCLGSAALALIEGKF NGELCIPQEI
BET2_YEAST 24 3.11e-10 RYIESLDTNK HNFEYWLTEHLRLNGIYWGLTALCVLDSPE TFVKEEVISF
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
BET2_YEAST 3.1e-10 23_[1]_19_[1]_21_[1]_18_[1]_21_
[1]_19_[1]_24
RATRABGERB 2.4e-14 82_[1]_18_[1]_18_[1]_18_[1]_19_[1]_26
CAL1_YEAST 1.1e-13 204_[1]_40_[1]_22_[1]_20
PFTB_RAT 4.3e-15 137_[1]_21_[1]_18_[1]_19_[1]_32_
[1]_60
RAM1_YEAST 1.3e-13 144_[1]_23_[1]_19_[1]_19_[1]_23_
[1]_53
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=30 seqs=24
BET2_YEAST ( 223) GGLNGRPSKLPDVCYSWWVLSSLAIIGRLD 1
RATRABGERB ( 227) GGLNGRPEKLPDVCYSWWVLASLKIIGRLH 1
CAL1_YEAST ( 275) GGFQGRENKFADTCYAFWCLNSLHLLTKDW 1
PFTB_RAT ( 237) GGIGGVPGMEAHGGYTFCGLAALVILKKER 1
PFTB_RAT ( 138) GGFGGGPGQYPHLAPTYAAVNALCIIGTEE 1
RATRABGERB ( 179) GGFGCRPGSESHAGQIYCCTGFLAITSQLH 1
RATRABGERB ( 131) GSFAGDIWGEIDTRFSFCAVATLALLGKLD 1
BET2_YEAST ( 172) GGFGLCPNAESHAAQAFTCLGALAIANKLD 1
RATRABGERB ( 276) GGFADRPGDMVDPFHTLFGIAGLSLLGEEQ 1
BET2_YEAST ( 124) GSFQGDRFGEVDTRFVYTALSALSILGELT 1
RAM1_YEAST ( 247) GFGSCPHVDEAHGGYTFCATASLAILRSMD 1
BET2_YEAST ( 272) GGISDRPENEVDVFHTVFGVAGLSLMGYDN 1
RAM1_YEAST ( 145) GPFGGGPGQLSHLASTYAAINALSLCDNID 1
PFTB_RAT ( 286) GGFQGRCNKLVDGCYSFWQAGLLPLLHRAL 1
RAM1_YEAST ( 296) RGFCGRSNKLVDGCYSFWVGGSAAILEAFG 1
PFTB_RAT ( 348) GGLLDKPGKSRDFYHTCYCLSGLSIAQHFG 1
RATRABGERB ( 83) GGVSASIGHDPHLLYTLSAVQILTLYDSIH 1
PFTB_RAT ( 189) GSFLMHVGGEVDVRSAYCAASVASLTNIIT 1
BET2_YEAST ( 73) GAFAPFPRHDAHLLTTLSAVQILATYDALD 1
CAL1_YEAST ( 205) YNGAFGAHNEPHSGYTSCALSTLALLSSLE 1
RAM1_YEAST ( 198) GFKTCLEVGEVDTRGIYCALSIATLLNILT 1
RAM1_YEAST ( 349) PGLRDKPGAHSDFYHTNYCLLGLAVAESSY 1
CAL1_YEAST ( 327) GGFSKNDEEDADLYHSCLGSAALALIEGKF 1
BET2_YEAST ( 24) HNFEYWLTEHLRLNGIYWGLTALCVLDSPE 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 20 w= 30 n= 1755 bayes= 6.12445 E= 2.2e-094
-218 -476 -324 -369 -492 351 -61 -474 -334 -558 -392 -225 -103 -392 -86 -303 -361 -418 -449 -109
-81 -470 -327 -377 -1 330 -398 -485 -347 -566 -404 54 -81 -396 -330 -9 -350 -421 -467 -482
-244 -349 -513 -434 367 -26 -384 59 -61 38 -123 -357 -404 -371 -364 -348 -238 -14 -322 -240
127 -17 -201 -5 -348 114 -187 -312 -81 -63 -205 120 -263 155 27 92 7 -262 -388 -304
-26 143 115 -207 -17 219 -252 -171 -9 -112 95 -186 -16 -179 -195 -235 -164 -152 -351 -13
-146 -17 33 -115 -32 45 38 -310 85 -143 -204 47 -13 -95 271 -53 -143 -50 83 -303
-47 -38 -90 6 -396 -374 0 15 -233 -169 -288 -259 375 -235 -26 -97 -231 -75 -473 -424
-148 -438 -204 99 -31 196 38 -302 -85 -335 -202 205 -266 -99 26 -54 6 33 83 -304
47 -444 33 57 -349 84 122 -315 209 -342 79 121 -263 109 -118 -53 -144 -265 -389 -305
-160 -416 82 250 -25 -316 123 -254 -111 61 85 -136 -283 -122 -146 -60 -156 -221 -375 -14
161 -320 -465 -373 -228 -392 -333 13 -325 -90 -101 -301 208 -309 -7 90 -181 221 -331 -288
-438 -650 318 -350 -594 -396 355 -672 -341 -686 -596 -158 -495 -373 4 -357 -386 -623 -637 -514
47 -316 -480 -387 82 91 -337 -111 -338 103 -98 -307 -15 -318 -312 -83 170 152 -328 -285
94 221 -398 -311 80 90 -301 -129 -266 -30 -111 21 -354 -263 179 -282 -178 -115 -329 139
-167 -305 -309 -259 149 -77 196 -221 -241 -249 -153 -216 -75 19 -217 -54 -68 -205 -133 341
71 -383 -460 -463 -428 -445 -427 86 -370 -442 -260 -234 -417 -351 -356 143 348 -55 -479 -484
-170 21 -317 -268 232 -354 -39 -217 -250 -54 -152 -36 -288 -261 -224 -116 -223 -78 132 328
46 272 -489 -397 84 -402 -334 -118 -347 -90 -105 -314 -378 -325 -320 -1 82 -106 351 88
277 240 -625 -594 -564 141 -583 -514 -585 -580 -446 -452 -451 4 -521 -277 -297 107 -614 -619
45 -317 -489 -395 -222 -96 -340 81 -346 184 -95 -313 -373 -323 -316 -85 81 179 -327 -285
211 -440 -247 -196 -412 97 -258 -374 -166 -146 -278 178 -325 106 -202 153 0 -314 -457 -377
213 -308 -476 -384 -5 88 -337 123 -337 -91 -99 -307 -372 -318 -311 118 79 12 -328 -287
87 -518 -675 -601 -320 -554 -562 -243 -564 290 -164 -543 -528 -491 -503 -489 -418 -296 -502 -500
317 38 -358 -284 -334 -229 -37 -276 -81 -332 -204 -260 -82 -270 -263 99 23 -47 -389 -383
-408 -489 -735 -670 -387 -688 -678 294 -638 194 -240 -597 -632 -619 -631 -623 -16 84 -602 -556
91 0 -492 -398 -220 -404 -343 158 -348 187 109 -317 -375 -324 -318 -313 78 -100 -329 80
-159 -454 121 100 -362 163 39 -329 20 -356 -221 172 -274 38 24 13 5 -279 -402 -316
47 -443 -200 57 -348 -88 38 37 160 -341 -205 47 -262 41 145 120 7 -264 -388 -19
-28 -364 22 86 69 -344 -250 108 -9 153 95 -185 -17 -174 -192 -72 -165 -153 -352 -294
-146 -443 171 100 -32 -6 175 -314 -80 -144 -205 47 -262 41 27 -178 126 -263 82 -19
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 20 w= 30 nsites= 24 E= 2.2e-094
0.000000 0.000000 0.000000 0.000000 0.000000 0.833333 0.041667 0.000000 0.000000 0.000000 0.000000 0.000000 0.041667 0.000000 0.041667 0.000000 0.000000 0.000000 0.000000 0.041667
0.041667 0.000000 0.000000 0.000000 0.083333 0.625000 0.000000 0.000000 0.000000 0.000000 0.000000 0.083333 0.041667 0.000000 0.000000 0.125000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.583333 0.083333 0.000000 0.083333 0.041667 0.166667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.041667 0.000000 0.000000
0.166667 0.041667 0.000000 0.041667 0.000000 0.208333 0.000000 0.000000 0.000000 0.083333 0.000000 0.083333 0.000000 0.125000 0.041667 0.166667 0.041667 0.000000 0.000000 0.000000
0.041667 0.125000 0.166667 0.000000 0.041667 0.416667 0.000000 0.000000 0.041667 0.041667 0.041667 0.000000 0.041667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.041667
0.000000 0.041667 0.083333 0.000000 0.041667 0.125000 0.041667 0.000000 0.083333 0.041667 0.000000 0.041667 0.041667 0.000000 0.333333 0.041667 0.000000 0.041667 0.041667 0.000000
0.041667 0.041667 0.041667 0.083333 0.000000 0.000000 0.041667 0.083333 0.000000 0.041667 0.000000 0.000000 0.500000 0.000000 0.041667 0.041667 0.000000 0.041667 0.000000 0.000000
0.000000 0.000000 0.000000 0.125000 0.041667 0.375000 0.041667 0.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.000000 0.041667 0.041667 0.041667 0.083333 0.041667 0.000000
0.083333 0.000000 0.083333 0.083333 0.000000 0.166667 0.083333 0.000000 0.250000 0.000000 0.041667 0.083333 0.000000 0.083333 0.000000 0.041667 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.125000 0.416667 0.041667 0.000000 0.083333 0.000000 0.000000 0.208333 0.041667 0.000000 0.000000 0.000000 0.000000 0.041667 0.000000 0.000000 0.000000 0.041667
0.208333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.041667 0.000000 0.041667 0.000000 0.000000 0.208333 0.000000 0.041667 0.166667 0.000000 0.291667 0.000000 0.000000
0.000000 0.000000 0.583333 0.000000 0.000000 0.000000 0.375000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.041667 0.000000 0.000000 0.000000 0.000000 0.000000
0.083333 0.000000 0.000000 0.000000 0.083333 0.166667 0.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.041667 0.000000 0.000000 0.041667 0.166667 0.166667 0.000000 0.000000
0.125000 0.208333 0.000000 0.000000 0.083333 0.166667 0.000000 0.000000 0.000000 0.083333 0.000000 0.041667 0.000000 0.000000 0.166667 0.000000 0.000000 0.000000 0.000000 0.125000
0.000000 0.000000 0.000000 0.000000 0.083333 0.083333 0.208333 0.000000 0.000000 0.000000 0.000000 0.000000 0.041667 0.083333 0.000000 0.083333 0.041667 0.000000 0.000000 0.375000
0.125000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.125000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.458333 0.041667 0.000000 0.000000
0.000000 0.083333 0.000000 0.000000 0.291667 0.000000 0.000000 0.000000 0.000000 0.125000 0.000000 0.041667 0.000000 0.000000 0.000000 0.041667 0.000000 0.041667 0.083333 0.291667
0.083333 0.291667 0.000000 0.000000 0.083333 0.000000 0.000000 0.000000 0.000000 0.041667 0.000000 0.000000 0.000000 0.000000 0.000000 0.083333 0.083333 0.000000 0.250000 0.083333
0.416667 0.208333 0.000000 0.000000 0.000000 0.208333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.041667 0.000000 0.000000 0.000000 0.125000 0.000000 0.000000
0.083333 0.000000 0.000000 0.000000 0.000000 0.041667 0.000000 0.083333 0.000000 0.458333 0.000000 0.000000 0.000000 0.000000 0.000000 0.041667 0.083333 0.208333 0.000000 0.000000
0.291667 0.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.000000 0.000000 0.041667 0.000000 0.125000 0.000000 0.083333 0.000000 0.250000 0.041667 0.000000 0.000000 0.000000
0.291667 0.000000 0.000000 0.000000 0.041667 0.166667 0.000000 0.125000 0.000000 0.041667 0.000000 0.000000 0.000000 0.000000 0.000000 0.208333 0.083333 0.041667 0.000000 0.000000
0.125000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.875000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.416667 0.083333 0.000000 0.000000 0.000000 0.000000 0.041667 0.000000 0.041667 0.000000 0.000000 0.000000 0.041667 0.000000 0.000000 0.250000 0.083333 0.041667 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.416667 0.000000 0.458333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.041667 0.083333 0.000000 0.000000
0.125000 0.041667 0.000000 0.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.458333 0.041667 0.000000 0.000000 0.000000 0.000000 0.000000 0.083333 0.000000 0.000000 0.083333
0.000000 0.000000 0.166667 0.125000 0.000000 0.291667 0.041667 0.000000 0.041667 0.000000 0.000000 0.125000 0.000000 0.041667 0.041667 0.083333 0.041667 0.000000 0.000000 0.000000
0.083333 0.000000 0.000000 0.083333 0.000000 0.041667 0.041667 0.083333 0.166667 0.000000 0.000000 0.041667 0.000000 0.041667 0.125000 0.208333 0.041667 0.000000 0.000000 0.041667
0.041667 0.000000 0.083333 0.125000 0.083333 0.000000 0.000000 0.125000 0.041667 0.375000 0.041667 0.000000 0.041667 0.000000 0.000000 0.041667 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.250000 0.125000 0.041667 0.083333 0.125000 0.000000 0.000000 0.041667 0.000000 0.041667 0.000000 0.041667 0.041667 0.000000 0.125000 0.000000 0.041667 0.041667
--------------------------------------------------------------------------------
Time 32.68 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 14 sites = 21 llr = 376 E-value = 3.1e-019
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A ::::111::::1::
pos.-specific C ::::::::::::61
probability D 12:11::1::::::
matrix E 1::61::2::::::
F 1:::::::5:::::
G ::::1:::::::::
H ::::::::::::::
I 5::::12::4::::
K ::313:::::11:1
L 11:::53::24:1:
M ::::::::::::::
N :4::::::::::::
P ::::::::::::::
Q ::1::::2:::::6
R ::1:::1::::11:
S ::::1::1:114::
T ::1::1::::::::
V :12::21::3::::
W ::::::::2:::::
Y ::::::::3:::::
bits 5.8
5.2
4.6
4.0
Information 3.5 *
content 2.9 * **
(25.8 bits) 2.3 * ** **
1.7 **** * ** **
1.2 **************
0.6 **************
0.0 --------------
Multilevel INKEKLLEFILSCQ
consensus YV
sequence WL
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Start P-value Site
------------- ----- --------- --------------
BET2_YEAST 254 2.24e-13 SLAIIGRLDW INYEKLTEFILKCQ DEKKGGISDR
RATRABGERB 258 1.30e-12 SLKIIGRLHW IDREKLRSFILACQ DEETGGFADR
RATRABGERB 162 4.20e-12 TLALLGKLDA INVEKAIEFVLSCM NFDGGFGCRP
RATRABGERB 66 9.60e-12 VMDLMGQLHR MNKEEILVFIKSCQ HECGGVSASI
RAM1_YEAST 278 5.08e-11 SLAILRSMDQ INVEKLLEWSSARQ LQEERGFCGR
CAL1_YEAST 190 5.01e-10 CRSKEDFDEY IDTEKLLGYIMSQQ CYNGAFGAHN
BET2_YEAST 55 6.90e-10 ALCVLDSPET FVKEEVISFVLSCW DDKYGAFAPF
RATRABGERB 114 1.57e-09 ILTLYDSIHV INVDKVVAYVQSLQ KEDGSFAGDI
PFTB_RAT 172 2.34e-09 IIGTEEAYNV INREKLLQYLYSLK QPDGSFLMHV
RAM1_YEAST 330 4.59e-09 ILEAFGYGQC FNKHALRDYILYCC QEKEQPGLRD
CAL1_YEAST 126 1.65e-08 LRDYEYFETI LDKRSLARFVSKCQ RPDRGSFVSC
PFTB_RAT 268 1.65e-08 ALVILKKERS LNLKSLLQWVTSRQ MRFEGGFQGR
PFTB_RAT 220 1.65e-08 VASLTNIITP DLFEGTAEWIARCQ NWEGGIGGVP
RAM1_YEAST 229 2.54e-08 IATLLNILTE ELTEGVLNYLKNCQ NYEGGFGSCP
PFTB_RAT 330 4.58e-08 DPALSMSHWM FHQQALQEYILMCC QCPAGGLLDK
CAL1_YEAST 239 5.86e-08 LLSSLEKLSD KFKEDTITWLLHRQ VSSHGCMKFE
PFTB_RAT 121 1.52e-07 LELLDEPIPQ IVATDVCQFLELCQ SPDGGFGGGP
CAL1_YEAST 362 1.91e-07 IEGKFNGELC IPQEIFNDFSKRCC F
BET2_YEAST 107 4.34e-07 TYDALDVLGK DRKVRLISFIRGNQ LEDGSFQGDR
BET2_YEAST 155 5.01e-07 ALSILGELTS EVVDPAVDFVLKCY NFDGGFGLCP
RAM1_YEAST 180 5.78e-07 CDNIDGCWDR IDRKGIYQWLISLK EPNGGFKTCL
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
BET2_YEAST 4.3e-07 54_[2]_38_[2]_34_[2]_85_[2]_58
RATRABGERB 1.6e-09 65_[2]_34_[2]_34_[2]_82_[2]_60
RAM1_YEAST 5.8e-07 179_[2]_35_[2]_35_[2]_38_[2]_88
CAL1_YEAST 5.9e-08 125_[2]_50_[2]_35_[2]_109_[2]_1
PFTB_RAT 2.3e-09 120_[2]_37_[2]_34_[2]_34_[2]_48_
[2]_94
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=14 seqs=21
BET2_YEAST ( 254) INYEKLTEFILKCQ 1
RATRABGERB ( 258) IDREKLRSFILACQ 1
RATRABGERB ( 162) INVEKAIEFVLSCM 1
RATRABGERB ( 66) MNKEEILVFIKSCQ 1
RAM1_YEAST ( 278) INVEKLLEWSSARQ 1
CAL1_YEAST ( 190) IDTEKLLGYIMSQQ 1
BET2_YEAST ( 55) FVKEEVISFVLSCW 1
RATRABGERB ( 114) INVDKVVAYVQSLQ 1
PFTB_RAT ( 172) INREKLLQYLYSLK 1
RAM1_YEAST ( 330) FNKHALRDYILYCC 1
CAL1_YEAST ( 126) LDKRSLARFVSKCQ 1
PFTB_RAT ( 268) LNLKSLLQWVTSRQ 1
PFTB_RAT ( 220) DLFEGTAEWIARCQ 1
RAM1_YEAST ( 229) ELTEGVLNYLKNCQ 1
PFTB_RAT ( 330) FHQQALQEYILMCC 1
CAL1_YEAST ( 239) KFKEDTITWLLHRQ 1
PFTB_RAT ( 121) IVATDVCQFLELCQ 1
CAL1_YEAST ( 362) IPQEIFNDFSKRCC 1
BET2_YEAST ( 107) DRKVRLISFIRGNQ 1
BET2_YEAST ( 155) EVVDPAVDFVLKCY 1
RAM1_YEAST ( 180) IDRKGIYQWLISLK 1
//
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Motif 2 position-specific scoring matrix
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log-odds matrix: alength= 20 w= 14 n= 1835 bayes= 7.42721 E= 3.1e-019
-180 -316 28 36 140 -376 -308 299 -24 -14 117 -265 -348 -268 -271 -280 -167 -65 -321 -275
-149 -393 133 -139 -11 -301 50 -227 -104 -40 -165 317 0 -117 32 -189 -143 106 -363 -290
-9 -383 -234 -146 -8 -309 -205 -210 224 -111 -154 -135 -277 119 160 -196 94 147 -356 0
-174 -491 57 300 -396 -328 51 -351 95 -378 -243 -145 -289 50 33 -217 12 -38 -433 -348
61 -430 48 71 -335 60 -173 -37 243 -328 -192 -95 2 -80 41 27 -130 -250 -375 -291
55 -332 -507 -413 10 -422 -361 96 -365 194 -94 -334 -390 -340 -334 -331 92 167 -344 -304
61 19 -456 -363 -205 -378 -316 176 -315 118 -79 32 -352 14 98 -285 19 91 -309 10
-6 -431 96 174 -336 -74 -174 -302 -67 -329 -193 61 -249 205 41 72 21 -37 -376 -291
-585 -591 -675 -658 339 -654 -303 -494 -585 -478 -424 -461 -604 -498 -508 -576 -538 -496 362 282
-333 -431 -610 -551 -351 -574 -548 290 -506 94 -192 -471 -535 -506 -502 6 -316 227 -516 -458
-7 -410 -200 4 -314 -290 -182 -28 139 137 97 -106 -256 51 38 25 20 -221 -366 -4
61 -428 -188 -102 -334 -74 52 -298 141 -130 93 61 -249 -81 112 195 -129 -248 -374 -5
-318 386 -431 -324 -470 -438 -297 -372 -61 20 -304 47 -439 41 186 -360 -300 -347 -474 -424
-264 97 -402 -180 -325 -446 -118 -335 29 -335 49 -229 -343 411 -155 -328 -274 -317 47 -50
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Motif 2 position-specific probability matrix
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letter-probability matrix: alength= 20 w= 14 nsites= 21 E= 3.1e-019
0.000000 0.000000 0.095238 0.095238 0.142857 0.000000 0.000000 0.476190 0.047619 0.095238 0.047619 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.190476 0.000000 0.047619 0.000000 0.047619 0.000000 0.000000 0.095238 0.000000 0.380952 0.047619 0.000000 0.047619 0.000000 0.000000 0.142857 0.000000 0.000000
0.047619 0.000000 0.000000 0.000000 0.047619 0.000000 0.000000 0.000000 0.285714 0.047619 0.000000 0.000000 0.000000 0.095238 0.142857 0.000000 0.095238 0.190476 0.000000 0.047619
0.000000 0.000000 0.095238 0.571429 0.000000 0.000000 0.047619 0.000000 0.095238 0.000000 0.000000 0.000000 0.000000 0.047619 0.047619 0.000000 0.047619 0.047619 0.000000 0.000000
0.095238 0.000000 0.095238 0.095238 0.000000 0.142857 0.000000 0.047619 0.333333 0.000000 0.000000 0.000000 0.047619 0.000000 0.047619 0.095238 0.000000 0.000000 0.000000 0.000000
0.095238 0.000000 0.000000 0.000000 0.047619 0.000000 0.000000 0.095238 0.000000 0.476190 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.095238 0.190476 0.000000 0.000000
0.095238 0.047619 0.000000 0.000000 0.000000 0.000000 0.000000 0.190476 0.000000 0.285714 0.000000 0.047619 0.000000 0.047619 0.095238 0.000000 0.047619 0.095238 0.000000 0.047619
0.047619 0.000000 0.142857 0.238095 0.000000 0.047619 0.000000 0.000000 0.000000 0.000000 0.000000 0.047619 0.000000 0.190476 0.047619 0.142857 0.047619 0.047619 0.000000 0.000000
0.000000 0.000000 0.000000 0.000000 0.476190 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.238095 0.285714
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.380952 0.000000 0.238095 0.000000 0.000000 0.000000 0.000000 0.000000 0.095238 0.000000 0.285714 0.000000 0.000000
0.047619 0.000000 0.000000 0.047619 0.000000 0.000000 0.000000 0.047619 0.142857 0.380952 0.047619 0.000000 0.000000 0.047619 0.047619 0.095238 0.047619 0.000000 0.000000 0.047619
0.095238 0.000000 0.000000 0.000000 0.000000 0.047619 0.047619 0.000000 0.142857 0.047619 0.047619 0.047619 0.000000 0.000000 0.095238 0.380952 0.000000 0.000000 0.000000 0.047619
0.000000 0.619048 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.142857 0.000000 0.047619 0.000000 0.047619 0.142857 0.000000 0.000000 0.000000 0.000000 0.000000
0.000000 0.142857 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.095238 0.000000 0.047619 0.000000 0.000000 0.619048 0.000000 0.000000 0.000000 0.000000 0.047619 0.047619
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Time 51.86 secs.
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SUMMARY OF MOTIFS
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Combined block diagrams: non-overlapping sites with p-value < 0.0001
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SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
RAM1_YEAST 2.14e-20 144_[1(1.27e-16)]_5_[2(5.78e-07)]_4_[1(1.33e-13)]_1_[2(2.54e-08)]_4_[1(5.00e-17)]_1_[2(5.08e-11)]_4_[1(3.47e-16)]_4_[2(4.59e-09)]_5_[1(3.52e-13)]_35_[2(9.16e-05)]_4
PFTB_RAT 2.44e-21 120_[2(1.52e-07)]_3_[1(4.30e-19)]_4_[2(2.34e-09)]_3_[1(2.81e-14)]_1_[2(1.65e-08)]_3_[1(1.15e-19)]_1_[2(1.65e-08)]_4_[1(3.17e-16)]_14_[2(4.58e-08)]_4_[1(4.30e-15)]_60
BET2_YEAST 1.02e-27 6_[2(5.17e-05)]_3_[1(3.11e-10)]_1_[2(6.90e-10)]_4_[1(7.78e-14)]_4_[2(4.34e-07)]_3_[1(3.41e-17)]_1_[2(5.01e-07)]_3_[1(2.10e-18)]_21_[1(7.28e-22)]_1_[2(2.24e-13)]_4_[1(6.64e-17)]_24
RATRABGERB 4.90e-26 65_[2(9.60e-12)]_3_[1(2.40e-14)]_1_[2(1.57e-09)]_3_[1(8.19e-19)]_1_[2(4.20e-12)]_3_[1(7.36e-19)]_18_[1(6.18e-21)]_1_[2(1.30e-12)]_4_[1(1.43e-17)]_26
CAL1_YEAST 3.16e-22 125_[2(1.65e-08)]_50_[2(5.01e-10)]_1_[1(1.14e-13)]_4_[2(5.86e-08)]_22_[1(9.17e-20)]_22_[1(5.47e-13)]_5_[2(1.91e-07)]_1
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Stopped because nmotifs = 2 reached.
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CPU: pmgm2
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