******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.5.1 (Release date: Sun Jan 29 10:33:12 2023 -0800) For further information on how to interpret these results please access https://meme-suite.org/meme. To get a copy of the MEME Suite software please access https://meme-suite.org. ******************************************************************************** ******************************************************************************** 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 ******************************************************************************** PRIMARY SEQUENCES= housekeeping.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ OJDOHDAK_00003 1.0000 100 OJDOHDAK_00043 1.0000 100 OJDOHDAK_00050 1.0000 100 OJDOHDAK_00087 1.0000 100 OJDOHDAK_00116 1.0000 100 OJDOHDAK_00147 1.0000 100 OJDOHDAK_00151 1.0000 100 OJDOHDAK_00177 1.0000 100 OJDOHDAK_00178 1.0000 100 OJDOHDAK_00181 1.0000 100 OJDOHDAK_00218 1.0000 100 OJDOHDAK_00236 1.0000 100 OJDOHDAK_00263 1.0000 100 OJDOHDAK_00264 1.0000 100 OJDOHDAK_00371 1.0000 100 OJDOHDAK_00386 1.0000 100 OJDOHDAK_00400 1.0000 100 OJDOHDAK_00420 1.0000 100 OJDOHDAK_00485 1.0000 100 OJDOHDAK_00493 1.0000 100 OJDOHDAK_00497 1.0000 100 OJDOHDAK_00500 1.0000 100 OJDOHDAK_00506 1.0000 100 OJDOHDAK_00511 1.0000 100 OJDOHDAK_00532 1.0000 100 OJDOHDAK_00533 1.0000 100 OJDOHDAK_00548 1.0000 100 OJDOHDAK_00564 1.0000 100 OJDOHDAK_00583 1.0000 100 OJDOHDAK_00630 1.0000 100 OJDOHDAK_00653 1.0000 100 OJDOHDAK_00663 1.0000 100 OJDOHDAK_00695 1.0000 100 OJDOHDAK_00722 1.0000 100 OJDOHDAK_00727 1.0000 100 OJDOHDAK_00736 1.0000 100 OJDOHDAK_00743 1.0000 100 OJDOHDAK_00768 1.0000 100 OJDOHDAK_00800 1.0000 100 OJDOHDAK_00801 1.0000 100 OJDOHDAK_00802 1.0000 100 OJDOHDAK_00805 1.0000 100 OJDOHDAK_00806 1.0000 100 OJDOHDAK_00895 1.0000 100 OJDOHDAK_00957 1.0000 100 OJDOHDAK_01011 1.0000 100 OJDOHDAK_01068 1.0000 100 OJDOHDAK_01076 1.0000 100 OJDOHDAK_01090 1.0000 100 OJDOHDAK_01091 1.0000 100 OJDOHDAK_01092 1.0000 100 OJDOHDAK_01100 1.0000 100 OJDOHDAK_01134 1.0000 100 OJDOHDAK_01163 1.0000 100 OJDOHDAK_01168 1.0000 100 OJDOHDAK_01188 1.0000 100 OJDOHDAK_01225 1.0000 100 OJDOHDAK_01226 1.0000 100 OJDOHDAK_01227 1.0000 100 OJDOHDAK_01228 1.0000 100 OJDOHDAK_01229 1.0000 100 OJDOHDAK_01243 1.0000 100 OJDOHDAK_01248 1.0000 100 OJDOHDAK_01265 1.0000 100 OJDOHDAK_01301 1.0000 100 OJDOHDAK_01338 1.0000 100 OJDOHDAK_01339 1.0000 100 OJDOHDAK_01380 1.0000 100 OJDOHDAK_01401 1.0000 100 OJDOHDAK_01408 1.0000 100 OJDOHDAK_01416 1.0000 100 OJDOHDAK_01422 1.0000 100 OJDOHDAK_01439 1.0000 100 OJDOHDAK_01443 1.0000 100 OJDOHDAK_01445 1.0000 100 OJDOHDAK_01446 1.0000 100 OJDOHDAK_01447 1.0000 100 OJDOHDAK_01453 1.0000 100 OJDOHDAK_01468 1.0000 100 OJDOHDAK_01493 1.0000 100 OJDOHDAK_01494 1.0000 100 OJDOHDAK_01506 1.0000 100 OJDOHDAK_01529 1.0000 100 OJDOHDAK_01532 1.0000 100 OJDOHDAK_01560 1.0000 100 OJDOHDAK_01578 1.0000 100 OJDOHDAK_01587 1.0000 100 OJDOHDAK_01610 1.0000 100 OJDOHDAK_01655 1.0000 100 OJDOHDAK_01665 1.0000 100 OJDOHDAK_01678 1.0000 100 OJDOHDAK_01730 1.0000 100 OJDOHDAK_01779 1.0000 100 OJDOHDAK_01822 1.0000 100 OJDOHDAK_01823 1.0000 100 OJDOHDAK_01839 1.0000 100 OJDOHDAK_01868 1.0000 100 OJDOHDAK_01871 1.0000 100 OJDOHDAK_01903 1.0000 100 OJDOHDAK_01909 1.0000 100 OJDOHDAK_01913 1.0000 100 OJDOHDAK_01916 1.0000 100 OJDOHDAK_01966 1.0000 100 OJDOHDAK_01978 1.0000 100 OJDOHDAK_01993 1.0000 100 OJDOHDAK_02019 1.0000 100 OJDOHDAK_02022 1.0000 100 OJDOHDAK_02023 1.0000 100 OJDOHDAK_02024 1.0000 100 OJDOHDAK_02025 1.0000 100 OJDOHDAK_02041 1.0000 100 OJDOHDAK_02052 1.0000 100 OJDOHDAK_02115 1.0000 100 OJDOHDAK_02125 1.0000 100 OJDOHDAK_02130 1.0000 100 OJDOHDAK_02140 1.0000 100 OJDOHDAK_02145 1.0000 100 OJDOHDAK_02164 1.0000 100 OJDOHDAK_02183 1.0000 100 OJDOHDAK_02195 1.0000 100 OJDOHDAK_02202 1.0000 100 OJDOHDAK_02263 1.0000 100 OJDOHDAK_02286 1.0000 100 OJDOHDAK_02287 1.0000 100 OJDOHDAK_02288 1.0000 100 OJDOHDAK_02289 1.0000 100 OJDOHDAK_02293 1.0000 100 OJDOHDAK_02294 1.0000 100 OJDOHDAK_02295 1.0000 100 OJDOHDAK_02296 1.0000 100 OJDOHDAK_02297 1.0000 100 OJDOHDAK_02298 1.0000 100 OJDOHDAK_02299 1.0000 100 OJDOHDAK_02300 1.0000 100 OJDOHDAK_02301 1.0000 100 OJDOHDAK_02302 1.0000 100 OJDOHDAK_02303 1.0000 100 OJDOHDAK_02304 1.0000 100 OJDOHDAK_02305 1.0000 100 OJDOHDAK_02306 1.0000 100 OJDOHDAK_02307 1.0000 100 OJDOHDAK_02308 1.0000 100 OJDOHDAK_02309 1.0000 100 OJDOHDAK_02310 1.0000 100 OJDOHDAK_02311 1.0000 100 OJDOHDAK_02312 1.0000 100 OJDOHDAK_02313 1.0000 100 OJDOHDAK_02314 1.0000 100 OJDOHDAK_02315 1.0000 100 OJDOHDAK_02316 1.0000 100 OJDOHDAK_02317 1.0000 100 OJDOHDAK_02320 1.0000 100 OJDOHDAK_02370 1.0000 100 OJDOHDAK_02412 1.0000 100 OJDOHDAK_02426 1.0000 100 OJDOHDAK_02496 1.0000 100 OJDOHDAK_02507 1.0000 100 OJDOHDAK_02518 1.0000 100 OJDOHDAK_02532 1.0000 100 OJDOHDAK_02566 1.0000 100 OJDOHDAK_02651 1.0000 100 OJDOHDAK_02667 1.0000 100 OJDOHDAK_02680 1.0000 100 OJDOHDAK_02693 1.0000 100 OJDOHDAK_02713 1.0000 100 OJDOHDAK_02754 1.0000 100 OJDOHDAK_02776 1.0000 100 OJDOHDAK_02800 1.0000 100 OJDOHDAK_02832 1.0000 100 OJDOHDAK_02844 1.0000 100 OJDOHDAK_02872 1.0000 100 OJDOHDAK_02889 1.0000 100 OJDOHDAK_02902 1.0000 100 OJDOHDAK_02913 1.0000 100 OJDOHDAK_02919 1.0000 100 OJDOHDAK_02921 1.0000 100 OJDOHDAK_02933 1.0000 100 OJDOHDAK_02935 1.0000 100 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme housekeeping.fasta -dna -mod zoops -nmotifs 3 -minw 6 -maxw 50 -maxsites 50 model: mod= zoops nmotifs= 3 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + width: minw= 6 maxw= 50 nsites: minsites= 2 maxsites= 50 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 trim: wg= 11 ws= 1 endgaps= yes data: n= 17800 N= 178 sample: seed= 0 hsfrac= 0 searchsize= 17800 norand= no csites= 1000 Letter frequencies in dataset: A 0.197 C 0.3 G 0.301 T 0.202 Background letter frequencies (from file dataset with add-one prior applied): A 0.197 C 0.3 G 0.301 T 0.202 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CGSSRCHWKKAGAGDCCAVBCSRTWYBWGAARRMTDSSTWVMRAVGRTBD MEME-1 width = 50 sites = 9 llr = 252 E-value = 8.3e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGSSRCHWKKAGAGDCCAVBCSRTWYBWGAARRMTDSSTWVMRAVGRTBD MEME-1 Description -------------------------------------------------------------------------------- Simplified A 2::16234::62922:29311:627:1327643413112424693141:2 pos.-specific C 7166162:::2211177:4467:::43::11:131134::46:13:::2: probability G :94331::67:6:64111221341:12:821661:2642:3:4:396:33 matrix T 1::::146432::122:::22::73437::2::183::66:::::::944 bits 2.3 2.1 1.9 * * * * 1.6 * * * * Relative 1.4 * * * * * * * * * Entropy 1.2 * * * * * * ** * * ** * * (40.5 bits) 0.9 * *** * * *** *** * * * *** *** 0.7 *** * ***** * *** ***** *** ** * ** *** *** * 0.5 ***** ******* **** ***** ****** * **** ********* 0.2 ******************* ****** *********************** 0.0 -------------------------------------------------- Multilevel CGCCACTTGGAGAGGCCACCCCATACCTGAAGGATAGCTTCCAAAGGTTT consensus A GGGAAATTCA AATA AGTGGATTTAAGTAAC TCGAAGAG C A GG sequence C TC T GT G G G A G CA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGSSRCHWKKAGAGDCCAVBCSRTWYBWGAARRMTDSSTWVMRAVGRTBD MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------------------------------------- OJDOHDAK_02935 11 9.63e-21 AGTCTGAAAG AGCCACAAGGAGAGGCCACCCCATACGAGAAGGCTAGCTACCAACGGTTT CTGACTATAG OJDOHDAK_00003 11 9.63e-21 AGTCTGAAAG AGCCACAAGGAGAGGCCACCCCATACGAGAAGGCTAGCTACCAACGGTTT CTGACTATAG OJDOHDAK_00116 26 2.02e-14 ATCCTCTGGC CGGGCATTTGAAATATCAAGTGATATCTGAAAATTTGGTTCCGAAAATCA GGACTTTTGA OJDOHDAK_02713 17 2.50e-13 CTATTGCGGG CGGCACCTTGCAAGTCCAATGCGAATTTGCAAAATCCGGTAAGCAGGTTT TGCAAAACAA OJDOHDAK_02024 39 2.50e-13 ATAGACTTGC TGCGGCTTTTAGAAGTGACTAGGAAGTTAGTAGATTAGTTCAAAAGGTTT CCTCAAAAAC OJDOHDAK_01401 10 3.98e-13 ATGGGGCCG CGCAGGTTTTTGACGCAAGACCATTTCTGGCAAATTGATTGAAAGGATGG GCGCCTGGCG OJDOHDAK_00147 46 4.13e-12 ACCGTATTTT CCGCAAAAGGCCAGACCGACTGGTTCATGAAGGAAACCAAGCGAGGGTCG AAGAG OJDOHDAK_01578 48 1.01e-11 CCAGCCGCCG CGCCATCTGGAGAACGCAGGCCAGTTCTGATGCCTGCCATAAAAGGAAGA ACC OJDOHDAK_00768 46 1.66e-11 GGTCTAAGGG CGGGGCTAGTTCCGTCAACCCCGTACTAAAGGGGCGGGGAGCGACGATGG CGGAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGSSRCHWKKAGAGDCCAVBCSRTWYBWGAARRMTDSSTWVMRAVGRTBD MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- OJDOHDAK_02935 9.6e-21 10_[+1]_40 OJDOHDAK_00003 9.6e-21 10_[+1]_40 OJDOHDAK_00116 2e-14 25_[+1]_25 OJDOHDAK_02713 2.5e-13 16_[+1]_34 OJDOHDAK_02024 2.5e-13 38_[+1]_12 OJDOHDAK_01401 4e-13 9_[+1]_41 OJDOHDAK_00147 4.1e-12 45_[+1]_5 OJDOHDAK_01578 1e-11 47_[+1]_3 OJDOHDAK_00768 1.7e-11 45_[+1]_5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGSSRCHWKKAGAGDCCAVBCSRTWYBWGAARRMTDSSTWVMRAVGRTBD MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CGSSRCHWKKAGAGDCCAVBCSRTWYBWGAARRMTDSSTWVMRAVGRTBD width=50 seqs=9 OJDOHDAK_02935 ( 11) AGCCACAAGGAGAGGCCACCCCATACGAGAAGGCTAGCTACCAACGGTTT 1 OJDOHDAK_00003 ( 11) AGCCACAAGGAGAGGCCACCCCATACGAGAAGGCTAGCTACCAACGGTTT 1 OJDOHDAK_00116 ( 26) CGGGCATTTGAAATATCAAGTGATATCTGAAAATTTGGTTCCGAAAATCA 1 OJDOHDAK_02713 ( 17) CGGCACCTTGCAAGTCCAATGCGAATTTGCAAAATCCGGTAAGCAGGTTT 1 OJDOHDAK_02024 ( 39) TGCGGCTTTTAGAAGTGACTAGGAAGTTAGTAGATTAGTTCAAAAGGTTT 1 OJDOHDAK_01401 ( 10) CGCAGGTTTTTGACGCAAGACCATTTCTGGCAAATTGATTGAAAGGATGG 1 OJDOHDAK_00147 ( 46) CCGCAAAAGGCCAGACCGACTGGTTCATGAAGGAAACCAAGCGAGGGTCG 1 OJDOHDAK_01578 ( 48) CGCCATCTGGAGAACGCAGGCCAGTTCTGATGCCTGCCATAAAAGGAAGA 1 OJDOHDAK_00768 ( 46) CGGGGCTAGTTCCGTCAACCCCGTACTAAAGGGGCGGGGAGCGACGATGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGSSRCHWKKAGAGDCCAVBCSRTWYBWGAARRMTDSSTWVMRAVGRTBD MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 50 n= 9078 bayes= 10.1112 E= 8.3e-007 17 115 -982 -86 -982 -143 156 -982 -982 89 56 -982 -83 89 15 -982 149 -143 15 -982 17 89 -143 -86 76 -43 -982 113 117 -982 -982 146 -982 -982 89 113 -982 -982 115 72 149 -43 -982 14 17 -43 89 -982 217 -143 -982 -982 17 -143 89 -86 17 -143 56 14 -982 115 -143 14 17 115 -143 -982 217 -982 -143 -982 76 57 -44 -982 -83 57 -44 14 -83 89 -143 14 -982 115 15 -982 149 -982 56 -982 17 -982 -143 172 176 -982 -982 72 -982 57 -143 113 -83 15 -44 72 76 -982 -982 172 17 -982 137 -982 176 -143 -44 -982 149 -143 -143 14 117 -982 89 -982 76 -143 89 -982 117 15 -143 -86 -83 -143 -982 194 76 -143 -44 72 -83 15 89 -982 -83 57 56 -982 17 -982 -44 146 117 -982 -982 146 17 57 15 -982 117 89 -982 -982 149 -982 56 -982 217 -143 -982 -982 76 15 15 -982 -83 -982 156 -982 117 -982 89 -982 -83 -982 -982 213 -982 -43 15 113 17 -982 15 113 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGSSRCHWKKAGAGDCCAVBCSRTWYBWGAARRMTDSSTWVMRAVGRTBD MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 50 nsites= 9 E= 8.3e-007 0.222222 0.666667 0.000000 0.111111 0.000000 0.111111 0.888889 0.000000 0.000000 0.555556 0.444444 0.000000 0.111111 0.555556 0.333333 0.000000 0.555556 0.111111 0.333333 0.000000 0.222222 0.555556 0.111111 0.111111 0.333333 0.222222 0.000000 0.444444 0.444444 0.000000 0.000000 0.555556 0.000000 0.000000 0.555556 0.444444 0.000000 0.000000 0.666667 0.333333 0.555556 0.222222 0.000000 0.222222 0.222222 0.222222 0.555556 0.000000 0.888889 0.111111 0.000000 0.000000 0.222222 0.111111 0.555556 0.111111 0.222222 0.111111 0.444444 0.222222 0.000000 0.666667 0.111111 0.222222 0.222222 0.666667 0.111111 0.000000 0.888889 0.000000 0.111111 0.000000 0.333333 0.444444 0.222222 0.000000 0.111111 0.444444 0.222222 0.222222 0.111111 0.555556 0.111111 0.222222 0.000000 0.666667 0.333333 0.000000 0.555556 0.000000 0.444444 0.000000 0.222222 0.000000 0.111111 0.666667 0.666667 0.000000 0.000000 0.333333 0.000000 0.444444 0.111111 0.444444 0.111111 0.333333 0.222222 0.333333 0.333333 0.000000 0.000000 0.666667 0.222222 0.000000 0.777778 0.000000 0.666667 0.111111 0.222222 0.000000 0.555556 0.111111 0.111111 0.222222 0.444444 0.000000 0.555556 0.000000 0.333333 0.111111 0.555556 0.000000 0.444444 0.333333 0.111111 0.111111 0.111111 0.111111 0.000000 0.777778 0.333333 0.111111 0.222222 0.333333 0.111111 0.333333 0.555556 0.000000 0.111111 0.444444 0.444444 0.000000 0.222222 0.000000 0.222222 0.555556 0.444444 0.000000 0.000000 0.555556 0.222222 0.444444 0.333333 0.000000 0.444444 0.555556 0.000000 0.000000 0.555556 0.000000 0.444444 0.000000 0.888889 0.111111 0.000000 0.000000 0.333333 0.333333 0.333333 0.000000 0.111111 0.000000 0.888889 0.000000 0.444444 0.000000 0.555556 0.000000 0.111111 0.000000 0.000000 0.888889 0.000000 0.222222 0.333333 0.444444 0.222222 0.000000 0.333333 0.444444 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGSSRCHWKKAGAGDCCAVBCSRTWYBWGAARRMTDSSTWVMRAVGRTBD MEME-1 regular expression -------------------------------------------------------------------------------- [CA]G[CG][CG][AG][CA][TAC][TA][GT][GT][ACT][GAC]A[GA][GAT][CT][CA]A[CAG][CGT][CT][CG][AG][TA][AT][CT][CTG][TA][GA][AG][AT][GA][GA][AC]T[ATG][GC][CG][TAG][TA][CGA][CA][AG]A[ACG]G[GA]T[TGC][TGA] -------------------------------------------------------------------------------- Time 16.17 secs. ******************************************************************************** ******************************************************************************** MOTIF KGCSGTTCTTCTWC MEME-2 width = 14 sites = 21 llr = 223 E-value = 2.7e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif KGCSGTTCTTCTWC MEME-2 Description -------------------------------------------------------------------------------- Simplified A :1::::2::1::3: pos.-specific C :1752219::91:8 probability G 66248::1::12:: matrix T 42:1:87:a9:772 bits 2.3 * 2.1 * 1.9 * 1.6 ** Relative 1.4 * ** * Entropy 1.2 ****** ** (15.4 bits) 0.9 * ********* 0.7 * * ********** 0.5 * ************ 0.2 ************** 0.0 -------------- Multilevel GGCCGTTCTTCTTC consensus T GG CA A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGCSGTTCTTCTWC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- OJDOHDAK_02288 34 7.52e-09 TTCGGCTAGC GGCCGTTCTTCTTC ATTAAGTGAC OJDOHDAK_02308 76 1.51e-07 GCCAGGGCAG TGCGCTTCTTCTTC TCCATTCTGG OJDOHDAK_02296 83 2.73e-07 AAGGCGTTCC TTCCCTTCTTCTTC ATTC OJDOHDAK_01779 76 2.73e-07 AGGCGCGCCT GGCTGTTCTTCTAC CCTCGCCGGA OJDOHDAK_01090 7 2.73e-07 GGCAGA GGCGGTTCTTCGTC GCGCTCGACA OJDOHDAK_02302 76 6.03e-07 TACAGGGCCG TTCGGCTCTTCTTC CTTGGCCTAG OJDOHDAK_02300 56 6.03e-07 CTTTGCTTCC TGCCGTTCTTCCAC GCGCAACGGC OJDOHDAK_02311 75 1.59e-06 CACGGGCTGC GGCCGCTCTTGTTC CTCCCGACTA OJDOHDAK_01225 3 3.73e-06 CT TCCGGTTCTTCGAC CGGCTTCTGC OJDOHDAK_00371 80 3.73e-06 CGTCCGGGCA GTCGGTTCTTCCTT ATATGCT OJDOHDAK_00532 76 4.10e-06 CGACGGGCGT TAGCGTTCTTGTTC CAATCGCGCA OJDOHDAK_02287 72 9.15e-06 CCGCCTACCG GTGGGTTCTTGTTT GGGGTCCCCT OJDOHDAK_02304 28 1.09e-05 AAGCTCGCGC GGCGCTACTTCGAC GGCTAGTTCT OJDOHDAK_00743 73 1.39e-05 CGACTAGCCG GGCTGTACTACTTT GAGCTGGAAG OJDOHDAK_00218 82 1.39e-05 AGTAGCGACG GGACGTCCTTCTAC GCGCG OJDOHDAK_00500 54 2.01e-05 GATGCGGCCT GGGCCTACTTCGAC GTCGCCCTGC OJDOHDAK_01227 8 2.33e-05 TTCAAGC TCCCGCTCTGCTTC CTGTTCTGGC OJDOHDAK_01134 84 2.33e-05 GTCGTCCCCC GACCGCCCTTCTAC TTG OJDOHDAK_00236 82 2.67e-05 ACCGACGACC TGGCGTAGTTCCTC GTAAG OJDOHDAK_01439 73 3.27e-05 CGGCTCGACC TCGCGTACTACTTT CTTTCCTTGC OJDOHDAK_02307 76 3.49e-05 GGCCCAGTGC GGCGTCTGTTCTTC CCGTTCGCGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGCSGTTCTTCTWC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- OJDOHDAK_02288 7.5e-09 33_[+2]_53 OJDOHDAK_02308 1.5e-07 75_[+2]_11 OJDOHDAK_02296 2.7e-07 82_[+2]_4 OJDOHDAK_01779 2.7e-07 75_[+2]_11 OJDOHDAK_01090 2.7e-07 6_[+2]_80 OJDOHDAK_02302 6e-07 75_[+2]_11 OJDOHDAK_02300 6e-07 55_[+2]_31 OJDOHDAK_02311 1.6e-06 74_[+2]_12 OJDOHDAK_01225 3.7e-06 2_[+2]_84 OJDOHDAK_00371 3.7e-06 79_[+2]_7 OJDOHDAK_00532 4.1e-06 75_[+2]_11 OJDOHDAK_02287 9.1e-06 71_[+2]_15 OJDOHDAK_02304 1.1e-05 27_[+2]_59 OJDOHDAK_00743 1.4e-05 72_[+2]_14 OJDOHDAK_00218 1.4e-05 81_[+2]_5 OJDOHDAK_00500 2e-05 53_[+2]_33 OJDOHDAK_01227 2.3e-05 7_[+2]_79 OJDOHDAK_01134 2.3e-05 83_[+2]_3 OJDOHDAK_00236 2.7e-05 81_[+2]_5 OJDOHDAK_01439 3.3e-05 72_[+2]_14 OJDOHDAK_02307 3.5e-05 75_[+2]_11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGCSGTTCTTCTWC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF KGCSGTTCTTCTWC width=14 seqs=21 OJDOHDAK_02288 ( 34) GGCCGTTCTTCTTC 1 OJDOHDAK_02308 ( 76) TGCGCTTCTTCTTC 1 OJDOHDAK_02296 ( 83) TTCCCTTCTTCTTC 1 OJDOHDAK_01779 ( 76) GGCTGTTCTTCTAC 1 OJDOHDAK_01090 ( 7) GGCGGTTCTTCGTC 1 OJDOHDAK_02302 ( 76) TTCGGCTCTTCTTC 1 OJDOHDAK_02300 ( 56) TGCCGTTCTTCCAC 1 OJDOHDAK_02311 ( 75) GGCCGCTCTTGTTC 1 OJDOHDAK_01225 ( 3) TCCGGTTCTTCGAC 1 OJDOHDAK_00371 ( 80) GTCGGTTCTTCCTT 1 OJDOHDAK_00532 ( 76) TAGCGTTCTTGTTC 1 OJDOHDAK_02287 ( 72) GTGGGTTCTTGTTT 1 OJDOHDAK_02304 ( 28) GGCGCTACTTCGAC 1 OJDOHDAK_00743 ( 73) GGCTGTACTACTTT 1 OJDOHDAK_00218 ( 82) GGACGTCCTTCTAC 1 OJDOHDAK_00500 ( 54) GGGCCTACTTCGAC 1 OJDOHDAK_01227 ( 8) TCCCGCTCTGCTTC 1 OJDOHDAK_01134 ( 84) GACCGCCCTTCTAC 1 OJDOHDAK_00236 ( 82) TGGCGTAGTTCCTC 1 OJDOHDAK_01439 ( 73) TCGCGTACTACTTT 1 OJDOHDAK_02307 ( 76) GGCGTCTGTTCTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGCSGTTCTTCTWC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 15486 bayes= 10.5117 E= 2.7e-002 -1104 -1104 93 108 -105 -107 93 -9 -205 125 -34 -1104 -1104 80 34 -109 -1104 -66 134 -208 -1104 -33 -1104 191 27 -165 -1104 172 -1104 159 -166 -1104 -1104 -1104 -1104 231 -105 -1104 -265 208 -1104 151 -107 -1104 -1104 -107 -66 172 76 -1104 -1104 172 -1104 143 -1104 -9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGCSGTTCTTCTWC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 21 E= 2.7e-002 0.000000 0.000000 0.571429 0.428571 0.095238 0.142857 0.571429 0.190476 0.047619 0.714286 0.238095 0.000000 0.000000 0.523810 0.380952 0.095238 0.000000 0.190476 0.761905 0.047619 0.000000 0.238095 0.000000 0.761905 0.238095 0.095238 0.000000 0.666667 0.000000 0.904762 0.095238 0.000000 0.000000 0.000000 0.000000 1.000000 0.095238 0.000000 0.047619 0.857143 0.000000 0.857143 0.142857 0.000000 0.000000 0.142857 0.190476 0.666667 0.333333 0.000000 0.000000 0.666667 0.000000 0.809524 0.000000 0.190476 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGCSGTTCTTCTWC MEME-2 regular expression -------------------------------------------------------------------------------- [GT]G[CG][CG]G[TC][TA]CTTCT[TA]C -------------------------------------------------------------------------------- Time 31.52 secs. ******************************************************************************** ******************************************************************************** MOTIF AVAATCCSAGTADSGTCCTBCCAT MEME-3 width = 24 sites = 4 llr = 103 E-value = 6.7e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif AVAATCCSAGTADSGTCCTBCCAT MEME-3 Description -------------------------------------------------------------------------------- Simplified A a38a3:::a3:83:::::::::8: pos.-specific C :3:::aa5:::3:5::aa:5aa3: probability G :5:::::5:8::35a3:::3:::: matrix T ::3:8:::::a:5::8::a3:::a bits 2.3 * * * * * * 2.1 * * * * * * 1.9 * * * * * * 1.6 * * ** * * * *** ** * Relative 1.4 * ***** * ** ***** **** Entropy 1.2 * ***** **** ***** **** (37.2 bits) 0.9 * ***** **** ***** **** 0.7 * ***************** **** 0.5 ************************ 0.2 ************************ 0.0 ------------------------ Multilevel AGAATCCCAGTATCGTCCTCCCAT consensus AT A G A CAG G G C sequence C G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AVAATCCSAGTADSGTCCTBCCAT MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------ OJDOHDAK_02935 72 8.55e-15 TGACTATAGC AGAATCCCAGTATGGTCCTCCCAT ACAGC OJDOHDAK_00003 72 8.55e-15 TGACTATAGC AGAATCCCAGTATGGTCCTCCCAT ACAGC OJDOHDAK_00485 9 2.72e-12 CAGCCTTT AAAAACCGAATAACGTCCTGCCAT CGCCGAACTG OJDOHDAK_01978 68 2.18e-11 AGGCGCCCTG ACTATCCGAGTCGCGGCCTTCCCT GCCTATTAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AVAATCCSAGTADSGTCCTBCCAT MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- OJDOHDAK_02935 8.6e-15 71_[+3]_5 OJDOHDAK_00003 8.6e-15 71_[+3]_5 OJDOHDAK_00485 2.7e-12 8_[+3]_68 OJDOHDAK_01978 2.2e-11 67_[+3]_9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AVAATCCSAGTADSGTCCTBCCAT MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AVAATCCSAGTADSGTCCTBCCAT width=24 seqs=4 OJDOHDAK_02935 ( 72) AGAATCCCAGTATGGTCCTCCCAT 1 OJDOHDAK_00003 ( 72) AGAATCCCAGTATGGTCCTCCCAT 1 OJDOHDAK_00485 ( 9) AAAAACCGAATAACGTCCTGCCAT 1 OJDOHDAK_01978 ( 68) ACTATCCGAGTCGCGGCCTTCCCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AVAATCCSAGTADSGTCCTBCCAT MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 24 n= 13706 bayes= 11.7421 E= 6.7e-001 234 -865 -865 -865 34 -26 73 -865 192 -865 -865 31 234 -865 -865 -865 34 -865 -865 189 -865 173 -865 -865 -865 173 -865 -865 -865 74 73 -865 234 -865 -865 -865 34 -865 132 -865 -865 -865 -865 230 192 -26 -865 -865 34 -865 -26 130 -865 74 73 -865 -865 -865 173 -865 -865 -865 -26 189 -865 173 -865 -865 -865 173 -865 -865 -865 -865 -865 230 -865 74 -26 31 -865 173 -865 -865 -865 173 -865 -865 192 -26 -865 -865 -865 -865 -865 230 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AVAATCCSAGTADSGTCCTBCCAT MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 24 nsites= 4 E= 6.7e-001 1.000000 0.000000 0.000000 0.000000 0.250000 0.250000 0.500000 0.000000 0.750000 0.000000 0.000000 0.250000 1.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.750000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 0.000000 1.000000 0.750000 0.250000 0.000000 0.000000 0.250000 0.000000 0.250000 0.500000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.250000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AVAATCCSAGTADSGTCCTBCCAT MEME-3 regular expression -------------------------------------------------------------------------------- A[GAC][AT]A[TA]CC[CG]A[GA]T[AC][TAG][CG]G[TG]CCT[CGT]CC[AC]T -------------------------------------------------------------------------------- Time 46.23 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- OJDOHDAK_00003 6.15e-28 10_[+1(9.63e-21)]_11_[+3(8.55e-15)]_\ 5 OJDOHDAK_00043 7.39e-02 100 OJDOHDAK_00050 3.95e-02 100 OJDOHDAK_00087 2.90e-01 100 OJDOHDAK_00116 1.52e-10 25_[+1(2.02e-14)]_25 OJDOHDAK_00147 2.70e-08 45_[+1(4.13e-12)]_5 OJDOHDAK_00151 6.40e-01 100 OJDOHDAK_00177 7.76e-01 100 OJDOHDAK_00178 8.18e-01 100 OJDOHDAK_00181 7.89e-01 100 OJDOHDAK_00218 3.93e-03 81_[+2(1.39e-05)]_5 OJDOHDAK_00236 4.00e-02 81_[+2(2.67e-05)]_5 OJDOHDAK_00263 2.41e-01 100 OJDOHDAK_00264 9.51e-01 100 OJDOHDAK_00371 1.13e-02 79_[+2(3.73e-06)]_7 OJDOHDAK_00386 2.12e-01 100 OJDOHDAK_00400 1.26e-01 100 OJDOHDAK_00420 3.46e-01 100 OJDOHDAK_00485 1.03e-09 8_[+3(2.72e-12)]_68 OJDOHDAK_00493 7.27e-01 100 OJDOHDAK_00497 7.65e-02 32_[+3(9.04e-05)]_44 OJDOHDAK_00500 4.43e-03 53_[+2(2.01e-05)]_33 OJDOHDAK_00506 5.53e-01 100 OJDOHDAK_00511 2.16e-01 100 OJDOHDAK_00532 9.70e-03 75_[+2(4.10e-06)]_11 OJDOHDAK_00533 7.99e-01 100 OJDOHDAK_00548 1.82e-01 100 OJDOHDAK_00564 7.11e-01 100 OJDOHDAK_00583 7.77e-01 100 OJDOHDAK_00630 4.27e-01 100 OJDOHDAK_00653 9.77e-01 100 OJDOHDAK_00663 4.03e-01 100 OJDOHDAK_00695 8.74e-01 100 OJDOHDAK_00722 1.37e-01 100 OJDOHDAK_00727 3.01e-01 100 OJDOHDAK_00736 2.97e-01 100 OJDOHDAK_00743 9.70e-03 72_[+2(1.39e-05)]_14 OJDOHDAK_00768 4.39e-08 45_[+1(1.66e-11)]_5 OJDOHDAK_00800 5.93e-01 100 OJDOHDAK_00801 1.08e-01 100 OJDOHDAK_00802 1.52e-01 100 OJDOHDAK_00805 4.39e-01 100 OJDOHDAK_00806 2.21e-01 100 OJDOHDAK_00895 5.90e-01 100 OJDOHDAK_00957 7.93e-01 100 OJDOHDAK_01011 9.65e-01 100 OJDOHDAK_01068 5.80e-01 100 OJDOHDAK_01076 7.88e-01 100 OJDOHDAK_01090 5.48e-04 6_[+2(2.73e-07)]_80 OJDOHDAK_01091 1.30e-01 100 OJDOHDAK_01092 4.20e-01 100 OJDOHDAK_01100 8.54e-01 100 OJDOHDAK_01134 8.38e-03 83_[+2(2.33e-05)]_3 OJDOHDAK_01163 5.15e-01 100 OJDOHDAK_01168 5.02e-01 100 OJDOHDAK_01188 2.73e-01 100 OJDOHDAK_01225 7.67e-03 2_[+2(3.73e-06)]_84 OJDOHDAK_01226 2.73e-01 100 OJDOHDAK_01227 1.80e-02 7_[+2(2.33e-05)]_79 OJDOHDAK_01228 6.50e-02 100 OJDOHDAK_01229 6.90e-01 100 OJDOHDAK_01243 2.58e-01 100 OJDOHDAK_01248 7.95e-01 100 OJDOHDAK_01265 5.38e-01 100 OJDOHDAK_01301 4.07e-01 100 OJDOHDAK_01338 4.57e-01 100 OJDOHDAK_01339 3.28e-01 100 OJDOHDAK_01380 6.89e-01 100 OJDOHDAK_01401 2.23e-10 9_[+1(3.98e-13)]_41 OJDOHDAK_01408 1.80e-02 35_[+3(1.50e-05)]_41 OJDOHDAK_01416 5.52e-01 100 OJDOHDAK_01422 8.97e-01 100 OJDOHDAK_01439 3.51e-02 72_[+2(3.27e-05)]_14 OJDOHDAK_01443 9.40e-01 100 OJDOHDAK_01445 7.96e-01 100 OJDOHDAK_01446 8.93e-01 100 OJDOHDAK_01447 8.34e-01 100 OJDOHDAK_01453 7.24e-01 100 OJDOHDAK_01468 6.88e-01 100 OJDOHDAK_01493 8.22e-01 100 OJDOHDAK_01494 8.92e-01 100 OJDOHDAK_01506 6.06e-01 100 OJDOHDAK_01529 7.25e-01 100 OJDOHDAK_01532 1.16e-01 100 OJDOHDAK_01560 6.51e-01 100 OJDOHDAK_01578 7.43e-08 47_[+1(1.01e-11)]_3 OJDOHDAK_01587 5.34e-01 100 OJDOHDAK_01610 2.42e-01 100 OJDOHDAK_01655 2.99e-01 100 OJDOHDAK_01665 9.15e-01 100 OJDOHDAK_01678 6.18e-01 100 OJDOHDAK_01730 7.15e-02 100 OJDOHDAK_01779 5.17e-04 75_[+2(2.73e-07)]_11 OJDOHDAK_01822 3.77e-01 100 OJDOHDAK_01823 7.23e-01 100 OJDOHDAK_01839 2.84e-01 100 OJDOHDAK_01868 8.83e-01 100 OJDOHDAK_01871 7.12e-01 100 OJDOHDAK_01903 7.44e-01 100 OJDOHDAK_01909 3.71e-01 100 OJDOHDAK_01913 2.00e-01 100 OJDOHDAK_01916 5.51e-01 100 OJDOHDAK_01966 9.93e-01 100 OJDOHDAK_01978 4.49e-08 67_[+3(2.18e-11)]_9 OJDOHDAK_01993 1.24e-01 100 OJDOHDAK_02019 2.08e-02 [+1(4.43e-05)]_50 OJDOHDAK_02022 3.39e-01 100 OJDOHDAK_02023 8.40e-01 100 OJDOHDAK_02024 1.88e-09 38_[+1(2.50e-13)]_12 OJDOHDAK_02025 5.83e-01 100 OJDOHDAK_02041 5.84e-01 100 OJDOHDAK_02052 3.81e-01 100 OJDOHDAK_02115 7.06e-01 100 OJDOHDAK_02125 9.79e-01 100 OJDOHDAK_02130 1.41e-01 100 OJDOHDAK_02140 5.44e-01 100 OJDOHDAK_02145 2.45e-01 100 OJDOHDAK_02164 8.79e-01 100 OJDOHDAK_02183 1.32e-01 100 OJDOHDAK_02195 2.85e-01 100 OJDOHDAK_02202 9.79e-01 100 OJDOHDAK_02263 4.55e-01 100 OJDOHDAK_02286 4.65e-01 100 OJDOHDAK_02287 1.87e-02 71_[+2(9.15e-06)]_15 OJDOHDAK_02288 2.07e-05 33_[+2(7.52e-09)]_53 OJDOHDAK_02289 7.32e-01 100 OJDOHDAK_02293 7.23e-01 100 OJDOHDAK_02294 5.44e-01 100 OJDOHDAK_02295 5.06e-01 100 OJDOHDAK_02296 2.79e-04 82_[+2(2.73e-07)]_4 OJDOHDAK_02297 5.92e-01 100 OJDOHDAK_02298 4.41e-01 100 OJDOHDAK_02299 5.56e-01 100 OJDOHDAK_02300 1.12e-03 55_[+2(6.03e-07)]_31 OJDOHDAK_02301 1.79e-01 100 OJDOHDAK_02302 1.11e-03 75_[+2(6.03e-07)]_11 OJDOHDAK_02303 3.69e-01 100 OJDOHDAK_02304 1.91e-02 27_[+2(1.09e-05)]_59 OJDOHDAK_02305 5.44e-02 100 OJDOHDAK_02306 4.36e-01 100 OJDOHDAK_02307 3.96e-03 75_[+2(3.49e-05)]_11 OJDOHDAK_02308 7.44e-04 75_[+2(1.51e-07)]_11 OJDOHDAK_02309 1.09e-01 100 OJDOHDAK_02310 3.20e-01 100 OJDOHDAK_02311 1.69e-03 74_[+2(1.59e-06)]_12 OJDOHDAK_02312 5.03e-01 100 OJDOHDAK_02313 2.78e-02 100 OJDOHDAK_02314 2.77e-01 100 OJDOHDAK_02315 7.08e-01 100 OJDOHDAK_02316 8.29e-01 100 OJDOHDAK_02317 5.84e-02 100 OJDOHDAK_02320 8.70e-01 100 OJDOHDAK_02370 3.56e-01 100 OJDOHDAK_02412 3.67e-02 84_[+2(8.79e-05)]_2 OJDOHDAK_02426 8.69e-01 100 OJDOHDAK_02496 9.81e-01 100 OJDOHDAK_02507 5.92e-01 100 OJDOHDAK_02518 7.68e-01 100 OJDOHDAK_02532 9.73e-01 100 OJDOHDAK_02566 1.05e-01 100 OJDOHDAK_02651 1.44e-04 31_[+3(1.18e-05)]_45 OJDOHDAK_02667 1.45e-01 100 OJDOHDAK_02680 2.25e-01 100 OJDOHDAK_02693 6.92e-01 100 OJDOHDAK_02713 7.87e-10 16_[+1(2.50e-13)]_34 OJDOHDAK_02754 7.25e-01 100 OJDOHDAK_02776 2.62e-01 100 OJDOHDAK_02800 9.51e-01 100 OJDOHDAK_02832 4.71e-01 100 OJDOHDAK_02844 8.35e-01 100 OJDOHDAK_02872 4.90e-01 100 OJDOHDAK_02889 8.65e-01 100 OJDOHDAK_02902 3.56e-01 100 OJDOHDAK_02913 7.86e-01 100 OJDOHDAK_02919 9.70e-02 100 OJDOHDAK_02921 9.80e-01 100 OJDOHDAK_02933 6.27e-02 100 OJDOHDAK_02935 6.15e-28 10_[+1(9.63e-21)]_11_[+3(8.55e-15)]_\ 5 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kodomo ********************************************************************************