******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.10.0 (Release date: Wed May 21 10:35:36 2014 +1000) 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= motifs/474/474.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10355 1.0000 500 10803 1.0000 500 1568 1.0000 500 16265 1.0000 500 17031 1.0000 500 20819 1.0000 500 20824 1.0000 500 21633 1.0000 500 21645 1.0000 500 21655 1.0000 500 21792 1.0000 500 22889 1.0000 500 22932 1.0000 500 23108 1.0000 500 23338 1.0000 500 23562 1.0000 500 23894 1.0000 500 24057 1.0000 500 24079 1.0000 500 24943 1.0000 500 25452 1.0000 500 261472 1.0000 500 261678 1.0000 500 263403 1.0000 500 263599 1.0000 500 263610 1.0000 500 264262 1.0000 500 269169 1.0000 500 269725 1.0000 500 33039 1.0000 500 37638 1.0000 500 37727 1.0000 500 39955 1.0000 500 40445 1.0000 500 4202 1.0000 500 7366 1.0000 500 7924 1.0000 500 8711 1.0000 500 9057 1.0000 500 9571 1.0000 500 9840 1.0000 500 bd1941 1.0000 500 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme motifs/474/474.seqs.fa -oc motifs/474 -dna -minw 12 -maxw 21 -nmotifs 3 -maxsize 500000 model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 12 maxw= 21 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 42 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 21000 N= 42 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.271 C 0.243 G 0.225 T 0.261 Background letter frequencies (from dataset with add-one prior applied): A 0.271 C 0.243 G 0.225 T 0.261 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 42 llr = 373 E-value = 7.8e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 34354162372164327564 pos.-specific C 457118157:6525542545 probability G :::1:12::::11::4:::: matrix T 2::35:13:313112:1::: bits 2.2 1.9 1.7 1.5 Relative 1.3 * Entropy 1.1 * * ** * (12.8 bits) 0.9 * * ** *** 0.6 ** ** ** **** 0.4 ** ******* ******* 0.2 ******************** 0.0 -------------------- Multilevel CCCATCACCACCACCGACAC consensus AAATA GTATATCAACCACA sequence T TA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 37638 207 7.06e-10 ACAGAACCCC CCCTACACCACCACACACAC ACCTGCGACT 22932 399 2.00e-08 ACAGCGAAGT CACTACACCACTACCGCCAC TACTATTGGA 10355 399 6.82e-08 ATACATGAAC CAATACACCACCACCCAACA ATAAGCATGA 263610 205 1.70e-07 ACTTCGCCCA CCCTTCTCCTCTACCGACAA CTCTACATCC 261472 323 2.39e-07 ACAACCTTCT TCCTTCACCAATACAGAACC TACCGTGACT 263599 205 5.35e-07 ACTTCTCCCA TCCTTCTCCTCTACCGACAA CTCTACATCC 20819 181 6.23e-07 TGGTGCCCCC TCCTTCTCCTCCAAAGAAAC CAAAGATTGA 24943 37 8.40e-07 TTTTTAAGCG AACAACGCCACCAAACCAAA AATAAAGATA 21633 480 1.70e-06 TCAGTCCTTC CACTTCGACTACACCAACAC C 16265 474 4.74e-06 CATCAACACA CACATCACCACCATTATCAA ATACTAA 21645 472 5.34e-06 GAGAGCCTCA CAAATCCCAACCAACCAACA CCGTCGACA bd1941 143 8.48e-06 CTAACTGCAT CCCTCCTCCACCGACGAAAA ACAATCTCCT 33039 201 8.48e-06 GGACACGTGT ACCATCACCACTCAACAAAG AGTCCAGCAG 23562 453 9.48e-06 TTTAACCTCA ACAAACAAAATCAACCACCC AAAGCACGGC 269169 460 1.06e-05 TGTGTTCTCC ACCTTCCTCACACCCCAACC TACCTCCCGA 263403 342 1.18e-05 AATACGGCCG TAAATCATAAACAACAACCA TGTGTCAGTG 23894 479 1.18e-05 TCTGCAGCCT CTCAACAACAACAACCACAA GC 269725 259 1.31e-05 GGGGAGTAGT CACATCATCATCATCATCAC GGAGTGTAAA 23108 472 1.31e-05 TTCCCAAACC CACCACATCACGCACAACAC AAACAAACC 7924 462 1.62e-05 ACCTGCCTAC CAACACACCACCTCACCCCC GGAGAACGAT 24079 4 1.99e-05 ATG ACAAACAACAAAACTAAAAC TCGCACTGCC 39955 246 2.43e-05 CTATGCCTAC TCCATCATCTCCCACTCCAC CCGATTTGGA 25452 226 2.95e-05 GAAAAGGAAC AAAGACACAACCGCAGACAA GAAAGGGAAG 9571 399 3.57e-05 AGGAGACAAC AACCTCCACAACACCGCAAC ACTCTTCCGC 4202 65 3.91e-05 GTCGTGAATG CACATCATAACACTTCAACC GACTAGGGTA 40445 375 5.61e-05 AGACCAACAC ACAATCGAATCCTATCACAC AAACCATTGC 24057 477 5.61e-05 TCGAGACAAT TCCATCACCTGAACAACACC ATCA 17031 346 6.66e-05 TACTGCCATC ACCATCAGCACTTCCGTCCA TTTGCATCAT 23338 451 9.30e-05 TGCAACAGTG TCAATCATCATGCAACCAAC GTCTTCAAGC 9057 420 1.01e-04 AGAGAACAAC AACACCGCGATCACCCACAA AGCCAAAGGA 7366 456 1.01e-04 TGCCAGCAAT CCAGTGGCCACAACTCAAAA CGATCGCAGC 261678 367 1.01e-04 GTGGAGAGAT GCCTTCGCCTCCCGTGAAAC GTTCATCAAA 21792 129 1.09e-04 CTCACCTTCT CCCAACGAAACAATTGCACC AATAAGACGA 8711 319 1.38e-04 ACACCCCCCC CCCTTCTTCTAGGCCAAACC ACTTCTCACT 37727 403 1.38e-04 TTTCTGCACT TGCTTCATATCTTCTGACAA GAGCTCCCAT 22889 428 1.49e-04 TTTGGTTTCG TCCAAAATCATCAAGAACAC GTAACAAGGA 21655 398 1.49e-04 AGCTTGGTGC TCCTTAACATCTACAGTACA ATCGCAACAA 264262 116 2.46e-04 GCGTCTGGTA AACACGAACAACGAAGACAC TGCGTTTAGT 20824 250 3.91e-04 AGTTTGATGT AGCAAAGCCTCTCAAGCAAC AGCAGAAGGC 10803 197 4.17e-04 TGGTGTGGGC CCAAAAATAAATTAAAAAAA ATTAAATGTA 1568 365 5.01e-04 GACAAATGTG CAACACACAAGTCCTCCCCA CAGTCTCTGG 9840 287 5.98e-04 ACATCACCAG GACGAGGTCATTACCGACCA GCCGACGACG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37638 7.1e-10 206_[+1]_274 22932 2e-08 398_[+1]_82 10355 6.8e-08 398_[+1]_82 263610 1.7e-07 204_[+1]_276 261472 2.4e-07 322_[+1]_158 263599 5.3e-07 204_[+1]_276 20819 6.2e-07 180_[+1]_300 24943 8.4e-07 36_[+1]_444 21633 1.7e-06 479_[+1]_1 16265 4.7e-06 473_[+1]_7 21645 5.3e-06 471_[+1]_9 bd1941 8.5e-06 142_[+1]_338 33039 8.5e-06 200_[+1]_280 23562 9.5e-06 452_[+1]_28 269169 1.1e-05 459_[+1]_21 263403 1.2e-05 341_[+1]_139 23894 1.2e-05 478_[+1]_2 269725 1.3e-05 258_[+1]_222 23108 1.3e-05 471_[+1]_9 7924 1.6e-05 461_[+1]_19 24079 2e-05 3_[+1]_477 39955 2.4e-05 245_[+1]_235 25452 3e-05 225_[+1]_255 9571 3.6e-05 398_[+1]_82 4202 3.9e-05 64_[+1]_416 40445 5.6e-05 374_[+1]_106 24057 5.6e-05 476_[+1]_4 17031 6.7e-05 345_[+1]_135 23338 9.3e-05 450_[+1]_30 9057 0.0001 419_[+1]_61 7366 0.0001 455_[+1]_25 261678 0.0001 366_[+1]_114 21792 0.00011 128_[+1]_352 8711 0.00014 318_[+1]_162 37727 0.00014 402_[+1]_78 22889 0.00015 427_[+1]_53 21655 0.00015 397_[+1]_83 264262 0.00025 115_[+1]_365 20824 0.00039 249_[+1]_231 10803 0.00042 196_[+1]_284 1568 0.0005 364_[+1]_116 9840 0.0006 286_[+1]_194 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=42 37638 ( 207) CCCTACACCACCACACACAC 1 22932 ( 399) CACTACACCACTACCGCCAC 1 10355 ( 399) CAATACACCACCACCCAACA 1 263610 ( 205) CCCTTCTCCTCTACCGACAA 1 261472 ( 323) TCCTTCACCAATACAGAACC 1 263599 ( 205) TCCTTCTCCTCTACCGACAA 1 20819 ( 181) TCCTTCTCCTCCAAAGAAAC 1 24943 ( 37) AACAACGCCACCAAACCAAA 1 21633 ( 480) CACTTCGACTACACCAACAC 1 16265 ( 474) CACATCACCACCATTATCAA 1 21645 ( 472) CAAATCCCAACCAACCAACA 1 bd1941 ( 143) CCCTCCTCCACCGACGAAAA 1 33039 ( 201) ACCATCACCACTCAACAAAG 1 23562 ( 453) ACAAACAAAATCAACCACCC 1 269169 ( 460) ACCTTCCTCACACCCCAACC 1 263403 ( 342) TAAATCATAAACAACAACCA 1 23894 ( 479) CTCAACAACAACAACCACAA 1 269725 ( 259) CACATCATCATCATCATCAC 1 23108 ( 472) CACCACATCACGCACAACAC 1 7924 ( 462) CAACACACCACCTCACCCCC 1 24079 ( 4) ACAAACAACAAAACTAAAAC 1 39955 ( 246) TCCATCATCTCCCACTCCAC 1 25452 ( 226) AAAGACACAACCGCAGACAA 1 9571 ( 399) AACCTCCACAACACCGCAAC 1 4202 ( 65) CACATCATAACACTTCAACC 1 40445 ( 375) ACAATCGAATCCTATCACAC 1 24057 ( 477) TCCATCACCTGAACAACACC 1 17031 ( 346) ACCATCAGCACTTCCGTCCA 1 23338 ( 451) TCAATCATCATGCAACCAAC 1 9057 ( 420) AACACCGCGATCACCCACAA 1 7366 ( 456) CCAGTGGCCACAACTCAAAA 1 261678 ( 367) GCCTTCGCCTCCCGTGAAAC 1 21792 ( 129) CCCAACGAAACAATTGCACC 1 8711 ( 319) CCCTTCTTCTAGGCCAAACC 1 37727 ( 403) TGCTTCATATCTTCTGACAA 1 22889 ( 428) TCCAAAATCATCAAGAACAC 1 21655 ( 398) TCCTTAACATCTACAGTACA 1 264262 ( 116) AACACGAACAACGAAGACAC 1 20824 ( 250) AGCAAAGCCTCTCAAGCAAC 1 10803 ( 197) CCAAAAATAAATTAAAAAAA 1 1568 ( 365) CAACACACAAGTCCTCCCCA 1 9840 ( 287) GACGAGGTCATTACCGACCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 20202 bayes= 8.90689 E= 7.8e-003 8 82 -224 -13 58 111 -224 -345 8 155 -1204 -1204 88 -135 -165 35 49 -177 -1204 107 -151 178 -165 -1204 113 -177 -7 -113 -51 104 -324 13 -5 155 -324 -1204 140 -1204 -1204 13 -34 129 -224 -87 -92 104 -165 13 108 -18 -124 -113 49 104 -324 -145 19 90 -324 -28 -19 55 76 -345 130 -3 -1204 -145 81 111 -1204 -1204 125 55 -1204 -1204 66 117 -324 -1204 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 42 E= 7.8e-003 0.285714 0.428571 0.047619 0.238095 0.404762 0.523810 0.047619 0.023810 0.285714 0.714286 0.000000 0.000000 0.500000 0.095238 0.071429 0.333333 0.380952 0.071429 0.000000 0.547619 0.095238 0.833333 0.071429 0.000000 0.595238 0.071429 0.214286 0.119048 0.190476 0.500000 0.023810 0.285714 0.261905 0.714286 0.023810 0.000000 0.714286 0.000000 0.000000 0.285714 0.214286 0.595238 0.047619 0.142857 0.142857 0.500000 0.071429 0.285714 0.571429 0.214286 0.095238 0.119048 0.380952 0.500000 0.023810 0.095238 0.309524 0.452381 0.023810 0.214286 0.238095 0.357143 0.380952 0.023810 0.666667 0.238095 0.000000 0.095238 0.476190 0.523810 0.000000 0.000000 0.642857 0.357143 0.000000 0.000000 0.428571 0.547619 0.023810 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CAT][CA][CA][AT][TA]C[AG][CT][CA][AT][CA][CT][AC][CA][CAT][GCA][AC][CA][AC][CA] -------------------------------------------------------------------------------- Time 13.07 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 35 llr = 328 E-value = 1.8e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 287126228225:48: pos.-specific C 3:23::5:15::42:1 probability G 42167328:3845429 matrix T 1::::11:2:::1::: bits 2.2 1.9 1.7 * 1.5 * Relative 1.3 * * ** Entropy 1.1 * * * ** (13.5 bits) 0.9 ** * ** ** ** 0.6 ***** ***** ** 0.4 ***** ********* 0.2 **************** 0.0 ---------------- Multilevel GAAGGACGACGAGGAG consensus C CAG A GAGCA sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 22889 223 8.61e-09 TTGCCGATGG AAAGGACGACGAGGAG CTTGGCTACA 264262 251 1.81e-07 CGATGCAACA GACCGACGACGACGAG CTGATATGAT 37727 170 4.05e-07 ACCAATCGAG AAAGGACGACGATCAG ACATCTCAAG 269725 350 6.54e-07 AAGCGAGTTA GAAGGTCAACGGGGAG ACGACAATGT 261472 423 8.78e-07 GAGACGGTTC CAACGGCGACGGCGGG AGCGTGGCAA 263403 68 1.32e-06 AGTTGTTGGT GGAGGGGGAGGGGCAG GTGTTGCTGG 25452 376 2.47e-06 CTGATGCTTA GAACGACGACGACAAC CACTTCTAGC 20824 103 2.47e-06 GAGAGAGTGA AAAGAGAGACGAGAAG AGGGTGAGGT 9057 482 2.80e-06 GTAACAACGA CAAGAACAAGGACAAG GAT 21655 102 3.17e-06 CGTTGCAAAG GGAGGAGGAGAGCGAG GAGCACATTG 22932 341 4.05e-06 GAGGCTACGA GAACGAGGCCGAGAAG CTCTCATTTG 21633 67 4.05e-06 ATGGAGCGAG TAACAGCGAGGAGAAG AACACCGTGG 7366 349 4.56e-06 ACGCACTGAG GAATGACGTCGGGGAG TTGTGACCAT 21792 467 4.56e-06 CTCGACGACG CAAAAACGACGAGGGG TGCTGCTCTT 263599 134 5.73e-06 GGGGTAGCAA AACGGGCGAAGGCCAG AATTGTCACT 23894 265 7.13e-06 TTGTCGCGTT TACGGACGTCGACCAG AACATTACAA 269169 204 1.19e-05 GGTGTATCTC GACGGATGAAGGTGAG AGGTATGGTG 9840 363 1.60e-05 TGTTCTCGAA GAAAGGCAAGAGCAAG CGGCAACGAC 39955 434 1.60e-05 TTGATTGAAG GGAGGTGGTCGAGCAG TTCCACTTCA 261678 471 1.60e-05 CGACGCAAAA TAACGACAACAGCAAG ACACAGGCTT 1568 188 1.60e-05 GTGGGTGGCC CGGCGGCGAAGAGGAG TTCGAAGGAA 20819 345 2.14e-05 GATTTCTATG GAAAGGAGAAAACAAG ACCGTACTCC 33039 64 2.35e-05 GCAGACAAAG CCACGAAGACGACAAG GGTTGGGCAC 23108 110 3.36e-05 GTTGCCTTTG CAAAGACGAGGCTGAG AAGCTGGAGA 21645 384 3.36e-05 TTGATCTTCT GAAGGAAGAGAGACAG TCAAACTCGA 10803 230 5.54e-05 AAATGTAGGT AACGAGCGCGGAGAAG TGCGTCCCAT 37638 380 6.00e-05 CAGAGCAAAA GAAGAGAAAAGAGAGG AGAGCTGAAA 10355 420 6.50e-05 CACCCAACAA TAAGCATGACGGCCAG ATTACACTGC 23562 26 7.61e-05 CCATTGAGTT GAAGGTTGTCGGTAGG TTGTTCTTTG 40445 310 8.86e-05 TGTACAGAGG CAACGAGGTAAGTGAG TGCTGTGACG 4202 411 9.55e-05 ACATTTCGTT CGAGGTGATGGGGGAG ACCCAGCCTC 8711 115 1.03e-04 TTGCCGCTTG GAGGGGAGAGGAGGGC GGATGCCGAG 24079 449 2.32e-04 TGGTGTAATA CAGGAATAACAGCCAG ACATTGACAT 24943 355 2.80e-04 TAATGAGATT AGCAAACGACAAGAGG CAATCCTTTG 263610 447 2.97e-04 GGACGTCCTT CTGGGACGAGGAGGAT TAATCACCGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 22889 8.6e-09 222_[+2]_262 264262 1.8e-07 250_[+2]_234 37727 4e-07 169_[+2]_315 269725 6.5e-07 349_[+2]_135 261472 8.8e-07 422_[+2]_62 263403 1.3e-06 67_[+2]_417 25452 2.5e-06 375_[+2]_109 20824 2.5e-06 102_[+2]_382 9057 2.8e-06 481_[+2]_3 21655 3.2e-06 101_[+2]_383 22932 4e-06 340_[+2]_144 21633 4e-06 66_[+2]_418 7366 4.6e-06 348_[+2]_136 21792 4.6e-06 466_[+2]_18 263599 5.7e-06 133_[+2]_351 23894 7.1e-06 264_[+2]_220 269169 1.2e-05 203_[+2]_281 9840 1.6e-05 362_[+2]_122 39955 1.6e-05 433_[+2]_51 261678 1.6e-05 470_[+2]_14 1568 1.6e-05 187_[+2]_297 20819 2.1e-05 344_[+2]_140 33039 2.4e-05 63_[+2]_421 23108 3.4e-05 109_[+2]_375 21645 3.4e-05 383_[+2]_101 10803 5.5e-05 229_[+2]_255 37638 6e-05 379_[+2]_105 10355 6.5e-05 419_[+2]_65 23562 7.6e-05 25_[+2]_459 40445 8.9e-05 309_[+2]_175 4202 9.5e-05 410_[+2]_74 8711 0.0001 114_[+2]_370 24079 0.00023 448_[+2]_36 24943 0.00028 354_[+2]_130 263610 0.0003 446_[+2]_38 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=35 22889 ( 223) AAAGGACGACGAGGAG 1 264262 ( 251) GACCGACGACGACGAG 1 37727 ( 170) AAAGGACGACGATCAG 1 269725 ( 350) GAAGGTCAACGGGGAG 1 261472 ( 423) CAACGGCGACGGCGGG 1 263403 ( 68) GGAGGGGGAGGGGCAG 1 25452 ( 376) GAACGACGACGACAAC 1 20824 ( 103) AAAGAGAGACGAGAAG 1 9057 ( 482) CAAGAACAAGGACAAG 1 21655 ( 102) GGAGGAGGAGAGCGAG 1 22932 ( 341) GAACGAGGCCGAGAAG 1 21633 ( 67) TAACAGCGAGGAGAAG 1 7366 ( 349) GAATGACGTCGGGGAG 1 21792 ( 467) CAAAAACGACGAGGGG 1 263599 ( 134) AACGGGCGAAGGCCAG 1 23894 ( 265) TACGGACGTCGACCAG 1 269169 ( 204) GACGGATGAAGGTGAG 1 9840 ( 363) GAAAGGCAAGAGCAAG 1 39955 ( 434) GGAGGTGGTCGAGCAG 1 261678 ( 471) TAACGACAACAGCAAG 1 1568 ( 188) CGGCGGCGAAGAGGAG 1 20819 ( 345) GAAAGGAGAAAACAAG 1 33039 ( 64) CCACGAAGACGACAAG 1 23108 ( 110) CAAAGACGAGGCTGAG 1 21645 ( 384) GAAGGAAGAGAGACAG 1 10803 ( 230) AACGAGCGCGGAGAAG 1 37638 ( 380) GAAGAGAAAAGAGAGG 1 10355 ( 420) TAAGCATGACGGCCAG 1 23562 ( 26) GAAGGTTGTCGGTAGG 1 40445 ( 310) CAACGAGGTAAGTGAG 1 4202 ( 411) CGAGGTGATGGGGGAG 1 8711 ( 115) GAGGGGAGAGGAGGGC 1 24079 ( 449) CAGGAATAACAGCCAG 1 24943 ( 355) AGCAAACGACAAGAGG 1 263610 ( 447) CTGGGACGAGGAGGAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 20370 bayes= 9.28505 E= 1.8e-005 -66 23 93 -119 151 -309 -39 -319 140 -50 -98 -1177 -92 8 135 -319 -25 -309 172 -1177 108 -1177 48 -119 -66 116 -39 -119 -44 -1177 183 -1177 151 -209 -1177 -61 -66 108 48 -1177 -25 -1177 178 -1177 100 -309 93 -1177 -324 61 102 -87 45 -9 83 -1177 161 -1177 -39 -1177 -1177 -209 202 -319 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 35 E= 1.8e-005 0.171429 0.285714 0.428571 0.114286 0.771429 0.028571 0.171429 0.028571 0.714286 0.171429 0.114286 0.000000 0.142857 0.257143 0.571429 0.028571 0.228571 0.028571 0.742857 0.000000 0.571429 0.000000 0.314286 0.114286 0.171429 0.542857 0.171429 0.114286 0.200000 0.000000 0.800000 0.000000 0.771429 0.057143 0.000000 0.171429 0.171429 0.514286 0.314286 0.000000 0.228571 0.000000 0.771429 0.000000 0.542857 0.028571 0.428571 0.000000 0.028571 0.371429 0.457143 0.142857 0.371429 0.228571 0.400000 0.000000 0.828571 0.000000 0.171429 0.000000 0.000000 0.057143 0.914286 0.028571 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GC]AA[GC][GA][AG]C[GA]A[CG][GA][AG][GC][GAC]AG -------------------------------------------------------------------------------- Time 25.46 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 17 llr = 204 E-value = 3.0e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :1:14151:::12::1 pos.-specific C :22:19::4:18::61 probability G a3282:3118::824: matrix T :4613:286292:8:9 bits 2.2 * 1.9 * 1.7 * * 1.5 * * ** * Relative 1.3 * * * ** ** * Entropy 1.1 * * * * ******* (17.3 bits) 0.9 * * * ********* 0.6 * ** * ********* 0.4 * ** *********** 0.2 **** *********** 0.0 ---------------- Multilevel GTTGACATTGTCGTCT consensus G T G C GG sequence C G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 23338 2 1.16e-09 T GGTGGCATTGTCGTCT GTGATATTTG 1568 149 1.07e-07 ATGATTAAGG GGTGGCTTTGTCGGGT GAAGGCGTGG bd1941 312 2.16e-07 TTCAACTTTT GATGTCATTGTCATCT AACCCAACAC 17031 397 3.03e-07 TTTCTACAAG GGTGTCATCGTCGTCC CCCGCCTACT 8711 211 4.14e-07 GGTCGGCGTA GTTGACGTCGCCGTCT CAGAGGCGTC 263610 390 5.09e-07 TGTTGAGTAA GCTGCCAACGTCGTCT AACCACGAAT 263599 390 5.09e-07 TGTTGAGTAA GCTGCCAACGTCGTCT AACCACGAAT 23108 154 6.86e-07 AGACATGATT GTGGGCTTTGTTGTGT TTGGCTTGGT 269169 112 9.95e-07 TGATGGTATA GACGACATTGTTGTGT GTGCGGTGGC 10355 228 1.30e-06 GCTATTTATA GTTAAAGTTGTCGTCT CCACCAACAG 39955 300 1.98e-06 GCAAAGACAA GGGATCTTTGTCGGCT CGTGATGCGA 21633 22 2.73e-06 CCTCGGCAGT GCTGTCATCGTCATCA TCCTCTGCAC 23894 381 2.95e-06 TGATCTCCGC GTCGTCGTCTTCATCT TTGGTCAGTC 7366 14 4.63e-06 ATGGCTTGAC GCTGGCAGTGTTGGGT CACCATTCAG 261472 54 5.34e-06 ACTGAGGCAG GGTTAATTTGTCGTGT TTGCTTGTGA 24057 149 5.72e-06 TTCGTCAGCT GTGGACGTTTTAGTGT GATTGACGCG 16265 175 5.72e-06 GCGGAATCTC GTCGACGTGTTCGGCT TCCTCGGTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 23338 1.2e-09 1_[+3]_483 1568 1.1e-07 148_[+3]_336 bd1941 2.2e-07 311_[+3]_173 17031 3e-07 396_[+3]_88 8711 4.1e-07 210_[+3]_274 263610 5.1e-07 389_[+3]_95 263599 5.1e-07 389_[+3]_95 23108 6.9e-07 153_[+3]_331 269169 9.9e-07 111_[+3]_373 10355 1.3e-06 227_[+3]_257 39955 2e-06 299_[+3]_185 21633 2.7e-06 21_[+3]_463 23894 3e-06 380_[+3]_104 7366 4.6e-06 13_[+3]_471 261472 5.3e-06 53_[+3]_431 24057 5.7e-06 148_[+3]_336 16265 5.7e-06 174_[+3]_310 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=17 23338 ( 2) GGTGGCATTGTCGTCT 1 1568 ( 149) GGTGGCTTTGTCGGGT 1 bd1941 ( 312) GATGTCATTGTCATCT 1 17031 ( 397) GGTGTCATCGTCGTCC 1 8711 ( 211) GTTGACGTCGCCGTCT 1 263610 ( 390) GCTGCCAACGTCGTCT 1 263599 ( 390) GCTGCCAACGTCGTCT 1 23108 ( 154) GTGGGCTTTGTTGTGT 1 269169 ( 112) GACGACATTGTTGTGT 1 10355 ( 228) GTTAAAGTTGTCGTCT 1 39955 ( 300) GGGATCTTTGTCGGCT 1 21633 ( 22) GCTGTCATCGTCATCA 1 23894 ( 381) GTCGTCGTCTTCATCT 1 7366 ( 14) GCTGGCAGTGTTGGGT 1 261472 ( 54) GGTTAATTTGTCGTGT 1 24057 ( 149) GTGGACGTTTTAGTGT 1 16265 ( 175) GTCGACGTGTTCGGCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 20370 bayes= 10.2951 E= 3.0e-003 -1073 -1073 215 -1073 -120 -5 39 44 -1073 -46 -35 131 -120 -1073 187 -215 38 -105 7 17 -120 186 -1073 -1073 80 -1073 39 -15 -120 -1073 -193 166 -1073 54 -193 117 -1073 -1073 187 -56 -1073 -204 -1073 185 -220 165 -1073 -56 -62 -1073 187 -1073 -1073 -1073 7 155 -1073 141 65 -1073 -220 -204 -1073 176 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 17 E= 3.0e-003 0.000000 0.000000 1.000000 0.000000 0.117647 0.235294 0.294118 0.352941 0.000000 0.176471 0.176471 0.647059 0.117647 0.000000 0.823529 0.058824 0.352941 0.117647 0.235294 0.294118 0.117647 0.882353 0.000000 0.000000 0.470588 0.000000 0.294118 0.235294 0.117647 0.000000 0.058824 0.823529 0.000000 0.352941 0.058824 0.588235 0.000000 0.000000 0.823529 0.176471 0.000000 0.058824 0.000000 0.941176 0.058824 0.764706 0.000000 0.176471 0.176471 0.000000 0.823529 0.000000 0.000000 0.000000 0.235294 0.764706 0.000000 0.647059 0.352941 0.000000 0.058824 0.058824 0.000000 0.882353 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[TGC]TG[ATG]C[AGT]T[TC]GTCG[TG][CG]T -------------------------------------------------------------------------------- Time 37.81 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10355 1.58e-07 227_[+3(1.30e-06)]_155_\ [+1(6.82e-08)]_1_[+2(6.50e-05)]_19_[+1(5.13e-05)]_26 10803 9.01e-02 229_[+2(5.54e-05)]_255 1568 1.29e-05 148_[+3(1.07e-07)]_23_\ [+2(1.60e-05)]_297 16265 4.08e-04 174_[+3(5.72e-06)]_62_\ [+1(3.57e-05)]_201_[+1(4.74e-06)]_7 17031 1.49e-04 345_[+1(6.66e-05)]_31_\ [+3(3.03e-07)]_88 20819 2.28e-04 180_[+1(6.23e-07)]_144_\ [+2(2.14e-05)]_140 20824 4.76e-03 102_[+2(2.47e-06)]_382 21633 4.68e-07 21_[+3(2.73e-06)]_29_[+2(4.05e-06)]_\ 62_[+3(5.26e-05)]_319_[+1(1.70e-06)]_1 21645 7.15e-04 383_[+2(3.36e-05)]_72_\ [+1(5.34e-06)]_9 21655 4.45e-03 101_[+2(3.17e-06)]_383 21792 1.93e-03 466_[+2(4.56e-06)]_18 22889 1.65e-06 82_[+3(6.23e-05)]_124_\ [+2(8.61e-09)]_262 22932 2.51e-06 340_[+2(4.05e-06)]_42_\ [+1(2.00e-08)]_82 23108 5.63e-06 109_[+2(3.36e-05)]_28_\ [+3(6.86e-07)]_302_[+1(1.31e-05)]_9 23338 2.32e-06 1_[+3(1.16e-09)]_433_[+1(9.30e-05)]_\ 30 23562 4.75e-03 25_[+2(7.61e-05)]_411_\ [+1(9.48e-06)]_28 23894 4.74e-06 264_[+2(7.13e-06)]_100_\ [+3(2.95e-06)]_82_[+1(1.18e-05)]_2 24057 3.45e-03 148_[+3(5.72e-06)]_312_\ [+1(5.61e-05)]_4 24079 1.28e-02 3_[+1(1.99e-05)]_477 24943 1.11e-03 36_[+1(8.40e-07)]_444 25452 6.22e-04 225_[+1(2.95e-05)]_130_\ [+2(2.47e-06)]_109 261472 3.59e-08 53_[+3(5.34e-06)]_253_\ [+1(2.39e-07)]_80_[+2(8.78e-07)]_62 261678 3.81e-03 470_[+2(1.60e-05)]_14 263403 3.06e-04 67_[+2(1.32e-06)]_258_\ [+1(1.18e-05)]_139 263599 4.86e-08 133_[+2(5.73e-06)]_55_\ [+1(5.35e-07)]_3_[+1(5.61e-05)]_142_[+3(5.09e-07)]_95 263610 5.83e-07 204_[+1(1.70e-07)]_3_[+1(5.61e-05)]_\ 142_[+3(5.09e-07)]_95 264262 7.66e-04 250_[+2(1.81e-07)]_234 269169 2.57e-06 111_[+3(9.95e-07)]_76_\ [+2(1.19e-05)]_240_[+1(1.06e-05)]_21 269725 1.03e-05 258_[+1(1.31e-05)]_19_\ [+1(7.89e-05)]_32_[+2(6.54e-07)]_116_[+3(7.03e-05)]_3 33039 1.90e-03 63_[+2(2.35e-05)]_121_\ [+1(8.48e-06)]_280 37638 2.33e-07 176_[+1(3.25e-05)]_10_\ [+1(7.06e-10)]_153_[+2(6.00e-05)]_105 37727 9.24e-04 169_[+2(4.05e-07)]_315 39955 1.29e-05 245_[+1(2.43e-05)]_34_\ [+3(1.98e-06)]_118_[+2(1.60e-05)]_51 40445 2.03e-02 309_[+2(8.86e-05)]_49_\ [+1(5.61e-05)]_106 4202 1.89e-02 64_[+1(3.91e-05)]_326_\ [+2(9.55e-05)]_74 7366 3.11e-05 13_[+3(4.63e-06)]_319_\ [+2(4.56e-06)]_136 7924 6.58e-02 461_[+1(1.62e-05)]_19 8711 7.34e-05 210_[+3(4.14e-07)]_274 9057 2.42e-03 481_[+2(2.80e-06)]_3 9571 1.76e-02 398_[+1(3.57e-05)]_82 9840 1.40e-02 362_[+2(1.60e-05)]_122 bd1941 5.05e-05 142_[+1(8.48e-06)]_149_\ [+3(2.16e-07)]_173 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************