******************************************************************************** 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/97/97.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 42574 1.0000 500 42743 1.0000 500 42914 1.0000 500 42946 1.0000 500 42993 1.0000 500 9158 1.0000 500 43122 1.0000 500 43196 1.0000 500 36284 1.0000 500 36337 1.0000 500 13028 1.0000 500 13706 1.0000 500 47045 1.0000 500 52174 1.0000 500 21410 1.0000 500 47179 1.0000 500 47205 1.0000 500 21455 1.0000 500 47517 1.0000 500 47734 1.0000 500 47761 1.0000 500 4344 1.0000 500 47965 1.0000 500 47992 1.0000 500 38652 1.0000 500 15016 1.0000 500 38865 1.0000 500 48451 1.0000 500 38917 1.0000 500 39117 1.0000 500 48735 1.0000 500 32848 1.0000 500 43757 1.0000 500 49115 1.0000 500 49227 1.0000 500 30352 1.0000 500 49507 1.0000 500 23281 1.0000 500 49838 1.0000 500 50016 1.0000 500 50280 1.0000 500 50365 1.0000 500 43956 1.0000 500 10628 1.0000 500 44165 1.0000 500 50429 1.0000 500 2845 1.0000 500 50635 1.0000 500 44270 1.0000 500 44271 1.0000 500 34026 1.0000 500 44947 1.0000 500 46249 1.0000 500 8598 1.0000 500 46392 1.0000 500 44469 1.0000 500 31453 1.0000 500 48333 1.0000 500 48434 1.0000 500 39065 1.0000 500 44194 1.0000 500 48673 1.0000 500 48674 1.0000 500 39317 1.0000 500 44300 1.0000 500 33755 1.0000 500 34868 1.0000 500 46380 1.0000 500 43546 1.0000 500 43823 1.0000 500 47397 1.0000 500 46513 1.0000 500 36590 1.0000 500 32962 1.0000 500 47533 1.0000 500 47534 1.0000 500 46659 1.0000 500 47592 1.0000 500 46705 1.0000 500 44848 1.0000 500 47738 1.0000 500 39650 1.0000 500 49082 1.0000 500 35642 1.0000 500 49129 1.0000 500 35036 1.0000 500 47053 1.0000 500 49269 1.0000 500 35856 1.0000 500 49302 1.0000 500 49467 1.0000 500 45019 1.0000 500 37463 1.0000 500 47359 1.0000 500 41098 1.0000 500 35525 1.0000 500 45552 1.0000 500 37774 1.0000 500 37787 1.0000 500 47557 1.0000 500 50129 1.0000 500 33588 1.0000 500 43718 1.0000 500 46000 1.0000 500 35694 1.0000 500 44464 1.0000 500 49304 1.0000 500 49305 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/97/97.seqs.fa -oc motifs/97 -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= 108 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= 54000 N= 108 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.275 C 0.235 G 0.220 T 0.270 Background letter frequencies (from dataset with add-one prior applied): A 0.275 C 0.235 G 0.220 T 0.270 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 13 sites = 68 llr = 603 E-value = 7.5e-017 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :41:19:5::194 pos.-specific C 513:4:a:::4:2 probability G 231:4:::a:413 matrix T 33691::4:a1:: bits 2.2 * * 2.0 * * 1.7 * * 1.5 * ** Relative 1.3 * ** ** * Entropy 1.1 * ** ** * (12.8 bits) 0.9 * ** ** * 0.7 * ***** * 0.4 * ******** * 0.2 ************* 0.0 ------------- Multilevel CATTCACAGTGAA consensus TGC G T C G sequence GT C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------- 47397 130 1.05e-07 AAGAGGATGC CATTGACAGTGAG TGCGCTAGGA 34026 159 1.05e-07 CTCCCATTAT CATTCACAGTCAA CAGACAGCGA 37463 63 6.26e-07 ACGGTGACAG CTTTCACAGTCAG CTAGCTCACA 47965 139 6.26e-07 ATTCCTTCCA CGTTGACTGTGAA TTTTGGATTC 47179 466 6.26e-07 AAAGAGGCAT CGTTCACTGTCAA CTAAATATAG 49302 120 1.06e-06 CGAAGCGAAG CATTCACTGTCAC TGTCAGTAAG 46249 452 1.06e-06 CAACGGATCC CATTGACTGTGAC CACAGTTTTT 50016 315 1.06e-06 TCTTTCTATT CTTTGACTGTGAG TGAGTGTTGC 47359 184 1.38e-06 TTTGCGATAT GATTCACAGTCAG TGATTTTTGC 49838 457 1.38e-06 TTGACGTTTG TATTCACAGTCAG TACAATCACC 44194 368 1.75e-06 AGAGCTGCGA CGCTCACAGTCAG TCGCCATCAC 30352 10 1.75e-06 GGTCGGCTG CGCTGACAGTGAA AGGTATTCGG 42946 345 2.64e-06 CAGATTCTCG CTTTGACTGTGAC ATGAAAGCAA 50280 301 3.11e-06 TCACCATGGT TTTTGACAGTGAA TCGTGGGCTT 49507 316 4.19e-06 TCCTTGGTGC TATTGACTGTGAC TGTCAACTGT 49115 422 4.19e-06 GCAAATTGCT GACTGACAGTGAG TTGCGAGGCT 36284 264 4.79e-06 AAATCTTGTT GGTTCACTGTGAC GTCGATTCCA 48451 152 5.44e-06 CAGAATGGTA CCTTGACTGTGAA AACAGTTTTG 43757 482 6.13e-06 CTCTTCTTTG GTCTCACAGTGAA GCCACT 39117 53 6.87e-06 GATGCAAAGC GGCTGACTGTGAA TGAAAACGAG 42743 235 6.87e-06 GACGGCTTGT GTCTCACAGTCAG CGTTGGGTCA 47053 465 1.08e-05 ACTGTATGTT CATTGACTGTGGA GGCTCAACTC 45019 380 1.22e-05 CGTTGATCAT CTTTCACAGTGGA TGTGCATTTC 46705 251 1.22e-05 GCAGAATGTC GCTTCACTGTCAG TAAATCGACG 48333 252 1.22e-05 TCACAGCTCA CGGTGACTGTGAG GGGGATGGCT 42993 233 1.22e-05 GTCTCGACGA TATTGACAGTAAG ATCTTCCCAA 43823 352 1.92e-05 TAATTGAAAA TATTCACAGTCGA TGCCTGTAAA 47738 160 2.40e-05 TACACAAATC AATTCACAGTCAG ATGTAAAATT 49467 96 2.66e-05 TTGATTGAAT TACTTACAGTCAA AGAATTTCCG 31453 295 2.66e-05 GAGTATGTTA CATTAACAGTAAG AGCTAGCCAA 44469 418 2.66e-05 AAGAGGCACC GACTAACTGTGAA GACCAATCAG 32848 131 2.66e-05 AGACTTTTTA CATTTACAGTTAG GGCTTTTTCC 47533 464 3.23e-05 GAGACGAGGC TTGTGACTGTGAA TACTCTGATC 33755 283 3.90e-05 TGCGATCGCC CATTCGCTGTCAC AAAACAAGAA 47761 236 4.28e-05 GACGCCACCA TGATCACTGTCAG TAAGGATAGA 47734 477 4.28e-05 TTGCTATTGC GATTCACTGTCAT CACGACCCGA 9158 451 4.28e-05 CGTTGTCGCG CACTCACAGCGAA ATTAAAGGCG 48674 20 5.10e-05 AATCCTGTGC AGCTCACAGTCAA TTGTGGAATG 43956 180 5.10e-05 TATAATACCT GATTGACAGCGAA GCACATATTT 49304 358 5.54e-05 TCGTGGCGTT CTTTTACAGTTAC AATTTACAGT 50365 473 5.54e-05 ACACACAATT TGTTCCCAGTCAG GTCGTCCCTC 23281 289 5.54e-05 TCCTTCGCCT TGTTCCCAGTCAG AGCAACGGCT 43196 217 5.54e-05 CCGACTGCCG TATTCACGGTCAC ATCATACTTT 44464 280 6.02e-05 GTCTGAAAAT GGATCACTGTCAC TGTTCTATAT 44270 407 6.02e-05 ACGATCATAT TATTTACTGTTAA AATTCGACAC 49305 132 6.54e-05 CTCCGCTATT CTCTTACAGTTAA TTAAAACTTC 39317 59 6.54e-05 TGGGATGCGG CGCTAACTGTAAA GCCTTTCCCA 50635 222 6.54e-05 AATATTAAAG CTTTCACTGTAGA TAGTTAGTTG 47592 480 7.12e-05 AGCTCACGTG CTTCCACAGTCAC GGTTAAAA 44271 254 7.12e-05 CTGTGTCGAA TTTTAACAGTAAA TAATATGATC 46392 332 7.75e-05 TCTGCGTTTG GCTTCACTGTCGG CAGGCAAAAA 37787 30 8.42e-05 TGTTGATTGT TGTGGACTGTGAG TAGTGGTGTG 13028 362 9.88e-05 TAGTCCTCGG CAGTGACGGTGAA GATGAATCAA 43122 234 9.88e-05 TAGAAGAACG GTTTGACAGTTGA GACACATACT 35642 186 1.07e-04 CGTTGGACAA GTTTGGCTGTCAC ACTTTGTGTA 49082 219 1.07e-04 AAATAGATAT TCCTCACTGTTAC TTTATATCAA 34868 270 1.07e-04 AATGTACATA CACACACAGTGAA GAGGGTAGGT 48735 336 1.07e-04 CAGCTGCACA TCATGACTGTGAA TCATGTCGTC 21410 467 1.07e-04 TGAATGCACA CATTGACAGTCGT GATGATATTA 44848 488 1.16e-04 GATGATTAGT GCCTAACTGTGAC 36337 371 1.25e-04 TGTTTTTGCC TGCCGACAGTGAA GCCAAACGCA 42574 47 1.25e-04 TACGAGAGAG CTCGGACTGTGAC TAAGAAAATT 35036 397 1.35e-04 TCTCAGCGAT CACTCACAGTCCC TTTGTACAAA 47534 63 1.45e-04 TTTTCACTAT CAGTCGCAGTCAC AGGTAATCCA 46513 114 1.45e-04 TTCTGTTGCA CGGTAACAGTAAG TGTTACCGAA 35525 206 1.68e-04 CAAACAACAA CGCTGACAGCTAG TAGCTGTGAC 47992 439 2.89e-04 TTTCGTTTCA TAATAACAGTAAA CAATACACAC 47557 295 3.28e-04 CCGAATGTGT CTTTTCCAGTTAG GTAGTCTTGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 47397 1.1e-07 129_[+1]_358 34026 1.1e-07 158_[+1]_329 37463 6.3e-07 62_[+1]_425 47965 6.3e-07 138_[+1]_349 47179 6.3e-07 465_[+1]_22 49302 1.1e-06 119_[+1]_368 46249 1.1e-06 451_[+1]_36 50016 1.1e-06 314_[+1]_173 47359 1.4e-06 183_[+1]_304 49838 1.4e-06 456_[+1]_31 44194 1.8e-06 367_[+1]_120 30352 1.8e-06 9_[+1]_478 42946 2.6e-06 344_[+1]_143 50280 3.1e-06 300_[+1]_187 49507 4.2e-06 315_[+1]_172 49115 4.2e-06 421_[+1]_66 36284 4.8e-06 263_[+1]_224 48451 5.4e-06 151_[+1]_336 43757 6.1e-06 481_[+1]_6 39117 6.9e-06 52_[+1]_435 42743 6.9e-06 234_[+1]_253 47053 1.1e-05 464_[+1]_23 45019 1.2e-05 379_[+1]_108 46705 1.2e-05 250_[+1]_237 48333 1.2e-05 251_[+1]_236 42993 1.2e-05 232_[+1]_255 43823 1.9e-05 351_[+1]_136 47738 2.4e-05 159_[+1]_328 49467 2.7e-05 95_[+1]_392 31453 2.7e-05 294_[+1]_193 44469 2.7e-05 417_[+1]_70 32848 2.7e-05 130_[+1]_357 47533 3.2e-05 463_[+1]_24 33755 3.9e-05 282_[+1]_205 47761 4.3e-05 235_[+1]_252 47734 4.3e-05 476_[+1]_11 9158 4.3e-05 450_[+1]_37 48674 5.1e-05 19_[+1]_468 43956 5.1e-05 179_[+1]_308 49304 5.5e-05 357_[+1]_130 50365 5.5e-05 472_[+1]_15 23281 5.5e-05 288_[+1]_199 43196 5.5e-05 216_[+1]_271 44464 6e-05 279_[+1]_208 44270 6e-05 406_[+1]_81 49305 6.5e-05 131_[+1]_356 39317 6.5e-05 58_[+1]_429 50635 6.5e-05 221_[+1]_266 47592 7.1e-05 479_[+1]_8 44271 7.1e-05 253_[+1]_234 46392 7.8e-05 331_[+1]_156 37787 8.4e-05 29_[+1]_458 13028 9.9e-05 361_[+1]_126 43122 9.9e-05 233_[+1]_254 35642 0.00011 185_[+1]_302 49082 0.00011 218_[+1]_269 34868 0.00011 269_[+1]_218 48735 0.00011 335_[+1]_152 21410 0.00011 466_[+1]_21 44848 0.00012 487_[+1] 36337 0.00012 370_[+1]_117 42574 0.00012 46_[+1]_441 35036 0.00013 396_[+1]_91 47534 0.00015 62_[+1]_425 46513 0.00015 113_[+1]_374 35525 0.00017 205_[+1]_282 47992 0.00029 438_[+1]_49 47557 0.00033 294_[+1]_193 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=13 seqs=68 47397 ( 130) CATTGACAGTGAG 1 34026 ( 159) CATTCACAGTCAA 1 37463 ( 63) CTTTCACAGTCAG 1 47965 ( 139) CGTTGACTGTGAA 1 47179 ( 466) CGTTCACTGTCAA 1 49302 ( 120) CATTCACTGTCAC 1 46249 ( 452) CATTGACTGTGAC 1 50016 ( 315) CTTTGACTGTGAG 1 47359 ( 184) GATTCACAGTCAG 1 49838 ( 457) TATTCACAGTCAG 1 44194 ( 368) CGCTCACAGTCAG 1 30352 ( 10) CGCTGACAGTGAA 1 42946 ( 345) CTTTGACTGTGAC 1 50280 ( 301) TTTTGACAGTGAA 1 49507 ( 316) TATTGACTGTGAC 1 49115 ( 422) GACTGACAGTGAG 1 36284 ( 264) GGTTCACTGTGAC 1 48451 ( 152) CCTTGACTGTGAA 1 43757 ( 482) GTCTCACAGTGAA 1 39117 ( 53) GGCTGACTGTGAA 1 42743 ( 235) GTCTCACAGTCAG 1 47053 ( 465) CATTGACTGTGGA 1 45019 ( 380) CTTTCACAGTGGA 1 46705 ( 251) GCTTCACTGTCAG 1 48333 ( 252) CGGTGACTGTGAG 1 42993 ( 233) TATTGACAGTAAG 1 43823 ( 352) TATTCACAGTCGA 1 47738 ( 160) AATTCACAGTCAG 1 49467 ( 96) TACTTACAGTCAA 1 31453 ( 295) CATTAACAGTAAG 1 44469 ( 418) GACTAACTGTGAA 1 32848 ( 131) CATTTACAGTTAG 1 47533 ( 464) TTGTGACTGTGAA 1 33755 ( 283) CATTCGCTGTCAC 1 47761 ( 236) TGATCACTGTCAG 1 47734 ( 477) GATTCACTGTCAT 1 9158 ( 451) CACTCACAGCGAA 1 48674 ( 20) AGCTCACAGTCAA 1 43956 ( 180) GATTGACAGCGAA 1 49304 ( 358) CTTTTACAGTTAC 1 50365 ( 473) TGTTCCCAGTCAG 1 23281 ( 289) TGTTCCCAGTCAG 1 43196 ( 217) TATTCACGGTCAC 1 44464 ( 280) GGATCACTGTCAC 1 44270 ( 407) TATTTACTGTTAA 1 49305 ( 132) CTCTTACAGTTAA 1 39317 ( 59) CGCTAACTGTAAA 1 50635 ( 222) CTTTCACTGTAGA 1 47592 ( 480) CTTCCACAGTCAC 1 44271 ( 254) TTTTAACAGTAAA 1 46392 ( 332) GCTTCACTGTCGG 1 37787 ( 30) TGTGGACTGTGAG 1 13028 ( 362) CAGTGACGGTGAA 1 43122 ( 234) GTTTGACAGTTGA 1 35642 ( 186) GTTTGGCTGTCAC 1 49082 ( 219) TCCTCACTGTTAC 1 34868 ( 270) CACACACAGTGAA 1 48735 ( 336) TCATGACTGTGAA 1 21410 ( 467) CATTGACAGTCGT 1 44848 ( 488) GCCTAACTGTGAC 1 36337 ( 371) TGCCGACAGTGAA 1 42574 ( 47) CTCGGACTGTGAC 1 35036 ( 397) CACTCACAGTCCC 1 47534 ( 63) CAGTCGCAGTCAC 1 46513 ( 114) CGGTAACAGTAAG 1 35525 ( 206) CGCTGACAGCTAG 1 47992 ( 439) TAATAACAGTAAA 1 47557 ( 295) CTTTTCCAGTTAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 52704 bayes= 9.66593 E= 7.5e-017 -322 105 0 -3 58 -141 18 -11 -223 25 -158 112 -422 -299 -290 178 -142 91 74 -161 173 -241 -232 -1273 -1273 209 -1273 -1273 98 -1273 -290 66 -1273 -1273 218 -1273 -1273 -241 -1273 182 -142 70 85 -120 168 -399 -110 -1273 58 0 56 -320 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 68 E= 7.5e-017 0.029412 0.485294 0.220588 0.264706 0.411765 0.088235 0.250000 0.250000 0.058824 0.279412 0.073529 0.588235 0.014706 0.029412 0.029412 0.926471 0.102941 0.441176 0.367647 0.088235 0.911765 0.044118 0.044118 0.000000 0.000000 1.000000 0.000000 0.000000 0.544118 0.000000 0.029412 0.426471 0.000000 0.000000 1.000000 0.000000 0.000000 0.044118 0.000000 0.955882 0.102941 0.382353 0.397059 0.117647 0.882353 0.014706 0.102941 0.000000 0.411765 0.235294 0.323529 0.029412 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CTG][AGT][TC]T[CG]AC[AT]GT[GC]A[AGC] -------------------------------------------------------------------------------- Time 77.24 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 7 llr = 137 E-value = 1.9e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 3::61a7::77a46::::a4: pos.-specific C 1991::13::::1:a:a3:19 probability G 61139:17a1::34:a:7::1 matrix T :::::::::13:1::::::4: bits 2.2 * *** 2.0 * * * *** * 1.7 * * * *** * 1.5 ** ** * * *** * * Relative 1.3 ** ** ** * ***** * Entropy 1.1 ** ** ** ** ****** * (28.3 bits) 0.9 ** ***** ** ****** * 0.7 ************ ****** * 0.4 ************ ******** 0.2 ********************* 0.0 --------------------- Multilevel GCCAGAAGGAAAAACGCGAAC consensus A G C T GG C T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 35856 177 7.17e-13 CGCCTTGTAC GCCAGAAGGAAAAACGCGAAC ACGATGGAAG 46000 177 1.86e-12 CGCCTTGTAC GCCGGAAGGAAAAACGCGAAC ACGATGGAAG 44165 455 7.98e-10 GGATTTTTCG ACCCGAACGAAAGACGCCATC CGTGGTACAA 38917 160 1.18e-09 GTTTGTTGTG GGCAGAGGGGAAGGCGCGAAC AGTCTGGAAT 42743 18 2.40e-09 CACAGGCTGG GCCGGACGGATAAACGCGACG GCCGCTCCGA 41098 277 4.10e-09 ATGGCGCGAA CCGAGAACGATATGCGCGATC AACAATTTGT 35642 440 5.08e-09 TTTGGCCCAA ACCAAAAGGTAACGCGCCATC GTGGCGACAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 35856 7.2e-13 176_[+2]_303 46000 1.9e-12 176_[+2]_303 44165 8e-10 454_[+2]_25 38917 1.2e-09 159_[+2]_320 42743 2.4e-09 17_[+2]_462 41098 4.1e-09 276_[+2]_203 35642 5.1e-09 439_[+2]_40 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=7 35856 ( 177) GCCAGAAGGAAAAACGCGAAC 1 46000 ( 177) GCCGGAAGGAAAAACGCGAAC 1 44165 ( 455) ACCCGAACGAAAGACGCCATC 1 38917 ( 160) GGCAGAGGGGAAGGCGCGAAC 1 42743 ( 18) GCCGGACGGATAAACGCGACG 1 41098 ( 277) CCGAGAACGATATGCGCGATC 1 35642 ( 440) ACCAAAAGGTAACGCGCCATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 51840 bayes= 13.46 E= 1.9e+000 5 -71 138 -945 -945 187 -62 -945 -945 187 -62 -945 105 -71 38 -945 -94 -945 196 -945 186 -945 -945 -945 137 -71 -62 -945 -945 28 170 -945 -945 -945 218 -945 137 -945 -62 -92 137 -945 -945 8 186 -945 -945 -945 64 -71 38 -92 105 -945 96 -945 -945 209 -945 -945 -945 -945 218 -945 -945 209 -945 -945 -945 28 170 -945 186 -945 -945 -945 64 -71 -945 66 -945 187 -62 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7 E= 1.9e+000 0.285714 0.142857 0.571429 0.000000 0.000000 0.857143 0.142857 0.000000 0.000000 0.857143 0.142857 0.000000 0.571429 0.142857 0.285714 0.000000 0.142857 0.000000 0.857143 0.000000 1.000000 0.000000 0.000000 0.000000 0.714286 0.142857 0.142857 0.000000 0.000000 0.285714 0.714286 0.000000 0.000000 0.000000 1.000000 0.000000 0.714286 0.000000 0.142857 0.142857 0.714286 0.000000 0.000000 0.285714 1.000000 0.000000 0.000000 0.000000 0.428571 0.142857 0.285714 0.142857 0.571429 0.000000 0.428571 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.285714 0.714286 0.000000 1.000000 0.000000 0.000000 0.000000 0.428571 0.142857 0.000000 0.428571 0.000000 0.857143 0.142857 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GA]CC[AG]GAA[GC]GA[AT]A[AG][AG]CGC[GC]A[AT]C -------------------------------------------------------------------------------- Time 151.94 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 12 llr = 153 E-value = 3.5e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::::::1::::: pos.-specific C 2::::a1:4:71 probability G ::1:::8:4::8 matrix T 8a9aa::a2a32 bits 2.2 * 2.0 * *** * * 1.7 * *** * * 1.5 ***** * * Relative 1.3 ******** * Entropy 1.1 ******** *** (18.4 bits) 0.9 ******** *** 0.7 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TTTTTCGTCTCG consensus G T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 47533 19 6.15e-08 GCGCGCAATA TTTTTCGTGTCG TATCCTTAAT 43546 447 1.98e-07 CCGGACCCAC TTTTTCGTGTTG GTTTTCCTTG 44464 89 2.73e-07 GCCATGGTGG TTTTTCGTCTTG GCCGTCGCAA 47359 93 4.60e-07 GGTCTAACGC CTTTTCGTCTCG TGTCATGCCT 46000 31 6.16e-07 GTCGTCGGCA TTTTTCGTCTCT ACTCCGCGGT 35856 31 6.16e-07 GTCGTCGGCA TTTTTCGTCTCT ACTCCGCGGT 31453 65 7.02e-07 AGGATTCGAC TTTTTCGTTTTG CTATCGAAAA 34026 141 1.00e-06 CACTTGCATA TTTTTCGTCTCC CATTATCATT 52174 96 1.13e-06 GTTCGCGCCT TTTTTCCTGTCG TTGTCAACAA 47053 141 1.37e-06 AAATAGCGAA TTTTTCATGTCG CAGAGGCCGA 35525 82 1.61e-06 GGCGCACACG CTTTTCGTTTCG TAAACGGAGT 42993 167 1.76e-06 GATGTTGTTG TTGTTCGTGTTG TTCTTGCAGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 47533 6.2e-08 18_[+3]_470 43546 2e-07 446_[+3]_42 44464 2.7e-07 88_[+3]_400 47359 4.6e-07 92_[+3]_396 46000 6.2e-07 30_[+3]_458 35856 6.2e-07 30_[+3]_458 31453 7e-07 64_[+3]_424 34026 1e-06 140_[+3]_348 52174 1.1e-06 95_[+3]_393 47053 1.4e-06 140_[+3]_348 35525 1.6e-06 81_[+3]_407 42993 1.8e-06 166_[+3]_322 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=12 47533 ( 19) TTTTTCGTGTCG 1 43546 ( 447) TTTTTCGTGTTG 1 44464 ( 89) TTTTTCGTCTTG 1 47359 ( 93) CTTTTCGTCTCG 1 46000 ( 31) TTTTTCGTCTCT 1 35856 ( 31) TTTTTCGTCTCT 1 31453 ( 65) TTTTTCGTTTTG 1 34026 ( 141) TTTTTCGTCTCC 1 52174 ( 96) TTTTTCCTGTCG 1 47053 ( 141) TTTTTCATGTCG 1 35525 ( 82) CTTTTCGTTTCG 1 42993 ( 167) TTGTTCGTGTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 52812 bayes= 11.7622 E= 3.5e+000 -1023 -49 -1023 162 -1023 -1023 -1023 189 -1023 -1023 -140 176 -1023 -1023 -1023 189 -1023 -1023 -1023 189 -1023 209 -1023 -1023 -172 -149 192 -1023 -1023 -1023 -1023 189 -1023 83 92 -70 -1023 -1023 -1023 189 -1023 151 -1023 30 -1023 -149 177 -70 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 12 E= 3.5e+000 0.000000 0.166667 0.000000 0.833333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.083333 0.916667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.083333 0.083333 0.833333 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.416667 0.416667 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.083333 0.750000 0.166667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- TTTTTCGT[CG]T[CT]G -------------------------------------------------------------------------------- Time 227.65 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42574 1.51e-01 500 42743 4.23e-08 17_[+2(2.40e-09)]_145_\ [+1(3.90e-05)]_38_[+1(6.87e-06)]_73_[+3(8.21e-05)]_168 42914 3.70e-01 500 42946 2.90e-04 17_[+2(2.39e-05)]_219_\ [+1(7.12e-05)]_74_[+1(2.64e-06)]_143 42993 2.01e-04 166_[+3(1.76e-06)]_54_\ [+1(1.22e-05)]_255 9158 4.62e-02 450_[+1(4.28e-05)]_37 43122 1.11e-01 233_[+1(9.88e-05)]_254 43196 1.62e-01 216_[+1(5.54e-05)]_271 36284 1.35e-03 263_[+1(4.79e-06)]_12_\ [+3(5.35e-05)]_200 36337 1.38e-02 500 13028 5.10e-02 361_[+1(9.88e-05)]_126 13706 8.80e-01 500 47045 9.98e-02 500 52174 1.40e-02 95_[+3(1.13e-06)]_393 21410 1.64e-01 500 47179 5.46e-03 465_[+1(6.26e-07)]_22 47205 2.13e-01 482_[+3(4.97e-05)]_6 21455 1.97e-01 500 47517 1.33e-02 74_[+2(3.91e-06)]_405 47734 8.77e-02 476_[+1(4.28e-05)]_11 47761 1.06e-01 235_[+1(4.28e-05)]_252 4344 2.57e-01 473_[+3(7.54e-05)]_15 47965 7.90e-04 138_[+1(6.26e-07)]_349 47992 1.54e-01 500 38652 6.35e-02 272_[+2(1.24e-05)]_207 15016 4.92e-01 500 38865 2.83e-01 500 48451 1.22e-03 151_[+1(5.44e-06)]_213_\ [+2(6.02e-05)]_102 38917 1.79e-05 159_[+2(1.18e-09)]_320 39117 8.02e-03 52_[+1(6.87e-06)]_435 48735 9.71e-02 500 32848 1.07e-02 130_[+1(2.66e-05)]_3_[+3(6.82e-05)]_\ 342 43757 5.33e-03 83_[+3(7.54e-05)]_105_\ [+3(9.95e-05)]_269_[+1(6.13e-06)]_6 49115 9.48e-03 421_[+1(4.19e-06)]_66 49227 3.98e-01 500 30352 4.27e-03 9_[+1(1.75e-06)]_478 49507 1.20e-02 67_[+1(4.28e-05)]_235_\ [+1(4.19e-06)]_172 23281 4.78e-02 288_[+1(5.54e-05)]_199 49838 1.60e-02 456_[+1(1.38e-06)]_31 50016 7.00e-03 314_[+1(1.06e-06)]_173 50280 3.41e-03 261_[+1(3.55e-05)]_26_\ [+1(3.11e-06)]_16_[+1(2.93e-05)]_158 50365 9.91e-02 472_[+1(5.54e-05)]_15 43956 3.50e-03 179_[+1(5.10e-05)]_118_\ [+3(1.20e-05)]_178 10628 1.85e-01 61_[+3(5.88e-05)]_427 44165 7.77e-06 454_[+2(7.98e-10)]_25 50429 5.93e-01 500 2845 7.07e-01 500 50635 9.57e-02 221_[+1(6.54e-05)]_266 44270 2.05e-02 276_[+3(8.21e-05)]_118_\ [+1(6.02e-05)]_81 44271 8.53e-03 166_[+3(7.54e-05)]_75_\ [+1(7.12e-05)]_234 34026 4.26e-06 140_[+3(1.00e-06)]_6_[+1(1.05e-07)]_\ 329 44947 1.51e-01 500 46249 2.47e-03 451_[+1(1.06e-06)]_36 8598 7.74e-01 500 46392 3.59e-02 331_[+1(7.75e-05)]_156 44469 4.14e-02 417_[+1(2.66e-05)]_70 31453 2.01e-04 64_[+3(7.02e-07)]_218_\ [+1(2.66e-05)]_193 48333 2.67e-03 251_[+1(1.22e-05)]_44_\ [+2(4.94e-05)]_171 48434 3.84e-01 500 39065 5.57e-01 500 44194 4.49e-03 367_[+1(1.75e-06)]_120 48673 3.98e-01 500 48674 2.43e-03 19_[+1(5.10e-05)]_11_[+2(7.79e-05)]_\ 313_[+3(8.98e-05)]_111 39317 4.99e-03 3_[+2(4.79e-05)]_34_[+1(6.54e-05)]_\ 429 44300 8.12e-01 500 33755 1.67e-02 282_[+1(3.90e-05)]_161_\ [+3(7.90e-05)]_32 34868 2.39e-01 500 46380 3.98e-01 500 43546 3.25e-03 446_[+3(1.98e-07)]_42 43823 9.75e-02 351_[+1(1.92e-05)]_136 47397 1.26e-03 129_[+1(1.05e-07)]_45_\ [+1(1.38e-06)]_300 46513 1.21e-01 500 36590 3.47e-01 500 32962 5.58e-01 500 47533 5.11e-05 18_[+3(6.15e-08)]_433_\ [+1(3.23e-05)]_24 47534 8.10e-02 500 46659 8.59e-01 500 47592 2.05e-01 479_[+1(7.12e-05)]_8 46705 6.95e-02 250_[+1(1.22e-05)]_237 44848 5.10e-02 500 47738 7.66e-03 159_[+1(2.40e-05)]_328 39650 2.38e-01 500 49082 4.36e-02 9_[+3(9.25e-05)]_479 35642 1.03e-05 439_[+2(5.08e-09)]_40 49129 5.32e-01 500 35036 1.51e-01 500 47053 2.20e-04 140_[+3(1.37e-06)]_312_\ [+1(1.08e-05)]_23 49269 2.32e-01 500 35856 2.91e-11 30_[+3(6.16e-07)]_134_\ [+2(7.17e-13)]_303 49302 1.31e-03 119_[+1(1.06e-06)]_42_\ [+1(6.87e-06)]_313 49467 1.01e-01 95_[+1(2.66e-05)]_392 45019 9.39e-03 379_[+1(1.22e-05)]_108 37463 9.81e-04 47_[+1(5.54e-05)]_2_[+1(6.26e-07)]_\ 2_[+1(5.10e-05)]_410 47359 1.45e-05 92_[+3(4.60e-07)]_79_[+1(1.38e-06)]_\ 304 41098 2.88e-05 276_[+2(4.10e-09)]_203 35525 2.51e-03 81_[+3(1.61e-06)]_407 45552 1.86e-01 500 37774 1.04e-01 500 37787 1.52e-01 29_[+1(8.42e-05)]_458 47557 2.09e-01 500 50129 2.71e-02 57_[+2(5.38e-05)]_422 33588 3.63e-01 500 43718 6.64e-01 500 46000 7.11e-11 30_[+3(6.16e-07)]_134_\ [+2(1.86e-12)]_303 35694 9.42e-01 500 44464 2.84e-04 88_[+3(2.73e-07)]_179_\ [+1(6.02e-05)]_208 49304 8.55e-02 357_[+1(5.54e-05)]_130 49305 3.24e-02 131_[+1(6.54e-05)]_356 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************