******************************************************************************** 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/468/468.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10638 1.0000 500 10761 1.0000 500 11391 1.0000 500 12008 1.0000 500 12185 1.0000 500 17312 1.0000 500 17735 1.0000 500 2003 1.0000 500 2004 1.0000 500 20848 1.0000 500 21882 1.0000 500 22487 1.0000 500 23159 1.0000 500 23432 1.0000 500 23915 1.0000 500 24468 1.0000 500 24871 1.0000 500 2509 1.0000 500 2657 1.0000 500 40385 1.0000 500 5155 1.0000 500 6126 1.0000 500 7767 1.0000 500 8221 1.0000 500 8506 1.0000 500 8700 1.0000 500 bd1948 1.0000 500 bd616 1.0000 500 bd827 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/468/468.seqs.fa -oc motifs/468 -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= 29 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= 14500 N= 29 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.265 C 0.247 G 0.221 T 0.267 Background letter frequencies (from dataset with add-one prior applied): A 0.265 C 0.247 G 0.221 T 0.267 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 19 sites = 29 llr = 275 E-value = 2.3e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 4:2315433:4439611a7 pos.-specific C 326:61421a1551:88:3 probability G :41131:2::2:1:1:::: matrix T 3417:2135:311:3:::1 bits 2.2 2.0 * * 1.7 * * 1.5 * * Relative 1.3 * * ** Entropy 1.1 * * *** (13.7 bits) 0.9 * * **** 0.7 * ** * ****** 0.4 ** ** * ** ******** 0.2 ******* ** ******** 0.0 ------------------- Multilevel AGCTCAAATCACCAACCAA consensus CT AGTCTA TAA T C sequence T G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 10761 403 5.51e-09 CGTAGCACCA AGCTCAAACCACCAACCAA AGACCACATT bd827 449 1.16e-08 AAGTCGATTC ATCTCACTTCACAATCCAA CAACAAGCCC 12185 449 1.16e-08 AAGTCGATTC ATCTCACTTCACAATCCAA CAACAAGCCC 20848 64 5.76e-07 GTGTGTTGAT AGCTCCAATCTCCAACAAA CGTATATCTC 6126 140 1.31e-06 CAAGAACACT CGCAGCATACTCCATCCAA ACTGAAGTCT 2003 460 1.70e-06 CAGCCACCTC CTCTCACAACCCAAAACAA CCACAACACA 10638 180 1.92e-06 TTGAGGTGGT TGCTGTAATCAACAACCAT TTCTCTCTGT 8700 383 2.76e-06 CTCTGCTCTT CCAACACATCTCAATCCAA ATCATCACAC 7767 428 3.91e-06 TCCCAACTTC ATCTCACTACTACAGCAAA TACCTCCCTT 2657 478 6.06e-06 CTAAAAAAAC TGATCACAACGAACACCAA CCCG 23915 351 6.06e-06 AACGGTCGTC CGCACTCGACGCTATCCAA CAGCAACAAA 17735 387 6.06e-06 TGACACGGCC AGATGTTTCCACCAACCAA CCAGCTCCAA 24871 14 8.28e-06 GGGAAGCACA ATCTGAATACTACCTCCAC TCGTCGGTGT 21882 140 8.28e-06 GCCGACAATA TTCGCAACCCCCCAACCAA CAGCGAACGA 12008 467 1.79e-05 AGCACAATCA CTATCTCGTCGTCAACAAA CAAACAACAC 24468 479 1.96e-05 TGCAGCACAT TGCTCACCTCCTCATCAAC ATC 23159 481 1.96e-05 CCAAACCACT TGAACAAAACACAAAACAC C 22487 133 2.15e-05 GATGATGTTT CGGAGGTGTCTACAACCAC GATGCTGCTG 11391 385 2.15e-05 TTCAATTAAT TTTTGCTCTCTCAAACCAA TGACCTTGTC 8221 284 2.79e-05 GAGATAGTCA CGCAAACTTCAAGAGCCAA TATAAGGTGT 23432 175 3.04e-05 GACTGTCTCG CGCTCGAGTCAACAACGAT AGTGATGTAC 17312 136 5.79e-05 CGAGATGATC ACCTCTCCCCGACGACCAA CTCGACGATG 2509 344 6.74e-05 TTCCGTGACG AGTTGCCAACTTAAAACAA CTTGTGGAAC 5155 279 7.81e-05 CACACTGACG TTGTTAAATCAAGAACCAC GTTAAGTAAA bd1948 422 9.68e-05 CAAAACCATA ATTTAGTTTCGTCAACCAA CCACACATCC 2004 318 1.55e-04 GAGCAGCTCA TTGAGAGGACGAAAGCCAA AACAGCGCGA 8506 141 1.76e-04 CACCTCCCCT CCGTCAAGACACTAATCAC ACTAGCGCCC 40385 475 2.11e-04 TGGCGTATCA CCTACGAGTCCACCTCCAC CGCGACC bd616 115 3.34e-04 TCTCGAGTGA ACCGGTACTCACAATGCAC AACAACTCCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10761 5.5e-09 402_[+1]_79 bd827 1.2e-08 448_[+1]_33 12185 1.2e-08 448_[+1]_33 20848 5.8e-07 63_[+1]_418 6126 1.3e-06 139_[+1]_342 2003 1.7e-06 459_[+1]_22 10638 1.9e-06 179_[+1]_302 8700 2.8e-06 382_[+1]_99 7767 3.9e-06 427_[+1]_54 2657 6.1e-06 477_[+1]_4 23915 6.1e-06 350_[+1]_131 17735 6.1e-06 386_[+1]_95 24871 8.3e-06 13_[+1]_468 21882 8.3e-06 139_[+1]_342 12008 1.8e-05 466_[+1]_15 24468 2e-05 478_[+1]_3 23159 2e-05 480_[+1]_1 22487 2.1e-05 132_[+1]_349 11391 2.1e-05 384_[+1]_97 8221 2.8e-05 283_[+1]_198 23432 3e-05 174_[+1]_307 17312 5.8e-05 135_[+1]_346 2509 6.7e-05 343_[+1]_138 5155 7.8e-05 278_[+1]_203 bd1948 9.7e-05 421_[+1]_60 2004 0.00015 317_[+1]_164 8506 0.00018 140_[+1]_341 40385 0.00021 474_[+1]_7 bd616 0.00033 114_[+1]_367 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=19 seqs=29 10761 ( 403) AGCTCAAACCACCAACCAA 1 bd827 ( 449) ATCTCACTTCACAATCCAA 1 12185 ( 449) ATCTCACTTCACAATCCAA 1 20848 ( 64) AGCTCCAATCTCCAACAAA 1 6126 ( 140) CGCAGCATACTCCATCCAA 1 2003 ( 460) CTCTCACAACCCAAAACAA 1 10638 ( 180) TGCTGTAATCAACAACCAT 1 8700 ( 383) CCAACACATCTCAATCCAA 1 7767 ( 428) ATCTCACTACTACAGCAAA 1 2657 ( 478) TGATCACAACGAACACCAA 1 23915 ( 351) CGCACTCGACGCTATCCAA 1 17735 ( 387) AGATGTTTCCACCAACCAA 1 24871 ( 14) ATCTGAATACTACCTCCAC 1 21882 ( 140) TTCGCAACCCCCCAACCAA 1 12008 ( 467) CTATCTCGTCGTCAACAAA 1 24468 ( 479) TGCTCACCTCCTCATCAAC 1 23159 ( 481) TGAACAAAACACAAAACAC 1 22487 ( 133) CGGAGGTGTCTACAACCAC 1 11391 ( 385) TTTTGCTCTCTCAAACCAA 1 8221 ( 284) CGCAAACTTCAAGAGCCAA 1 23432 ( 175) CGCTCGAGTCAACAACGAT 1 17312 ( 136) ACCTCTCCCCGACGACCAA 1 2509 ( 344) AGTTGCCAACTTAAAACAA 1 5155 ( 279) TTGTTAAATCAAGAACCAC 1 bd1948 ( 422) ATTTAGTTTCGTCAACCAA 1 2004 ( 318) TTGAGAGGACGAAAGCCAA 1 8506 ( 141) CCGTCAAGACACTAATCAC 1 40385 ( 475) CCTACGAGTCCACCTCCAC 1 bd616 ( 115) ACCGGTACTCACAATGCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 13978 bayes= 8.90989 E= 2.3e-003 51 48 -1150 5 -1150 -52 102 51 -62 116 -68 -95 6 -1150 -168 129 -194 125 49 -295 96 -84 -68 -37 64 74 -267 -95 23 -52 13 5 38 -84 -1150 95 -1150 202 -1150 -1150 51 -84 -9 5 51 97 -1150 -95 38 107 -168 -195 170 -125 -267 -1150 114 -1150 -109 22 -136 174 -267 -295 -94 174 -267 -1150 191 -1150 -1150 -1150 130 16 -1150 -195 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 29 E= 2.3e-003 0.379310 0.344828 0.000000 0.275862 0.000000 0.172414 0.448276 0.379310 0.172414 0.551724 0.137931 0.137931 0.275862 0.000000 0.068966 0.655172 0.068966 0.586207 0.310345 0.034483 0.517241 0.137931 0.137931 0.206897 0.413793 0.413793 0.034483 0.137931 0.310345 0.172414 0.241379 0.275862 0.344828 0.137931 0.000000 0.517241 0.000000 1.000000 0.000000 0.000000 0.379310 0.137931 0.206897 0.275862 0.379310 0.482759 0.000000 0.137931 0.344828 0.517241 0.068966 0.068966 0.862069 0.103448 0.034483 0.000000 0.586207 0.000000 0.103448 0.310345 0.103448 0.827586 0.034483 0.034483 0.137931 0.827586 0.034483 0.000000 1.000000 0.000000 0.000000 0.000000 0.655172 0.275862 0.000000 0.068966 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [ACT][GT]C[TA][CG][AT][AC][ATG][TA]C[ATG][CA][CA]A[AT]CCA[AC] -------------------------------------------------------------------------------- Time 6.40 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 21 llr = 239 E-value = 8.0e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::121::7:5:22523223:2 pos.-specific C :::::1:1::2:3:323:3:: probability G :94:83329:75324424:9: matrix T a148:56::5:2131133417 bits 2.2 2.0 * 1.7 * 1.5 ** * * Relative 1.3 ** * * * Entropy 1.1 ** * * * * (16.4 bits) 0.9 ** ** **** ** 0.7 ** ********* ** 0.4 ************ * *** 0.2 **************** **** 0.0 --------------------- Multilevel TGTTGTTAGAGGCAGGCGTGT consensus G GG TCAGTCATTA A sequence TA GAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 2657 258 4.86e-09 GCTATCATTG TGGTGGTAGAGGAACCGGCGT TGTGCTATCT 12185 125 1.07e-07 TTCTCAAACT TGGAGTGAGTGGGAGGTGATT TGGCCCAAGA 2509 387 1.39e-07 CCTCGGAGAA TTTTGTGAGAGGGAGTTGCGT GCGGTAACTT 2003 36 3.59e-07 AAAAAATGGA TGGTGGTGGACAGAGGAGTGA AGCAACAAAC 8506 228 5.00e-07 ATATCTCCTT TGGAGGGAGAGGCGCGCTTGA ACTCCGCCGC 17312 103 5.57e-07 TGACTGCTGT TGGTATGAGACGCGGGTATGT GTCGAGATGA bd616 412 8.46e-07 GGGAAGAACA TGATGTTAATGGGAAATGAGT TTAAGAGGAA 40385 151 8.46e-07 TTGACATCTT TGTTGTTAGTGTTGTGTTAGT GTTTGTTGAG 6126 114 1.52e-06 GCTCAGCCAG TGTAGGTAGAGTATCACAAGA ACACTCGCAG bd827 118 1.67e-06 CTCATTCTTG TGGAGCGAGTGAGAGGTGATT GGCCCAAGAT 22487 253 1.84e-06 TGCGTTCTCT TGTTGGTGGACTTTGAGTCGT TGACGTGTGT 21882 369 1.84e-06 TGAGTGAGAT TGTCGTTAGTGACGACGGAGT AGGGATTGAT 8700 140 2.02e-06 CGATGAGGGC TGTTGCTAGAGGCATTGATGA GTTGGTTGTC 2004 26 2.88e-06 AGATGTTGAA TGATCTTAGTGACTGAATTGT GGTAGAGTGC 24871 212 4.06e-06 CGATGGACGA TGATGGTCGACGATGAAGCGA GATGCACACC 23432 364 4.06e-06 CGTTCTTTGT TGTTGTGGCAGTCACGGATGT AAACGAAGCT 23159 350 5.19e-06 CACACTAAAG TGGTATCAGTCGCTCCCGCGT CATTGGTCAT 24468 357 1.20e-05 TTTATCATAT TGTTATAAGTGTAAAAATAGT TCCCAAAAGC 12008 162 1.29e-05 CTCTTTTGTG TGCTGTTGGTTGGTCCCATGT CTCCTGCATG bd1948 294 1.48e-05 AACTGGTCCC TTTTGGTAGTGAGTGACTTTG CAACAGCCCG 17735 316 1.82e-05 CTCCTTCCAG TTGTGCTCGAGGAAAGCCCGT GGTGACAAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 2657 4.9e-09 257_[+2]_222 12185 1.1e-07 124_[+2]_355 2509 1.4e-07 386_[+2]_93 2003 3.6e-07 35_[+2]_444 8506 5e-07 227_[+2]_252 17312 5.6e-07 102_[+2]_377 bd616 8.5e-07 411_[+2]_68 40385 8.5e-07 150_[+2]_329 6126 1.5e-06 113_[+2]_366 bd827 1.7e-06 117_[+2]_362 22487 1.8e-06 252_[+2]_227 21882 1.8e-06 368_[+2]_111 8700 2e-06 139_[+2]_340 2004 2.9e-06 25_[+2]_454 24871 4.1e-06 211_[+2]_268 23432 4.1e-06 363_[+2]_116 23159 5.2e-06 349_[+2]_130 24468 1.2e-05 356_[+2]_123 12008 1.3e-05 161_[+2]_318 bd1948 1.5e-05 293_[+2]_186 17735 1.8e-05 315_[+2]_164 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=21 2657 ( 258) TGGTGGTAGAGGAACCGGCGT 1 12185 ( 125) TGGAGTGAGTGGGAGGTGATT 1 2509 ( 387) TTTTGTGAGAGGGAGTTGCGT 1 2003 ( 36) TGGTGGTGGACAGAGGAGTGA 1 8506 ( 228) TGGAGGGAGAGGCGCGCTTGA 1 17312 ( 103) TGGTATGAGACGCGGGTATGT 1 bd616 ( 412) TGATGTTAATGGGAAATGAGT 1 40385 ( 151) TGTTGTTAGTGTTGTGTTAGT 1 6126 ( 114) TGTAGGTAGAGTATCACAAGA 1 bd827 ( 118) TGGAGCGAGTGAGAGGTGATT 1 22487 ( 253) TGTTGGTGGACTTTGAGTCGT 1 21882 ( 369) TGTCGTTAGTGACGACGGAGT 1 8700 ( 140) TGTTGCTAGAGGCATTGATGA 1 2004 ( 26) TGATCTTAGTGACTGAATTGT 1 24871 ( 212) TGATGGTCGACGATGAAGCGA 1 23432 ( 364) TGTTGTGGCAGTCACGGATGT 1 23159 ( 350) TGGTATCAGTCGCTCCCGCGT 1 24468 ( 357) TGTTATAAGTGTAAAAATAGT 1 12008 ( 162) TGCTGTTGGTTGGTCCCATGT 1 bd1948 ( 294) TTTTGGTAGTGAGTGACTTTG 1 17735 ( 316) TTGTGCTCGAGGAAAGCCCGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 13920 bayes= 9.67565 E= 8.0e-002 -1104 -1104 -1104 190 -1104 -1104 196 -90 -89 -237 79 68 -48 -237 -1104 151 -89 -237 187 -1104 -1104 -79 60 97 -248 -237 37 121 143 -137 -21 -1104 -248 -237 204 -1104 98 -1104 -1104 83 -1104 -5 169 -248 -16 -1104 125 -17 -16 43 60 -149 84 -1104 -21 32 -48 21 96 -149 33 -37 79 -149 -48 21 11 10 -16 -237 96 10 33 21 -1104 51 -1104 -1104 196 -90 -16 -1104 -221 142 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 21 E= 8.0e-002 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.857143 0.142857 0.142857 0.047619 0.380952 0.428571 0.190476 0.047619 0.000000 0.761905 0.142857 0.047619 0.809524 0.000000 0.000000 0.142857 0.333333 0.523810 0.047619 0.047619 0.285714 0.619048 0.714286 0.095238 0.190476 0.000000 0.047619 0.047619 0.904762 0.000000 0.523810 0.000000 0.000000 0.476190 0.000000 0.238095 0.714286 0.047619 0.238095 0.000000 0.523810 0.238095 0.238095 0.333333 0.333333 0.095238 0.476190 0.000000 0.190476 0.333333 0.190476 0.285714 0.428571 0.095238 0.333333 0.190476 0.380952 0.095238 0.190476 0.285714 0.238095 0.285714 0.238095 0.047619 0.428571 0.285714 0.333333 0.285714 0.000000 0.380952 0.000000 0.000000 0.857143 0.142857 0.238095 0.000000 0.047619 0.714286 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- TG[TG]TG[TG][TG]AG[AT][GC][GAT][CGA][AT][GC][GA][CTG][GTA][TAC]G[TA] -------------------------------------------------------------------------------- Time 12.46 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 13 llr = 179 E-value = 2.3e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 1:::414:324::1:71874: pos.-specific C :11211::221::6::8:2:: probability G 1:482231222:4:83:2:2a matrix T 895:4739454a632:1:14: bits 2.2 * 2.0 * * 1.7 * * 1.5 * * * * Relative 1.3 * * * * * * * Entropy 1.1 ** * * ** **** * (19.9 bits) 0.9 ** * * ** ***** * 0.7 **** * * ******** * 0.4 **** *** ********** 0.2 ******** ************ 0.0 --------------------- Multilevel TTTGATATTTATTCGACAAAG consensus GCT G AGT GTTG GCT sequence T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 8221 26 2.24e-10 TGGCAAGGGA TTTGATTTGTATTCGACAATG AAAACTTCAC bd827 25 2.58e-08 CCTAACAGCA TTGCAGATCTTTTCGACAAAG TTTAGTTCTC 12185 34 2.58e-08 CCTATCAGCA TTGCAGATCTTTTCGACAAAG TTTAGTTCTC 24871 172 2.88e-08 GCCTCATTGA ATTGTTGTTGTTTTGACAATG GTGTGCCGAC 12008 43 1.43e-07 CCGGTGTCAG TTTGTTGGATGTTCGGCGATG CGATATAGCG 23432 14 1.87e-07 GCGACAGTCG TTGGATGTATCTTTGACATGG TGTCTTGATG 23159 373 1.87e-07 TCCCGCGTCA TTGGTCATTATTGCTACAAGG AATGATAAGT 22487 189 2.03e-07 CTCAGTTGAA TTTGATTTGAATGCGGCGCGG TTCTTAGGGT 17735 57 4.23e-07 GAGTAGGTGT TTTGCTTTACATTAGACACAG GCATTTTTTG 2657 97 5.31e-07 CCTCCTCACC TTCGTTGTTTGTGCGATGAAG GGCAGCAGCG 20848 439 6.61e-07 AATCACGCTG TTGGGTATACTTGTGAAACAG AGTGGTGACT 10761 296 8.16e-07 TACAATCAGA TCTCTTATTGATTTTGCAATG CAACTACGAA 8506 282 2.11e-06 GGAGACGTTT GTTGGATTTGATGCTGCAATG GAAGAGGCTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8221 2.2e-10 25_[+3]_454 bd827 2.6e-08 24_[+3]_455 12185 2.6e-08 33_[+3]_446 24871 2.9e-08 171_[+3]_308 12008 1.4e-07 42_[+3]_437 23432 1.9e-07 13_[+3]_466 23159 1.9e-07 372_[+3]_107 22487 2e-07 188_[+3]_291 17735 4.2e-07 56_[+3]_423 2657 5.3e-07 96_[+3]_383 20848 6.6e-07 438_[+3]_41 10761 8.2e-07 295_[+3]_184 8506 2.1e-06 281_[+3]_198 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=13 8221 ( 26) TTTGATTTGTATTCGACAATG 1 bd827 ( 25) TTGCAGATCTTTTCGACAAAG 1 12185 ( 34) TTGCAGATCTTTTCGACAAAG 1 24871 ( 172) ATTGTTGTTGTTTTGACAATG 1 12008 ( 43) TTTGTTGGATGTTCGGCGATG 1 23432 ( 14) TTGGATGTATCTTTGACATGG 1 23159 ( 373) TTGGTCATTATTGCTACAAGG 1 22487 ( 189) TTTGATTTGAATGCGGCGCGG 1 17735 ( 57) TTTGCTTTACATTAGACACAG 1 2657 ( 97) TTCGTTGTTTGTGCGATGAAG 1 20848 ( 439) TTGGGTATACTTGTGAAACAG 1 10761 ( 296) TCTCTTATTGATTTTGCAATG 1 8506 ( 282) GTTGGATTTGATGCTGCAATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 13920 bayes= 10.594 E= 2.3e+000 -178 -1035 -152 166 -1035 -168 -1035 179 -1035 -168 80 101 -1035 -10 180 -1035 53 -168 -52 53 -178 -168 -52 137 53 -1035 48 20 -1035 -1035 -152 179 21 -68 -52 53 -79 -68 6 79 53 -168 -52 53 -1035 -1035 -1035 190 -1035 -1035 80 120 -178 132 -1035 20 -1035 -1035 180 -21 138 -1035 48 -1035 -178 178 -1035 -179 153 -1035 6 -1035 138 -10 -1035 -179 53 -1035 6 53 -1035 -1035 218 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 13 E= 2.3e+000 0.076923 0.000000 0.076923 0.846154 0.000000 0.076923 0.000000 0.923077 0.000000 0.076923 0.384615 0.538462 0.000000 0.230769 0.769231 0.000000 0.384615 0.076923 0.153846 0.384615 0.076923 0.076923 0.153846 0.692308 0.384615 0.000000 0.307692 0.307692 0.000000 0.000000 0.076923 0.923077 0.307692 0.153846 0.153846 0.384615 0.153846 0.153846 0.230769 0.461538 0.384615 0.076923 0.153846 0.384615 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.384615 0.615385 0.076923 0.615385 0.000000 0.307692 0.000000 0.000000 0.769231 0.230769 0.692308 0.000000 0.307692 0.000000 0.076923 0.846154 0.000000 0.076923 0.769231 0.000000 0.230769 0.000000 0.692308 0.230769 0.000000 0.076923 0.384615 0.000000 0.230769 0.384615 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- TT[TG][GC][AT]T[AGT]T[TA][TG][AT]T[TG][CT][GT][AG]C[AG][AC][ATG]G -------------------------------------------------------------------------------- Time 18.33 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10638 1.30e-03 179_[+1(1.92e-06)]_302 10761 6.83e-08 295_[+3(8.16e-07)]_86_\ [+1(5.51e-09)]_79 11391 7.97e-02 384_[+1(2.15e-05)]_97 12008 7.64e-07 42_[+3(1.43e-07)]_98_[+2(1.29e-05)]_\ 242_[+3(3.21e-05)]_21_[+1(1.79e-05)]_15 12185 2.09e-12 33_[+3(2.58e-08)]_70_[+2(1.07e-07)]_\ 64_[+1(8.40e-05)]_18_[+2(7.60e-05)]_181_[+1(1.16e-08)]_33 17312 2.14e-04 102_[+2(5.57e-07)]_12_\ [+1(5.79e-05)]_346 17735 1.04e-06 56_[+3(4.23e-07)]_238_\ [+2(1.82e-05)]_50_[+1(6.06e-06)]_95 2003 1.58e-05 35_[+2(3.59e-07)]_403_\ [+1(1.70e-06)]_22 2004 4.13e-03 25_[+2(2.88e-06)]_427_\ [+2(5.81e-05)]_6 20848 6.23e-06 63_[+1(5.76e-07)]_356_\ [+3(6.61e-07)]_41 21882 1.66e-04 139_[+1(8.28e-06)]_210_\ [+2(1.84e-06)]_111 22487 2.12e-07 132_[+1(2.15e-05)]_37_\ [+3(2.03e-07)]_43_[+2(1.84e-06)]_227 23159 4.63e-07 349_[+2(5.19e-06)]_2_[+3(1.87e-07)]_\ 62_[+1(8.40e-05)]_6_[+1(1.96e-05)]_1 23432 5.50e-07 13_[+3(1.87e-07)]_140_\ [+1(3.04e-05)]_25_[+3(6.76e-05)]_124_[+2(4.06e-06)]_116 23915 7.58e-03 350_[+1(6.06e-06)]_131 24468 1.63e-03 356_[+2(1.20e-05)]_101_\ [+1(1.96e-05)]_3 24871 3.08e-08 13_[+1(8.28e-06)]_139_\ [+3(2.88e-08)]_19_[+2(4.06e-06)]_268 2509 1.20e-05 98_[+3(7.97e-05)]_224_\ [+1(6.74e-05)]_24_[+2(1.39e-07)]_93 2657 6.85e-10 96_[+3(5.31e-07)]_140_\ [+2(4.86e-09)]_199_[+1(6.06e-06)]_4 40385 3.87e-04 150_[+2(8.46e-07)]_329 5155 5.88e-02 278_[+1(7.81e-05)]_203 6126 5.53e-05 113_[+2(1.52e-06)]_5_[+1(1.31e-06)]_\ 342 7767 3.18e-02 427_[+1(3.91e-06)]_54 8221 1.84e-07 25_[+3(2.24e-10)]_237_\ [+1(2.79e-05)]_198 8506 3.47e-06 227_[+2(5.00e-07)]_33_\ [+3(2.11e-06)]_198 8700 4.42e-05 139_[+2(2.02e-06)]_222_\ [+1(2.76e-06)]_99 bd1948 1.27e-02 293_[+2(1.48e-05)]_107_\ [+1(9.68e-05)]_60 bd616 2.68e-03 411_[+2(8.46e-07)]_68 bd827 2.75e-11 24_[+3(2.58e-08)]_72_[+2(1.67e-06)]_\ 63_[+1(6.74e-05)]_18_[+2(6.14e-05)]_189_[+1(1.16e-08)]_33 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************