******************************************************************************** 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/113/113.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10907 1.0000 500 11486 1.0000 500 1747 1.0000 500 18503 1.0000 500 20892 1.0000 500 20993 1.0000 500 20998 1.0000 500 21341 1.0000 500 2145 1.0000 500 21734 1.0000 500 21965 1.0000 500 22097 1.0000 500 22443 1.0000 500 22742 1.0000 500 22830 1.0000 500 22996 1.0000 500 23126 1.0000 500 23148 1.0000 500 25127 1.0000 500 25179 1.0000 500 261702 1.0000 500 263182 1.0000 500 263354 1.0000 500 264339 1.0000 500 28523 1.0000 500 32029 1.0000 500 32459 1.0000 500 33829 1.0000 500 34018 1.0000 500 37596 1.0000 500 39038 1.0000 500 40073 1.0000 500 42992 1.0000 500 444 1.0000 500 4829 1.0000 500 5116 1.0000 500 6052 1.0000 500 6809 1.0000 500 8673 1.0000 500 926 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/113/113.seqs.fa -oc motifs/113 -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= 40 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= 20000 N= 40 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.259 C 0.242 G 0.239 T 0.260 Background letter frequencies (from dataset with add-one prior applied): A 0.259 C 0.242 G 0.239 T 0.260 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 40 llr = 384 E-value = 1.1e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 62:4142:241:22:61:543 pos.-specific C 24847616636554a:59136 probability G ::1:1:11211::::21111: matrix T 24132173:32524:33:331 bits 2.1 1.9 * 1.7 * 1.4 * * Relative 1.2 * * Entropy 1.0 * * * * (13.8 bits) 0.8 * * * * * * 0.6 * * ***** ** ** * * 0.4 ********* ********* * 0.2 ********************* 0.0 --------------------- Multilevel ACCACCTCCACCCCCACCAAC consensus TT C A TACTTAT TT TCA sequence T T TA T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 20993 375 3.16e-08 TCGGAAATAA ACCCCCTCCCCCTCCTCCGTC TCTTCGTTGC 42992 471 1.03e-07 CGCCGCCGCC TTCCCCTCCTCCACCAACAAC GGAGACGTT 10907 476 1.64e-07 ACACCTCTAT ATCACATCAGCTCCCATCAAC AGCC 20892 453 1.91e-07 TGGTGTTTGG ACGACCTTCTCTCTCACCACA CCCACTCCTC 444 65 3.44e-07 TCCCTGCGCC ACCAACTCCCTTATCACCAAC TGACGACGGA 28523 398 4.56e-07 AGGCGACAAC CTCCTCTCCTCCCCCACCTAT ATCGGAGGCA 22742 158 6.85e-07 TTTGCTTGCA ATCCCATCCGCCCTCGTCTAA AGGAAACAGT 21341 4 8.92e-07 TCT ACCTCATCCTTTTCCGTCATC GCATTGGCAT 32459 98 1.02e-06 GTCGTCTTAG TCTCCCTCCACCCCCACCTTT GAATGTGAGA 37596 431 1.15e-06 ATCTAATGCA TTCTCATTCTCTCTCGCCGAC GCTCGTGCTT 261702 90 1.15e-06 CCCCGATGTT ACCTCCTCCACCGCCAACATC CGCAGAAGCA 6052 475 1.68e-06 ACCCAAAACG TACAACTCGCCCCTCACCAAC CCACG 22443 46 1.90e-06 CACCACCAAT ATCCCATTGCTTTACACCACC CTATCAACTC 32029 462 2.14e-06 CAATAATGAA ACCATCGCAACTCTCATCACA ATAATATCAA 11486 216 2.71e-06 GTGCTCCGAT TCCTTCTTGACCTTCACCACC ATCATTTGGA 25127 9 3.41e-06 ACAATGCC ACCAGCTTCTTCCCCTTCAAA GCAGACACTG 263354 7 3.82e-06 CATGAT ATCAGCTTCTTCATCATCATC GCGTCTCCAA 40073 49 4.27e-06 TCCTTTGCGT CCCCCTTCCACCACCGCCACA AGCAAGTCAA 18503 477 5.32e-06 CACCCACTGG TTGCTCTTCACTCTCATCTCC ATC 926 24 8.13e-06 GACTCAATGC ACCACCTGCCGTCTCAACAAT AGTAGTTGCC 39038 465 8.13e-06 GTACAAACAC AACCAAGCCTCCAACACCAAC AGCACTGCTG 4829 379 9.01e-06 AAAACACCGT CCGACCTCCACCACCACGTCC CGTCTTATCT 20998 465 1.48e-05 GAACGAAACG ATCCCAACCAACCACAGCAGC ACCACAGAGC 25179 453 2.17e-05 ACGTCGACGG TTCACCACCCTCTTCGTCTGC GTGCCCGACC 2145 165 2.85e-05 CTAAAGAATG ATGTCATTACCTCCCAACGTC ACGGGCGGAT 5116 480 4.04e-05 CAGTCGCAAT AACACACCAACTCTCTCGACA 264339 75 4.04e-05 CGATCGATCC AACCGATCCACTTACTCGTAC GCTTCTCGAA 23148 449 4.04e-05 ATGACGACGG TTCTCTTCGCGTCTCTCCTTC GACACAAACC 22830 328 4.40e-05 TGAGACTACA ACCACAGTCACTCAATTCAAC GCTTCGCTTG 8673 22 5.65e-05 AGTTTACGTT CGCATCACCCCTCTCTCCGAC GTGATCGTCA 23126 58 5.65e-05 CTCTATGCAT ACTCTATGATCTTCCACCTCA GATGAGTTTG 21965 460 5.65e-05 ACACGTGGAA ATTCCCAGCACCACCACCCAA CACCATAGTA 6809 44 7.20e-05 TACATTATTG AACACCACAATTAACATCGCA GCACTGATGT 21734 284 8.42e-05 CCTTAGATAT CACTCCCGAACCCCCTTCTTC CAGCTGCAGT 34018 402 9.10e-05 CTGATCCTTT ATTCCATTGTCTTCCTGCTAA CCCCTTGCTT 263182 412 1.14e-04 AGAACTTCCG CCCACCGCCCGCCACGCCCGC CACGCCGCTG 22996 448 1.23e-04 CAGCCGAGCG ACCCCACCACACCACAGCAGA ACGTCGACGT 1747 58 1.88e-04 CTTCTTAGAG TCCTTCTTGTGCCTCTTCTTT GAGTTTGAGT 33829 432 2.30e-04 GTATTCAAAA ATATCATCATTTTTCTCCTTT GCATAGATAA 22097 476 2.46e-04 CAACCGAGCA ATCTCAACCCACACCGCTACA GCAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 20993 3.2e-08 374_[+1]_105 42992 1e-07 470_[+1]_9 10907 1.6e-07 475_[+1]_4 20892 1.9e-07 452_[+1]_27 444 3.4e-07 64_[+1]_415 28523 4.6e-07 397_[+1]_82 22742 6.9e-07 157_[+1]_322 21341 8.9e-07 3_[+1]_476 32459 1e-06 97_[+1]_382 37596 1.2e-06 430_[+1]_49 261702 1.2e-06 89_[+1]_390 6052 1.7e-06 474_[+1]_5 22443 1.9e-06 45_[+1]_434 32029 2.1e-06 461_[+1]_18 11486 2.7e-06 215_[+1]_264 25127 3.4e-06 8_[+1]_471 263354 3.8e-06 6_[+1]_473 40073 4.3e-06 48_[+1]_431 18503 5.3e-06 476_[+1]_3 926 8.1e-06 23_[+1]_456 39038 8.1e-06 464_[+1]_15 4829 9e-06 378_[+1]_101 20998 1.5e-05 464_[+1]_15 25179 2.2e-05 452_[+1]_27 2145 2.8e-05 164_[+1]_315 5116 4e-05 479_[+1] 264339 4e-05 74_[+1]_405 23148 4e-05 448_[+1]_31 22830 4.4e-05 327_[+1]_152 8673 5.7e-05 21_[+1]_458 23126 5.7e-05 57_[+1]_422 21965 5.7e-05 459_[+1]_20 6809 7.2e-05 43_[+1]_436 21734 8.4e-05 283_[+1]_196 34018 9.1e-05 401_[+1]_78 263182 0.00011 411_[+1]_68 22996 0.00012 447_[+1]_32 1747 0.00019 57_[+1]_422 33829 0.00023 431_[+1]_48 22097 0.00025 475_[+1]_4 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=40 20993 ( 375) ACCCCCTCCCCCTCCTCCGTC 1 42992 ( 471) TTCCCCTCCTCCACCAACAAC 1 10907 ( 476) ATCACATCAGCTCCCATCAAC 1 20892 ( 453) ACGACCTTCTCTCTCACCACA 1 444 ( 65) ACCAACTCCCTTATCACCAAC 1 28523 ( 398) CTCCTCTCCTCCCCCACCTAT 1 22742 ( 158) ATCCCATCCGCCCTCGTCTAA 1 21341 ( 4) ACCTCATCCTTTTCCGTCATC 1 32459 ( 98) TCTCCCTCCACCCCCACCTTT 1 37596 ( 431) TTCTCATTCTCTCTCGCCGAC 1 261702 ( 90) ACCTCCTCCACCGCCAACATC 1 6052 ( 475) TACAACTCGCCCCTCACCAAC 1 22443 ( 46) ATCCCATTGCTTTACACCACC 1 32029 ( 462) ACCATCGCAACTCTCATCACA 1 11486 ( 216) TCCTTCTTGACCTTCACCACC 1 25127 ( 9) ACCAGCTTCTTCCCCTTCAAA 1 263354 ( 7) ATCAGCTTCTTCATCATCATC 1 40073 ( 49) CCCCCTTCCACCACCGCCACA 1 18503 ( 477) TTGCTCTTCACTCTCATCTCC 1 926 ( 24) ACCACCTGCCGTCTCAACAAT 1 39038 ( 465) AACCAAGCCTCCAACACCAAC 1 4829 ( 379) CCGACCTCCACCACCACGTCC 1 20998 ( 465) ATCCCAACCAACCACAGCAGC 1 25179 ( 453) TTCACCACCCTCTTCGTCTGC 1 2145 ( 165) ATGTCATTACCTCCCAACGTC 1 5116 ( 480) AACACACCAACTCTCTCGACA 1 264339 ( 75) AACCGATCCACTTACTCGTAC 1 23148 ( 449) TTCTCTTCGCGTCTCTCCTTC 1 22830 ( 328) ACCACAGTCACTCAATTCAAC 1 8673 ( 22) CGCATCACCCCTCTCTCCGAC 1 23126 ( 58) ACTCTATGATCTTCCACCTCA 1 21965 ( 460) ATTCCCAGCACCACCACCCAA 1 6809 ( 44) AACACCACAATTAACATCGCA 1 21734 ( 284) CACTCCCGAACCCCCTTCTTC 1 34018 ( 402) ATTCCATTGTCTTCCTGCTAA 1 263182 ( 412) CCCACCGCCCGCCACGCCCGC 1 22996 ( 448) ACCCCACCACACCACAGCAGA 1 1747 ( 58) TCCTTCTTGTGCCTCTTCTTT 1 33829 ( 432) ATATCATCATTTTTCTCCTTT 1 22097 ( 476) ATCTCAACCCACACCGCTACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 19200 bayes= 8.90388 E= 1.1e-010 127 -69 -1197 -21 -79 81 -325 62 -337 168 -125 -138 54 63 -1197 -6 -179 148 -167 -57 63 118 -1197 -238 -79 -169 -125 137 -1197 137 -125 8 -20 137 -67 -1197 44 31 -225 20 -179 137 -125 -38 -1197 111 -1197 87 -20 111 -325 -21 -37 72 -1197 62 -337 201 -1197 -1197 109 -1197 -45 8 -137 111 -167 20 -1197 189 -167 -338 95 -228 -93 32 54 18 -125 -6 21 125 -1197 -106 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 40 E= 1.1e-010 0.625000 0.150000 0.000000 0.225000 0.150000 0.425000 0.025000 0.400000 0.025000 0.775000 0.100000 0.100000 0.375000 0.375000 0.000000 0.250000 0.075000 0.675000 0.075000 0.175000 0.400000 0.550000 0.000000 0.050000 0.150000 0.075000 0.100000 0.675000 0.000000 0.625000 0.100000 0.275000 0.225000 0.625000 0.150000 0.000000 0.350000 0.300000 0.050000 0.300000 0.075000 0.625000 0.100000 0.200000 0.000000 0.525000 0.000000 0.475000 0.225000 0.525000 0.025000 0.225000 0.200000 0.400000 0.000000 0.400000 0.025000 0.975000 0.000000 0.000000 0.550000 0.000000 0.175000 0.275000 0.100000 0.525000 0.075000 0.300000 0.000000 0.900000 0.075000 0.025000 0.500000 0.050000 0.125000 0.325000 0.375000 0.275000 0.100000 0.250000 0.300000 0.575000 0.000000 0.125000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AT][CT]C[ACT]C[CA]T[CT][CA][ACT][CT][CT][CAT][CTA]C[AT][CT]C[AT][ACT][CA] -------------------------------------------------------------------------------- Time 17.25 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 17 llr = 233 E-value = 1.4e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :4::11212::74:8314133 pos.-specific C :1:::::::1::1:::31:1: probability G 8512656745a:5a:545757 matrix T 2:98342245:3::222121: bits 2.1 * * 1.9 * * 1.7 * * 1.4 * * * Relative 1.2 * ** * ** * Entropy 1.0 * ** ** ** * (19.7 bits) 0.8 ***** ** ****** * * 0.6 ******** ******* * * 0.4 **************** **** 0.2 ********************* 0.0 --------------------- Multilevel GGTTGGGGTGGAGGAGGGGGG consensus TA TT GT TA TACA AA sequence A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 21734 240 7.13e-10 CGTCTTATGT GGTTGTGGTGGAGGAGCAGTG CAGATTTGTA 33829 366 1.84e-08 CCACACGGTT TGTGGGGGATGAAGAAGGGGG GAGGGGCGGC 22443 264 2.66e-08 CGGGGGAGAA GGTTGTGGTGGAGGAGTCGTA TCGGCGCGCC 10907 221 4.24e-08 AGTCATTTGC TATTGTGAGTGTGGAGCGGGG TAGTCTTTCT 444 257 5.29e-08 GAGATGCGTT GGTTGGGGGGGAGGATAATGG TGTACTCATC 261702 295 5.29e-08 TTGCTTGAGT GATTTGGGGGGAGGTTGGTGG TCAGATGATG 22097 211 8.14e-08 CTCAGTTGTT GGTTGTGGTTGTAGTAGGGCG TCCTCGGAAA 18503 309 1.22e-07 TATCCAATGA GATTTGGTATGTAGAGGAGGA CCTCGTTGGC 5116 70 1.98e-07 ATGCGATGAC GATTGTTGTGGACGTGGAGAG CTTTGGCTGC 25179 257 2.17e-07 TCCGTTGGCT GGTTTGATTTGAGGAGTAGAA TTAGTGATTT 23148 320 3.69e-07 TAACTGTTTC GGTGTTGGGTGTGGTGCGAGG CCAACACAAT 21341 63 4.75e-07 TCTTTGGTTT TGTTGGTTAGGAAGAGGAAGG AATCAATGAG 6052 400 5.15e-07 TCAGCTTTCT GCGTGGAGTTGAAGAAGGGAG GTGCTTCGCA 4829 94 5.15e-07 TTTCGTTGTC TAGTTGAGAGGAGGAACGGGG GATACTTTGA 263182 53 8.21e-07 GCTTTCTATT GATGGTGGTCGTAGAACGTGG CGTGATGAAT 1747 369 2.28e-06 GTGCCCGAGT GGTTAAGGGGGAAGATTCGAA ATCTTCTGAC 42992 207 3.06e-06 GGAATGGAAA GATTGATAGTGAGGAGTTGAA GGAGTTGTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21734 7.1e-10 239_[+2]_240 33829 1.8e-08 365_[+2]_114 22443 2.7e-08 263_[+2]_216 10907 4.2e-08 220_[+2]_259 444 5.3e-08 256_[+2]_223 261702 5.3e-08 294_[+2]_185 22097 8.1e-08 210_[+2]_269 18503 1.2e-07 308_[+2]_171 5116 2e-07 69_[+2]_410 25179 2.2e-07 256_[+2]_223 23148 3.7e-07 319_[+2]_160 21341 4.7e-07 62_[+2]_417 6052 5.1e-07 399_[+2]_80 4829 5.1e-07 93_[+2]_386 263182 8.2e-07 52_[+2]_427 1747 2.3e-06 368_[+2]_111 42992 3.1e-06 206_[+2]_273 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=17 21734 ( 240) GGTTGTGGTGGAGGAGCAGTG 1 33829 ( 366) TGTGGGGGATGAAGAAGGGGG 1 22443 ( 264) GGTTGTGGTGGAGGAGTCGTA 1 10907 ( 221) TATTGTGAGTGTGGAGCGGGG 1 444 ( 257) GGTTGGGGGGGAGGATAATGG 1 261702 ( 295) GATTTGGGGGGAGGTTGGTGG 1 22097 ( 211) GGTTGTGGTTGTAGTAGGGCG 1 18503 ( 309) GATTTGGTATGTAGAGGAGGA 1 5116 ( 70) GATTGTTGTGGACGTGGAGAG 1 25179 ( 257) GGTTTGATTTGAGGAGTAGAA 1 23148 ( 320) GGTGTTGGGTGTGGTGCGAGG 1 21341 ( 63) TGTTGGTTAGGAAGAGGAAGG 1 6052 ( 400) GCGTGGAGTTGAAGAAGGGAG 1 4829 ( 94) TAGTTGAGAGGAGGAACGGGG 1 263182 ( 53) GATGGTGGTCGTAGAACGTGG 1 1747 ( 369) GGTTAAGGGGGAAGATTCGAA 1 42992 ( 207) GATTGATAGTGAGGAGTTGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 19200 bayes= 11.9065 E= 1.4e-005 -1073 -1073 168 -15 67 -204 115 -1073 -1073 -1073 -102 176 -1073 -1073 -43 166 -213 -1073 144 18 -114 -1073 98 66 -55 -1073 144 -56 -114 -1073 156 -56 -14 -1073 56 66 -1073 -204 98 85 -1073 -1073 207 -1073 145 -1073 -1073 18 67 -204 115 -1073 -1073 -1073 207 -1073 156 -1073 -1073 -15 19 -1073 115 -56 -213 28 79 -15 45 -104 98 -214 -114 -1073 156 -56 19 -204 115 -114 19 -1073 156 -1073 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 17 E= 1.4e-005 0.000000 0.000000 0.764706 0.235294 0.411765 0.058824 0.529412 0.000000 0.000000 0.000000 0.117647 0.882353 0.000000 0.000000 0.176471 0.823529 0.058824 0.000000 0.647059 0.294118 0.117647 0.000000 0.470588 0.411765 0.176471 0.000000 0.647059 0.176471 0.117647 0.000000 0.705882 0.176471 0.235294 0.000000 0.352941 0.411765 0.000000 0.058824 0.470588 0.470588 0.000000 0.000000 1.000000 0.000000 0.705882 0.000000 0.000000 0.294118 0.411765 0.058824 0.529412 0.000000 0.000000 0.000000 1.000000 0.000000 0.764706 0.000000 0.000000 0.235294 0.294118 0.000000 0.529412 0.176471 0.058824 0.294118 0.411765 0.235294 0.352941 0.117647 0.470588 0.058824 0.117647 0.000000 0.705882 0.176471 0.294118 0.058824 0.529412 0.117647 0.294118 0.000000 0.705882 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT][GA]TT[GT][GT]GG[TGA][GT]G[AT][GA]G[AT][GA][GCT][GA]G[GA][GA] -------------------------------------------------------------------------------- Time 34.20 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 27 llr = 277 E-value = 7.0e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :92344381:74:76: pos.-specific C 413:23::6::1:::4 probability G 6:46:1712a3:a325 matrix T :11:42::1::5::31 bits 2.1 * * 1.9 * * 1.7 * * 1.4 * * Relative 1.2 * ** * * Entropy 1.0 ** ** ** ** (14.8 bits) 0.8 ** * ** ** ** 0.6 ** * ** ******* 0.4 ** ** ********** 0.2 **************** 0.0 ---------------- Multilevel GAGGAAGACGATGAAG consensus C CATCA G GA GTC sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 926 1 1.96e-08 . GAGGAAGACGATGGAC TCAATGCACC 263182 123 2.81e-07 TCCTCCTCGC GAAGAAGACGAAGAGG AGGTTGAGGC 23126 105 3.97e-07 CCCTTGCCAA GAGGCAGAGGAAGAAC GATACATTCG 1747 103 4.72e-07 CCGTTCAGTT GAGGAAGAGGATGAAT TGTCGTCATC 6052 5 8.83e-07 ATCT GATGACGGCGATGAAG CTAACAACGA 21965 11 8.83e-07 TTCCGTATTA CAAGAAAACGGTGAAG GGATTGTGCG 33829 139 1.02e-06 GGGATGAGAT CAGATTGACGAAGGAG TACCTTTGGT 28523 254 1.02e-06 ATACTACGAC GACGACGACGGTGAAT CCATCAGCTC 21341 396 1.35e-06 TCCTGGACGG CAGACAGACGGAGAAC AGCGCCCCTC 8673 140 2.01e-06 TTGTCTCCAG GAGAACGAGGAAGATC TCGGAAGCAT 18503 214 2.91e-06 CGAATGATGA CACATAGAGGATGATC GCGAAAGCCC 20993 210 5.69e-06 TGTTGGTGTT GATATTGACGGTGAGG GGTGATTGTC 22830 187 6.97e-06 GACGTCTTGT GACGACGGAGATGATG CAGCCTTTGC 25179 38 7.70e-06 ATTTGGAAGG GCCGACGACGACGAAG TGCTGCTCAT 20892 254 1.34e-05 GAGGGTACAA CATGTTGCCGATGAAG AGACAACTAC 40073 299 1.87e-05 GAGATGCACC GATACCAACGATGAAT ACTCATATCT 22996 265 1.87e-05 GCAATTGATA CAGGACAGCGACGATG CTACGGCGAC 444 237 2.02e-05 GTCGTAGTTG GAGGTTGGAGGAGATG CGTTGGTTGG 32459 362 2.02e-05 TTGTGAGGTT CAGGTGAAGGGTGATG TCTGGATATA 5116 181 2.19e-05 AAGCCCGTAC CAAGTGGAGGGAGGAG GGAGAGAATT 32029 266 2.55e-05 AATAGAGTAT CCCATAAACGAAGAAC CAAGAAATAT 22742 286 2.74e-05 GCATATGAGT GACGTAAAAGGTGGGC GTGTCATTGG 22443 361 2.94e-05 GTTGCAGGTG GTGGCCGACGACGGAC GTTGATCGAA 34018 73 3.16e-05 TTCGGGCCGT CTCGTTGACGATGGGC GTTGGAGCAC 6809 92 3.39e-05 AATGCAACAT GAAACAGAAGGAGGTG GACGACAAAA 22097 184 3.39e-05 CACTTCTTAG CAGCATGATGATGAAC GCTCAGTTGT 11486 391 6.70e-05 ATGGGGGGGG CAAAAAAATGAAGGGG AAACAACTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 926 2e-08 [+3]_484 263182 2.8e-07 122_[+3]_362 23126 4e-07 104_[+3]_380 1747 4.7e-07 102_[+3]_382 6052 8.8e-07 4_[+3]_480 21965 8.8e-07 10_[+3]_474 33829 1e-06 138_[+3]_346 28523 1e-06 253_[+3]_231 21341 1.4e-06 395_[+3]_89 8673 2e-06 139_[+3]_345 18503 2.9e-06 213_[+3]_271 20993 5.7e-06 209_[+3]_275 22830 7e-06 186_[+3]_298 25179 7.7e-06 37_[+3]_447 20892 1.3e-05 253_[+3]_231 40073 1.9e-05 298_[+3]_186 22996 1.9e-05 264_[+3]_220 444 2e-05 236_[+3]_248 32459 2e-05 361_[+3]_123 5116 2.2e-05 180_[+3]_304 32029 2.5e-05 265_[+3]_219 22742 2.7e-05 285_[+3]_199 22443 2.9e-05 360_[+3]_124 34018 3.2e-05 72_[+3]_412 6809 3.4e-05 91_[+3]_393 22097 3.4e-05 183_[+3]_301 11486 6.7e-05 390_[+3]_94 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=27 926 ( 1) GAGGAAGACGATGGAC 1 263182 ( 123) GAAGAAGACGAAGAGG 1 23126 ( 105) GAGGCAGAGGAAGAAC 1 1747 ( 103) GAGGAAGAGGATGAAT 1 6052 ( 5) GATGACGGCGATGAAG 1 21965 ( 11) CAAGAAAACGGTGAAG 1 33829 ( 139) CAGATTGACGAAGGAG 1 28523 ( 254) GACGACGACGGTGAAT 1 21341 ( 396) CAGACAGACGGAGAAC 1 8673 ( 140) GAGAACGAGGAAGATC 1 18503 ( 214) CACATAGAGGATGATC 1 20993 ( 210) GATATTGACGGTGAGG 1 22830 ( 187) GACGACGGAGATGATG 1 25179 ( 38) GCCGACGACGACGAAG 1 20892 ( 254) CATGTTGCCGATGAAG 1 40073 ( 299) GATACCAACGATGAAT 1 22996 ( 265) CAGGACAGCGACGATG 1 444 ( 237) GAGGTTGGAGGAGATG 1 32459 ( 362) CAGGTGAAGGGTGATG 1 5116 ( 181) CAAGTGGAGGGAGGAG 1 32029 ( 266) CCCATAAACGAAGAAC 1 22742 ( 286) GACGTAAAAGGTGGGC 1 22443 ( 361) GTGGCCGACGACGGAC 1 34018 ( 73) CTCGTTGACGATGGGC 1 6809 ( 92) GAAACAGAAGGAGGTG 1 22097 ( 184) CAGCATGATGATGAAC 1 11486 ( 391) CAAAAAAATGAAGGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 19400 bayes= 11.1388 E= 7.0e-005 -1140 87 122 -1140 172 -171 -1140 -181 -48 10 77 -81 37 -271 140 -1140 78 -39 -1140 51 66 29 -169 -23 0 -1140 163 -1140 165 -271 -69 -1140 -80 120 -10 -181 -1140 -1140 207 -1140 137 -1140 48 -1140 52 -112 -1140 99 -1140 -1140 207 -1140 144 -1140 31 -1140 110 -1140 -37 -1 -1140 61 112 -123 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 27 E= 7.0e-005 0.000000 0.444444 0.555556 0.000000 0.851852 0.074074 0.000000 0.074074 0.185185 0.259259 0.407407 0.148148 0.333333 0.037037 0.629630 0.000000 0.444444 0.185185 0.000000 0.370370 0.407407 0.296296 0.074074 0.222222 0.259259 0.000000 0.740741 0.000000 0.814815 0.037037 0.148148 0.000000 0.148148 0.555556 0.222222 0.074074 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.370370 0.111111 0.000000 0.518519 0.000000 0.000000 1.000000 0.000000 0.703704 0.000000 0.296296 0.000000 0.555556 0.000000 0.185185 0.259259 0.000000 0.370370 0.518519 0.111111 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GC]A[GC][GA][AT][ACT][GA]A[CG]G[AG][TA]G[AG][AT][GC] -------------------------------------------------------------------------------- Time 49.45 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10907 3.61e-07 220_[+2(4.24e-08)]_234_\ [+1(1.64e-07)]_4 11486 1.71e-03 215_[+1(2.71e-06)]_154_\ [+3(6.70e-05)]_94 1747 3.77e-06 102_[+3(4.72e-07)]_250_\ [+2(2.28e-06)]_111 18503 5.74e-08 213_[+3(2.91e-06)]_79_\ [+2(1.22e-07)]_147_[+1(5.32e-06)]_3 20892 2.31e-05 253_[+3(1.34e-05)]_183_\ [+1(1.91e-07)]_27 20993 4.80e-07 209_[+3(5.69e-06)]_149_\ [+1(3.16e-08)]_105 20998 2.95e-02 464_[+1(1.48e-05)]_15 21341 1.92e-08 3_[+1(8.92e-07)]_38_[+2(4.75e-07)]_\ 156_[+2(7.22e-05)]_135_[+3(1.35e-06)]_89 2145 9.44e-02 164_[+1(2.85e-05)]_315 21734 1.53e-06 239_[+2(7.13e-10)]_23_\ [+1(8.42e-05)]_196 21965 5.04e-04 10_[+3(8.83e-07)]_433_\ [+1(5.65e-05)]_20 22097 1.09e-05 183_[+3(3.39e-05)]_11_\ [+2(8.14e-08)]_269 22443 4.57e-08 45_[+1(1.90e-06)]_197_\ [+2(2.66e-08)]_76_[+3(2.94e-05)]_124 22742 8.28e-05 157_[+1(6.85e-07)]_107_\ [+3(2.74e-05)]_199 22830 1.33e-03 186_[+3(6.97e-06)]_125_\ [+1(4.40e-05)]_152 22996 4.38e-03 155_[+3(5.00e-05)]_93_\ [+3(1.87e-05)]_220 23126 2.13e-04 57_[+1(5.65e-05)]_26_[+3(3.97e-07)]_\ 380 23148 9.84e-06 319_[+2(3.69e-07)]_94_\ [+3(3.88e-05)]_50 25127 1.68e-02 8_[+1(3.41e-06)]_471 25179 8.34e-07 37_[+3(7.70e-06)]_203_\ [+2(2.17e-07)]_175_[+1(2.17e-05)]_27 261702 1.43e-06 89_[+1(1.15e-06)]_184_\ [+2(5.29e-08)]_185 263182 6.13e-07 52_[+2(8.21e-07)]_49_[+3(2.81e-07)]_\ 362 263354 2.52e-02 6_[+1(3.82e-06)]_473 264339 6.38e-02 74_[+1(4.04e-05)]_405 28523 1.03e-05 253_[+3(1.02e-06)]_128_\ [+1(4.56e-07)]_82 32029 8.48e-04 265_[+3(2.55e-05)]_180_\ [+1(2.14e-06)]_18 32459 1.05e-04 97_[+1(1.02e-06)]_243_\ [+3(2.02e-05)]_123 33829 1.17e-07 138_[+3(1.02e-06)]_211_\ [+2(1.84e-08)]_114 34018 1.13e-02 72_[+3(3.16e-05)]_313_\ [+1(9.10e-05)]_78 37596 4.70e-03 430_[+1(1.15e-06)]_49 39038 6.83e-02 464_[+1(8.13e-06)]_15 40073 1.29e-03 48_[+1(4.27e-06)]_229_\ [+3(1.87e-05)]_52_[+1(4.04e-05)]_113 42992 4.10e-06 24_[+1(1.80e-05)]_2_[+1(3.40e-05)]_\ 138_[+2(3.06e-06)]_243_[+1(1.03e-07)]_9 444 1.27e-08 64_[+1(3.44e-07)]_151_\ [+3(2.02e-05)]_4_[+2(5.29e-08)]_223 4829 5.91e-05 93_[+2(5.15e-07)]_264_\ [+1(9.01e-06)]_101 5116 3.40e-06 69_[+2(1.98e-07)]_90_[+3(2.19e-05)]_\ 95_[+2(4.09e-05)]_167_[+1(4.04e-05)] 6052 2.50e-08 4_[+3(8.83e-07)]_379_[+2(5.15e-07)]_\ 54_[+1(1.68e-06)]_5 6809 1.97e-02 43_[+1(7.20e-05)]_27_[+3(3.39e-05)]_\ 393 8673 6.66e-04 21_[+1(5.65e-05)]_97_[+3(2.01e-06)]_\ 345 926 2.20e-06 [+3(1.96e-08)]_7_[+1(8.13e-06)]_456 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************