******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.5.1 (Release date: Sun Jan 29 10:33:12 2023 -0800) For further information on how to interpret these results please access https://meme-suite.org/meme. To get a copy of the MEME Suite software please access https://meme-suite.org. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** PRIMARY SEQUENCES= train.fa CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ seq1_Taq 1.0000 100 seq2_Taq 1.0000 100 seq3_Taq 1.0000 100 seq4_Taq 1.0000 100 seq5_Taq 1.0000 100 seq6_Taq 1.0000 100 seq7_Taq 1.0000 100 seq8_Taq 1.0000 100 seq9_Taq 1.0000 100 seq10_Taq 1.0000 100 seq11_Taq 1.0000 100 seq12_Taq 1.0000 100 seq13_Taq 1.0000 100 seq14_Taq 1.0000 100 seq15_Taq 1.0000 100 seq16_Taq 1.0000 100 seq17_Taq 1.0000 100 seq18_Taq 1.0000 100 seq19_Taq 1.0000 100 seq20_Taq 1.0000 100 seq21_Taq 1.0000 100 seq22_Taq 1.0000 100 seq23_Taq 1.0000 100 seq24_Taq 1.0000 100 seq25_Taq 1.0000 100 seq26_Taq 1.0000 100 seq27_Taq 1.0000 100 seq28_Taq 1.0000 100 seq29_Taq 1.0000 100 seq30_Taq 1.0000 100 seq31_Taq 1.0000 100 seq32_Taq 1.0000 100 seq33_Taq 1.0000 100 seq34_Taq 1.0000 100 seq35_Taq 1.0000 100 seq36_Taq 1.0000 100 seq37_Taq 1.0000 100 seq38_Taq 1.0000 100 seq39_Taq 1.0000 50 seq40_Taq 1.0000 100 seq41_Taq 1.0000 100 seq42_Taq 1.0000 100 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme train.fa -dna -mod zoops -nmotifs 3 -minw 6 -maxw 50 -maxsites 50 model: mod= zoops nmotifs= 3 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + width: minw= 6 maxw= 50 nsites: minsites= 2 maxsites= 42 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 trim: wg= 11 ws= 1 endgaps= yes data: n= 4150 N= 42 sample: seed= 0 hsfrac= 0 searchsize= 4150 norand= no csites= 1000 Letter frequencies in dataset: A 0.192 C 0.323 G 0.312 T 0.173 Background letter frequencies (from file dataset with add-one prior applied): A 0.192 C 0.323 G 0.312 T 0.173 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CCHCCTYCAGG MEME-1 width = 11 sites = 27 llr = 211 E-value = 2.2e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCHCCTYCAGG MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::3:::::6:1 pos.-specific C a926936913: probability G :::1:::1279 matrix T :143174:11: bits 2.5 2.3 2.0 1.8 Relative 1.5 * * Entropy 1.3 ** ** * * (11.3 bits) 1.0 ** **** * 0.8 *** **** * 0.5 *********** 0.3 *********** 0.0 ----------- Multilevel CCTCCTCCAGG consensus AT CT C sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCHCCTYCAGG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------- seq11_Taq 2 3.40e-07 C CCTCCTTCAGG GTGTAGCGGC seq4_Taq 13 2.58e-06 GGGTAGGAGG CCACCTCCAGG GCCCGCCTCC seq1_Taq 17 2.58e-06 TCGGAAAGGG CCACCTCCAGG GGCTCCCGGG seq5_Taq 3 3.16e-06 CT CCATCTCCAGG TAGGCCTCGA seq9_Taq 41 4.69e-06 AGGGGCCGCC CCTCTTCCAGG AGGTGGCTGT seq2_Taq 40 7.73e-06 TCCCCGGGCT CCCCCTCCAGG ACGTACCAGG seq26_Taq 15 2.35e-05 TCCGCCGCCA CCACCCTCAGG TTCCCGTCCC seq28_Taq 59 4.45e-05 AGGGTATAAT CCTCCTTCGCG CGGCCTGCCG seq19_Taq 36 5.11e-05 GCCTCGAGGG CCTCTTCCTGG GGGAAGGGCG seq12_Taq 34 5.40e-05 AAGGCGGCCA CCCTTTCCAGG GGGGCCTTGA seq8_Taq 58 5.75e-05 CCCACTATAC CCTTCCTCACG CCTTTCACCT seq6_Taq 16 7.56e-05 CGCATCTCCA CCACCTCCTCG CTTAGCGCTA seq31_Taq 17 8.41e-05 GGCCACGTTC CCTCCTTCCCG CCCCCCGGGC seq29_Taq 39 1.21e-04 CGGGGCAATC CTTCCCTCAGG GATAGTCCCC seq39_Taq 7 1.32e-04 CAACTC CCAGCTCCACG CACTGGAGGA seq37_Taq 67 1.32e-04 GGGCTTTTTC CCTTCCCCATG GGCAAATCCG seq30_Taq 49 1.32e-04 GGGAAGGCCT CCTTCCCCGGG CGGATCTTGA seq35_Taq 43 1.46e-04 CCCAAAACCA CCCACTCCAGG ATGTCGCGCA seq23_Taq 86 1.85e-04 GGGCTTTCTG CTACCCTCAGG CCCA seq15_Taq 32 2.03e-04 GCCTTCATGG CCTCCTTGATG GTCTCCTTGA seq38_Taq 76 2.18e-04 GGTTTTGTAC CCCTCTTCACA AAAGGGAGGC seq3_Taq 39 2.18e-04 AAGGCCTTGG CCTCCTCGGGG GTGAAGCCCG seq40_Taq 78 2.69e-04 CACCAAGCCC CCCTTTCCGGG GGGCTTCTTT seq18_Taq 20 3.16e-04 GGGTGAGGTG CCCCCTCCGGA AGGCGGAGAG seq25_Taq 57 3.92e-04 CAGCGGCCAA ACTCCTCCCGG TCCAAGGGCA seq7_Taq 26 4.72e-04 ACGCCCAAAC CCACCTTCCCA TGGTGGCTCT seq20_Taq 14 7.14e-04 GCGTGCCGGA CCAGCCCCTGG GCAGGGGAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCHCCTYCAGG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- seq11_Taq 3.4e-07 1_[+1]_88 seq4_Taq 2.6e-06 12_[+1]_77 seq1_Taq 2.6e-06 16_[+1]_73 seq5_Taq 3.2e-06 2_[+1]_87 seq9_Taq 4.7e-06 40_[+1]_49 seq2_Taq 7.7e-06 39_[+1]_50 seq26_Taq 2.3e-05 14_[+1]_75 seq28_Taq 4.5e-05 58_[+1]_31 seq19_Taq 5.1e-05 35_[+1]_54 seq12_Taq 5.4e-05 33_[+1]_56 seq8_Taq 5.7e-05 57_[+1]_32 seq6_Taq 7.6e-05 15_[+1]_74 seq31_Taq 8.4e-05 16_[+1]_73 seq29_Taq 0.00012 38_[+1]_51 seq39_Taq 0.00013 6_[+1]_33 seq37_Taq 0.00013 66_[+1]_23 seq30_Taq 0.00013 48_[+1]_41 seq35_Taq 0.00015 42_[+1]_47 seq23_Taq 0.00018 85_[+1]_4 seq15_Taq 0.0002 31_[+1]_58 seq38_Taq 0.00022 75_[+1]_14 seq3_Taq 0.00022 38_[+1]_51 seq40_Taq 0.00027 77_[+1]_12 seq18_Taq 0.00032 19_[+1]_70 seq25_Taq 0.00039 56_[+1]_33 seq7_Taq 0.00047 25_[+1]_64 seq20_Taq 0.00071 13_[+1]_76 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCHCCTYCAGG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCHCCTYCAGG width=11 seqs=27 seq11_Taq ( 2) CCTCCTTCAGG 1 seq4_Taq ( 13) CCACCTCCAGG 1 seq1_Taq ( 17) CCACCTCCAGG 1 seq5_Taq ( 3) CCATCTCCAGG 1 seq9_Taq ( 41) CCTCTTCCAGG 1 seq2_Taq ( 40) CCCCCTCCAGG 1 seq26_Taq ( 15) CCACCCTCAGG 1 seq28_Taq ( 59) CCTCCTTCGCG 1 seq19_Taq ( 36) CCTCTTCCTGG 1 seq12_Taq ( 34) CCCTTTCCAGG 1 seq8_Taq ( 58) CCTTCCTCACG 1 seq6_Taq ( 16) CCACCTCCTCG 1 seq31_Taq ( 17) CCTCCTTCCCG 1 seq29_Taq ( 39) CTTCCCTCAGG 1 seq39_Taq ( 7) CCAGCTCCACG 1 seq37_Taq ( 67) CCTTCCCCATG 1 seq30_Taq ( 49) CCTTCCCCGGG 1 seq35_Taq ( 43) CCCACTCCAGG 1 seq23_Taq ( 86) CTACCCTCAGG 1 seq15_Taq ( 32) CCTCCTTGATG 1 seq38_Taq ( 76) CCCTCTTCACA 1 seq3_Taq ( 39) CCTCCTCGGGG 1 seq40_Taq ( 78) CCCTTTCCGGG 1 seq18_Taq ( 20) CCCCCTCCGGA 1 seq25_Taq ( 57) ACTCCTCCCGG 1 seq7_Taq ( 26) CCACCTTCCCA 1 seq20_Taq ( 14) CCAGCCCCTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCHCCTYCAGG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 3730 bayes= 8.29967 E= 2.2e-005 -237 157 -1140 -1140 -1140 152 -1140 -123 80 -54 -1140 136 -237 96 -207 58 -1140 140 -1140 -23 -1140 -32 -1140 210 -1140 96 -1140 110 -1140 152 -207 -1140 163 -154 -75 -64 -1140 -32 110 -123 -79 -1140 151 -1140 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCHCCTYCAGG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 27 E= 2.2e-005 0.037037 0.962963 0.000000 0.000000 0.000000 0.925926 0.000000 0.074074 0.333333 0.222222 0.000000 0.444444 0.037037 0.629630 0.074074 0.259259 0.000000 0.851852 0.000000 0.148148 0.000000 0.259259 0.000000 0.740741 0.000000 0.629630 0.000000 0.370370 0.000000 0.925926 0.074074 0.000000 0.592593 0.111111 0.185185 0.111111 0.000000 0.259259 0.666667 0.074074 0.111111 0.000000 0.888889 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCHCCTYCAGG MEME-1 regular expression -------------------------------------------------------------------------------- CC[TAC][CT]C[TC][CT]CA[GC]G -------------------------------------------------------------------------------- Time 2.06 secs. ******************************************************************************** ******************************************************************************** MOTIF CYCCAYGSCTYYAKYMTA MEME-2 width = 18 sites = 17 llr = 187 E-value = 7.4e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif CYCCAYGSCTYYAKYMTA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1:125:::::219:14:9 pos.-specific C 646824256255:134:1 probability G 111:::84311::4111: matrix T 252:26:11635155191 bits 2.5 2.3 * 2.0 * 1.8 * ** Relative 1.5 * ** Entropy 1.3 * * ** (15.8 bits) 1.0 * * * * ** 0.8 * **** * *** ** 0.5 ******* ** **** ** 0.3 ****************** 0.0 ------------------ Multilevel CTCCATGCCTCCATTATA consensus C CCCGGCTT GCC sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CYCCAYGSCTYYAKYMTA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------ seq35_Taq 71 1.39e-08 GCAGGGTCCT TTCCATGCCTTCAGCATA CACTGAAAAA seq11_Taq 33 8.08e-08 GCATCTGGAC CTTCATGGGTCCAGTTTA AGGGAAGGGG seq36_Taq 43 4.61e-07 TCACCTCCTG CGCCACGCCTCCATCCTA GCCCTTGAGG seq2_Taq 77 4.61e-07 AAAGCTCCGG CTCCACCGGTCCATAATA CCCTCG seq1_Taq 63 6.46e-07 GGATGAGGAC CTTCATGCCCCCATTATC GCCCGGTTAG seq41_Taq 71 7.20e-07 CCGCGGCGCG TTCCATGCCTTTAGGGTA CGCTAAGGCC seq23_Taq 31 1.22e-06 GTATAGCCCA CCCCTCGCCTTTTTCCTA GGGCATAAAC seq4_Taq 77 1.22e-06 AAAGGTCGGG CCGCATGCGGATATTCTA AAGGTA seq28_Taq 19 3.87e-06 GGCCTAAGGG CCCCCTGGGTCTTTTATT GGGGGGCGAA seq15_Taq 64 3.87e-06 GGCCTCGTAG ATCATCCCCTCCAGTCTA GCGGGTACAA seq8_Taq 39 5.50e-06 CCCCGCCAGG CTCACCGCCCCCACTATA CCCTTCCTCA seq34_Taq 75 5.99e-06 CGGTGGAAAG CTCCATGGCGGTATAGTA CCCAAAGA seq22_Taq 64 7.09e-06 GTACATGGCA CCTCCTCTTTTCATCATA CCGTCGTAGA seq16_Taq 46 9.06e-06 GGAAGGCCCG CGCCTTGGGTATAGTAGA AGACCGGTAG seq9_Taq 78 1.24e-05 CGTAGCCCAG GCGCATGGCTATACTTTA GGGCA seq19_Taq 63 2.98e-05 GGCGCGTCCA TCACCTGCCCCAAGTCTA AGCCCTAAAC seq25_Taq 77 4.42e-05 GTCCAAGGGC ACCATCCTCCTTATCCTA AGGGGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CYCCAYGSCTYYAKYMTA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- seq35_Taq 1.4e-08 70_[+2]_12 seq11_Taq 8.1e-08 32_[+2]_50 seq36_Taq 4.6e-07 42_[+2]_40 seq2_Taq 4.6e-07 76_[+2]_6 seq1_Taq 6.5e-07 62_[+2]_20 seq41_Taq 7.2e-07 70_[+2]_12 seq23_Taq 1.2e-06 30_[+2]_52 seq4_Taq 1.2e-06 76_[+2]_6 seq28_Taq 3.9e-06 18_[+2]_64 seq15_Taq 3.9e-06 63_[+2]_19 seq8_Taq 5.5e-06 38_[+2]_44 seq34_Taq 6e-06 74_[+2]_8 seq22_Taq 7.1e-06 63_[+2]_19 seq16_Taq 9.1e-06 45_[+2]_37 seq9_Taq 1.2e-05 77_[+2]_5 seq19_Taq 3e-05 62_[+2]_20 seq25_Taq 4.4e-05 76_[+2]_6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CYCCAYGSCTYYAKYMTA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CYCCAYGSCTYYAKYMTA width=18 seqs=17 seq35_Taq ( 71) TTCCATGCCTTCAGCATA 1 seq11_Taq ( 33) CTTCATGGGTCCAGTTTA 1 seq36_Taq ( 43) CGCCACGCCTCCATCCTA 1 seq2_Taq ( 77) CTCCACCGGTCCATAATA 1 seq1_Taq ( 63) CTTCATGCCCCCATTATC 1 seq41_Taq ( 71) TTCCATGCCTTTAGGGTA 1 seq23_Taq ( 31) CCCCTCGCCTTTTTCCTA 1 seq4_Taq ( 77) CCGCATGCGGATATTCTA 1 seq28_Taq ( 19) CCCCCTGGGTCTTTTATT 1 seq15_Taq ( 64) ATCATCCCCTCCAGTCTA 1 seq8_Taq ( 39) CTCACCGCCCCCACTATA 1 seq34_Taq ( 75) CTCCATGGCGGTATAGTA 1 seq22_Taq ( 64) CCTCCTCTTTTCATCATA 1 seq16_Taq ( 46) CGCCTTGGGTATAGTAGA 1 seq9_Taq ( 78) GCGCATGGCTATACTTTA 1 seq19_Taq ( 63) TCACCTGCCCCAAGTCTA 1 seq25_Taq ( 77) ACCATCCTCCTTATCCTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CYCCAYGSCTYYAKYMTA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 18 n= 3436 bayes= 7.72177 E= 7.4e-005 -70 100 -240 3 -1073 35 -140 144 -170 100 -140 3 -12 135 -1073 -1073 147 -46 -1073 44 -1073 13 -1073 190 -1073 -46 129 -1073 -1073 71 18 -56 -1073 100 -8 -156 -1073 -46 -140 190 -12 54 -240 76 -170 54 -1073 144 220 -1073 -1073 -56 -1073 -146 18 161 -70 -14 -240 161 110 13 -140 -56 -1073 -1073 -240 244 220 -245 -1073 -156 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CYCCAYGSCTYYAKYMTA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 18 nsites= 17 E= 7.4e-005 0.117647 0.647059 0.058824 0.176471 0.000000 0.411765 0.117647 0.470588 0.058824 0.647059 0.117647 0.176471 0.176471 0.823529 0.000000 0.000000 0.529412 0.235294 0.000000 0.235294 0.000000 0.352941 0.000000 0.647059 0.000000 0.235294 0.764706 0.000000 0.000000 0.529412 0.352941 0.117647 0.000000 0.647059 0.294118 0.058824 0.000000 0.235294 0.117647 0.647059 0.176471 0.470588 0.058824 0.294118 0.058824 0.470588 0.000000 0.470588 0.882353 0.000000 0.000000 0.117647 0.000000 0.117647 0.352941 0.529412 0.117647 0.294118 0.058824 0.529412 0.411765 0.352941 0.117647 0.117647 0.000000 0.000000 0.058824 0.941176 0.882353 0.058824 0.000000 0.058824 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CYCCAYGSCTYYAKYMTA MEME-2 regular expression -------------------------------------------------------------------------------- C[TC]CC[ACT][TC][GC][CG][CG][TC][CT][CT]A[TG][TC][AC]TA -------------------------------------------------------------------------------- Time 3.79 secs. ******************************************************************************** ******************************************************************************** MOTIF WARAGG MEME-3 width = 6 sites = 30 llr = 188 E-value = 4.7e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif WARAGG MEME-3 Description -------------------------------------------------------------------------------- Simplified A 577a:: pos.-specific C :::::: probability G 233:aa matrix T 3::::: bits 2.5 2.3 * 2.0 * 1.8 *** Relative 1.5 *** Entropy 1.3 ***** (9.0 bits) 1.0 ***** 0.8 ****** 0.5 ****** 0.3 ****** 0.0 ------ Multilevel AAAAGG consensus TGG sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WARAGG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------ seq29_Taq 16 1.32e-04 GGAGGGGCCC AAAAGG GCTATCCCGG seq28_Taq 46 1.32e-04 TGGGGGGCGA AAAAGG GTATAATCCT seq27_Taq 78 1.32e-04 GCGGAGCGGG AAAAGG GGGTATAGTA seq20_Taq 46 1.32e-04 TCCCTGGGGA AAAAGG CCGGCCCGCA seq17_Taq 22 1.32e-04 TCAACGCGGA AAAAGG CTACGGGTTC seq16_Taq 87 1.32e-04 CTAAGGGCCC AAAAGG GGAGGCCA seq13_Taq 81 1.32e-04 CCCGAAAGGC AAAAGG CGCCAGGAAA seq38_Taq 2 2.51e-04 C TAAAGG GGATGGCCTA seq37_Taq 3 2.51e-04 GA TAAAGG GCAGGGATTT seq14_Taq 5 2.51e-04 CTCT TAAAGG TGAAGCCTCG seq9_Taq 28 2.51e-04 GCCGCAGAGG TAAAGG GGCCGCCCCT seq35_Taq 27 4.66e-04 CACCACCACC AAGAGG CCCAAAACCA seq31_Taq 44 4.66e-04 GGGCGGTTTG AAGAGG CATCTTAGCC seq12_Taq 58 6.81e-04 GCCTTGACGT GAAAGG AGAGGAAGCT seq4_Taq 66 6.81e-04 GGGCACACGG GAAAGG TCGGGCCGCA seq1_Taq 10 6.81e-04 GCGTGCTCG GAAAGG GCCACCTCCA seq34_Taq 31 8.96e-04 GGGCCTGAGG AGAAGG GCCTTGGGGT seq30_Taq 92 8.96e-04 AAGTCCAAGA AGAAGG GAG seq19_Taq 21 8.96e-04 TTTAGGGTAA AGAAGG CCTCGAGGGC seq8_Taq 18 8.96e-04 GTAGCGCTTA AGAAGG GTCTTCCCCG seq24_Taq 88 1.09e-03 CGCTTTCCCT TAGAGG TGACGCA seq10_Taq 91 1.09e-03 CGGTAAGCTT TAGAGG ATTA seq6_Taq 71 1.09e-03 AGGAGCGGGT TAGAGG CCCCCCTGGT seq33_Taq 94 1.63e-03 GCTTAAGGAG GAGAGG A seq18_Taq 36 1.63e-03 CCGGAAGGCG GAGAGG ACCACGGCGT seq41_Taq 36 1.98e-03 CCTCCGGGCA AGGAGG CGGAGGGCGT seq21_Taq 88 1.98e-03 GCGTTTTGCT AGGAGG TGAGGGA seq32_Taq 92 2.33e-03 GCTGGCCCCA GGAAGG ATA seq11_Taq 53 2.33e-03 CCAGTTTAAG GGAAGG GGCCCCCCAC seq39_Taq 21 2.65e-03 CTCCACGCAC TGGAGG AGCTGCGGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WARAGG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- seq29_Taq 0.00013 15_[+3]_79 seq28_Taq 0.00013 45_[+3]_49 seq27_Taq 0.00013 77_[+3]_17 seq20_Taq 0.00013 45_[+3]_49 seq17_Taq 0.00013 21_[+3]_73 seq16_Taq 0.00013 86_[+3]_8 seq13_Taq 0.00013 80_[+3]_14 seq38_Taq 0.00025 1_[+3]_93 seq37_Taq 0.00025 2_[+3]_92 seq14_Taq 0.00025 4_[+3]_90 seq9_Taq 0.00025 27_[+3]_67 seq35_Taq 0.00047 26_[+3]_68 seq31_Taq 0.00047 43_[+3]_51 seq12_Taq 0.00068 57_[+3]_37 seq4_Taq 0.00068 65_[+3]_29 seq1_Taq 0.00068 9_[+3]_85 seq34_Taq 0.0009 30_[+3]_64 seq30_Taq 0.0009 91_[+3]_3 seq19_Taq 0.0009 20_[+3]_74 seq8_Taq 0.0009 17_[+3]_77 seq24_Taq 0.0011 87_[+3]_7 seq10_Taq 0.0011 90_[+3]_4 seq6_Taq 0.0011 70_[+3]_24 seq33_Taq 0.0016 93_[+3]_1 seq18_Taq 0.0016 35_[+3]_59 seq41_Taq 0.002 35_[+3]_59 seq21_Taq 0.002 87_[+3]_7 seq32_Taq 0.0023 91_[+3]_3 seq11_Taq 0.0023 52_[+3]_42 seq39_Taq 0.0026 20_[+3]_24 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WARAGG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF WARAGG width=6 seqs=30 seq29_Taq ( 16) AAAAGG 1 seq28_Taq ( 46) AAAAGG 1 seq27_Taq ( 78) AAAAGG 1 seq20_Taq ( 46) AAAAGG 1 seq17_Taq ( 22) AAAAGG 1 seq16_Taq ( 87) AAAAGG 1 seq13_Taq ( 81) AAAAGG 1 seq38_Taq ( 2) TAAAGG 1 seq37_Taq ( 3) TAAAGG 1 seq14_Taq ( 5) TAAAGG 1 seq9_Taq ( 28) TAAAGG 1 seq35_Taq ( 27) AAGAGG 1 seq31_Taq ( 44) AAGAGG 1 seq12_Taq ( 58) GAAAGG 1 seq4_Taq ( 66) GAAAGG 1 seq1_Taq ( 10) GAAAGG 1 seq34_Taq ( 31) AGAAGG 1 seq30_Taq ( 92) AGAAGG 1 seq19_Taq ( 21) AGAAGG 1 seq8_Taq ( 18) AGAAGG 1 seq24_Taq ( 88) TAGAGG 1 seq10_Taq ( 91) TAGAGG 1 seq6_Taq ( 71) TAGAGG 1 seq33_Taq ( 94) GAGAGG 1 seq18_Taq ( 36) GAGAGG 1 seq41_Taq ( 36) AGGAGG 1 seq21_Taq ( 88) AGGAGG 1 seq32_Taq ( 92) GGAAGG 1 seq11_Taq ( 53) GGAAGG 1 seq39_Taq ( 21) TGGAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WARAGG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 3940 bayes= 8.30716 E= 4.7e-001 138 -1155 -42 62 187 -1155 -6 -1155 180 -1155 10 -1155 238 -1155 -1155 -1155 -1155 -1155 168 -1155 -1155 -1155 168 -1155 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WARAGG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 30 E= 4.7e-001 0.500000 0.000000 0.233333 0.266667 0.700000 0.000000 0.300000 0.000000 0.666667 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WARAGG MEME-3 regular expression -------------------------------------------------------------------------------- [ATG][AG][AG]AGG -------------------------------------------------------------------------------- Time 5.30 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- seq1_Taq 1.89e-07 16_[+1(2.58e-06)]_35_[+2(6.46e-07)]_\ 20 seq2_Taq 2.95e-06 39_[+1(7.73e-06)]_26_[+2(4.61e-07)]_\ 6 seq3_Taq 1.69e-01 100 seq4_Taq 1.39e-07 12_[+1(2.58e-06)]_53_[+2(1.22e-06)]_\ 6 seq5_Taq 3.97e-03 2_[+1(3.16e-06)]_87 seq6_Taq 8.71e-03 15_[+1(7.56e-05)]_74 seq7_Taq 4.50e-02 100 seq8_Taq 2.62e-05 38_[+2(5.50e-06)]_1_[+1(5.75e-05)]_\ 32 seq9_Taq 1.94e-06 40_[+1(4.69e-06)]_26_[+2(1.24e-05)]_\ 5 seq10_Taq 1.91e-01 100 seq11_Taq 1.27e-08 1_[+1(3.40e-07)]_20_[+2(8.08e-08)]_\ 50 seq12_Taq 5.75e-03 33_[+1(5.40e-05)]_56 seq13_Taq 5.16e-02 100 seq14_Taq 2.16e-02 100 seq15_Taq 4.28e-04 63_[+2(3.87e-06)]_19 seq16_Taq 6.31e-04 45_[+2(9.06e-06)]_37 seq17_Taq 3.58e-02 100 seq18_Taq 6.46e-02 100 seq19_Taq 1.03e-04 35_[+1(5.11e-05)]_16_[+2(2.98e-05)]_\ 20 seq20_Taq 1.91e-02 100 seq21_Taq 3.65e-01 100 seq22_Taq 1.15e-02 63_[+2(7.09e-06)]_19 seq23_Taq 1.69e-04 30_[+2(1.22e-06)]_52 seq24_Taq 1.01e-01 100 seq25_Taq 3.64e-03 76_[+2(4.42e-05)]_6 seq26_Taq 3.29e-02 14_[+1(2.35e-05)]_75 seq27_Taq 9.85e-02 100 seq28_Taq 2.89e-06 18_[+2(3.87e-06)]_22_[+1(4.45e-05)]_\ 31 seq29_Taq 1.18e-03 100 seq30_Taq 2.62e-02 100 seq31_Taq 4.13e-03 16_[+1(8.41e-05)]_73 seq32_Taq 4.30e-01 100 seq33_Taq 1.60e-01 100 seq34_Taq 2.10e-03 74_[+2(5.99e-06)]_8 seq35_Taq 1.60e-07 70_[+2(1.39e-08)]_12 seq36_Taq 8.06e-04 42_[+2(4.61e-07)]_40 seq37_Taq 7.66e-04 100 seq38_Taq 1.42e-03 100 seq39_Taq 1.89e-02 50 seq40_Taq 1.27e-01 100 seq41_Taq 3.70e-04 70_[+2(7.20e-07)]_12 seq42_Taq 2.36e-01 100 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kodomo ********************************************************************************