******************************************************************************** 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= /home/students/y22/mkd57/public_html/term4/learn.fa CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1 1.0000 100 2 1.0000 100 3 1.0000 100 4 1.0000 100 5 1.0000 100 6 1.0000 100 7 1.0000 100 8 1.0000 100 9 1.0000 100 10 1.0000 100 11 1.0000 100 12 1.0000 100 13 1.0000 100 14 1.0000 100 15 1.0000 100 16 1.0000 100 17 1.0000 100 18 1.0000 100 19 1.0000 100 20 1.0000 100 21 1.0000 100 22 1.0000 100 23 1.0000 100 24 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 /home/students/y22/mkd57/public_html/term4/learn.fa -dna -nmotifs 3 -minw 6 -text 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= 24 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= 2400 N= 24 sample: seed= 0 hsfrac= 0 searchsize= 2400 norand= no csites= 1000 Letter frequencies in dataset: A 0.138 C 0.337 G 0.382 T 0.144 Background letter frequencies (from file dataset with add-one prior applied): A 0.138 C 0.337 G 0.381 T 0.144 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TCTGGTABAGTYMYYHCHBGTT MEME-1 width = 22 sites = 7 llr = 132 E-value = 9.4e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCTGGTABAGTYMYYHCHBGTT MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::1:::a17:::3:13:3:::: pos.-specific C :71:1::33::44334643::: probability G 33179::3:a::11::1:47:3 matrix T 7:63:a:3::a616633333a7 bits 2.9 ** * * 2.6 ** * * 2.3 ** * * 2.0 ** * * Relative 1.7 ** * * * Entropy 1.4 * ** **** ** (27.3 bits) 1.1 * ** **** * ** 0.9 * ***** **** *** * *** 0.6 ******* **** ***** *** 0.3 ******* ************** 0.0 ---------------------- Multilevel TCTGGTACAGTTCTTCCCGGTT consensus GG T GC CACCATACT G sequence T T TT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTGGTABAGTYMYYHCHBGTT MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------------- 17 5 4.24e-11 GGTT TCTGGTACCGTCATTCTAGGTT CGAGTCCTGG 1 48 2.92e-10 GCGTCGGCGT TCCTGTACAGTCATCTCCTGTT GTGAACGGCG 14 48 7.76e-10 GGCGGGTGGC TCTGGTAAAGTTCCATCCGTTG TCCGAACGGC 6 51 1.12e-09 ACTCGGAGGC TCTGCTAGAGTTTCCACTCGTT GCGAAAGCGG 16 9 1.72e-09 CGCCCGGA GGGTGTAGAGTTCTTACTCGTT GCCGGAGAGA 9 55 2.03e-09 ACCCGGTGTG GCTGGTATAGTCGGTCTCTGTT GGATTCAGGT 11 56 6.34e-09 CGGCGCCGCC TGAGGTATCGTTCTTCGAGTTG TCACCCCCAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTGGTABAGTYMYYHCHBGTT MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 17 4.2e-11 4_[+1]_74 1 2.9e-10 47_[+1]_31 14 7.8e-10 47_[+1]_31 6 1.1e-09 50_[+1]_28 16 1.7e-09 8_[+1]_70 9 2e-09 54_[+1]_24 11 6.3e-09 55_[+1]_23 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTGGTABAGTYMYYHCHBGTT MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TCTGGTABAGTYMYYHCHBGTT width=22 seqs=7 17 ( 5) TCTGGTACCGTCATTCTAGGTT 1 1 ( 48) TCCTGTACAGTCATCTCCTGTT 1 14 ( 48) TCTGGTAAAGTTCCATCCGTTG 1 6 ( 51) TCTGCTAGAGTTTCCACTCGTT 1 16 ( 9) GGGTGTAGAGTTCTTACTCGTT 1 9 ( 55) GCTGGTATAGTCGGTCTCTGTT 1 11 ( 56) TGAGGTATCGTTCTTCGAGTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTGGTABAGTYMYYHCHBGTT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 22 n= 1896 bayes= 9.3015 E= 9.4e-008 -945 -945 -42 231 -945 108 -42 -945 5 -123 -141 199 -945 -945 90 99 -945 -123 117 -945 -945 -945 -945 279 285 -945 -945 -945 5 -24 -42 99 237 -24 -945 -945 -945 -945 139 -945 -945 -945 -945 279 -945 35 -945 199 105 35 -141 -1 -945 -24 -141 199 5 -24 -945 199 105 35 -945 99 -945 76 -141 99 105 35 -945 99 -945 -24 17 99 -945 -945 90 99 -945 -945 -945 279 -945 -945 -42 231 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTGGTABAGTYMYYHCHBGTT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 22 nsites= 7 E= 9.4e-008 0.000000 0.000000 0.285714 0.714286 0.000000 0.714286 0.285714 0.000000 0.142857 0.142857 0.142857 0.571429 0.000000 0.000000 0.714286 0.285714 0.000000 0.142857 0.857143 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.142857 0.285714 0.285714 0.285714 0.714286 0.285714 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.428571 0.000000 0.571429 0.285714 0.428571 0.142857 0.142857 0.000000 0.285714 0.142857 0.571429 0.142857 0.285714 0.000000 0.571429 0.285714 0.428571 0.000000 0.285714 0.000000 0.571429 0.142857 0.285714 0.285714 0.428571 0.000000 0.285714 0.000000 0.285714 0.428571 0.285714 0.000000 0.000000 0.714286 0.285714 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.285714 0.714286 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTGGTABAGTYMYYHCHBGTT MEME-1 regular expression -------------------------------------------------------------------------------- [TG][CG]T[GT]GTA[CGT][AC]GT[TC][CA][TC][TC][CAT][CT][CAT][GCT][GT]T[TG] -------------------------------------------------------------------------------- Time 0.66 secs. ******************************************************************************** ******************************************************************************** MOTIF KGTASGVTGGW MEME-2 width = 11 sites = 9 llr = 89 E-value = 1.8e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif KGTASGVTGGW MEME-2 Description -------------------------------------------------------------------------------- Simplified A 12:a1:3::17 pos.-specific C ::::223::1: probability G 471:483:a8: matrix T 419:2::a::3 bits 2.9 * * 2.6 * * 2.3 * * 2.0 ** * * Relative 1.7 ** * * Entropy 1.4 ** ** * (14.2 bits) 1.1 ** ** * 0.9 * ** ** * 0.6 **** * **** 0.3 **** ****** 0.0 ----------- Multilevel GGTAGGATGGA consensus TA CCC T sequence T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGTASGVTGGW MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------- 15 63 1.02e-06 GAGCCCCGTC GGTAGGATGGA CGGGTCCCGC 10 53 2.63e-06 GCCCGGGCCT TGTACGCTGGA AGGGCTGGCC 8 50 2.63e-06 CGCGTGTCTG GTTATGATGGA GCCTGCCCTC 24 57 7.47e-06 GCCGGGCTGG TGTAAGGTGGT GCCCGCGCCG 21 24 8.23e-06 GCGGGGACCG TGTACGCTGGT CGAGTTGCCA 16 62 1.99e-05 CAAGCTCATG AATATGATGCA CATCGGTCAG 19 80 2.14e-05 CTCGCTCACC GGTAGCCTGGA CGGACACCGG 23 65 3.64e-05 CCGGGGCGCT GATAGGGTGAT CGAGTCCCGC 6 20 8.29e-05 GAACGGCACG TGGAGCGTGGA TTTGCATGAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGTASGVTGGW MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 15 1e-06 62_[+2]_27 10 2.6e-06 52_[+2]_37 8 2.6e-06 49_[+2]_40 24 7.5e-06 56_[+2]_33 21 8.2e-06 23_[+2]_66 16 2e-05 61_[+2]_28 19 2.1e-05 79_[+2]_10 23 3.6e-05 64_[+2]_25 6 8.3e-05 19_[+2]_70 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGTASGVTGGW MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF KGTASGVTGGW width=11 seqs=9 15 ( 63) GGTAGGATGGA 1 10 ( 53) TGTACGCTGGA 1 8 ( 50) GTTATGATGGA 1 24 ( 57) TGTAAGGTGGT 1 21 ( 24) TGTACGCTGGT 1 16 ( 62) AATATGATGCA 1 19 ( 80) GGTAGCCTGGA 1 23 ( 65) GATAGGGTGAT 1 6 ( 20) TGGAGCGTGGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGTASGVTGGW MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 2160 bayes= 8.75154 E= 1.8e+001 -31 -982 22 163 69 -982 80 -37 -982 -982 -178 263 285 -982 -982 -982 -31 -60 22 63 -982 -60 103 -982 127 -1 -19 -982 -982 -982 -982 280 -982 -982 139 -982 -31 -160 103 -982 227 -982 -982 121 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGTASGVTGGW MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 9 E= 1.8e+001 0.111111 0.000000 0.444444 0.444444 0.222222 0.000000 0.666667 0.111111 0.000000 0.000000 0.111111 0.888889 1.000000 0.000000 0.000000 0.000000 0.111111 0.222222 0.444444 0.222222 0.000000 0.222222 0.777778 0.000000 0.333333 0.333333 0.333333 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.111111 0.111111 0.777778 0.000000 0.666667 0.000000 0.000000 0.333333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KGTASGVTGGW MEME-2 regular expression -------------------------------------------------------------------------------- [GT][GA]TA[GCT][GC][ACG]TGG[AT] -------------------------------------------------------------------------------- Time 1.11 secs. ******************************************************************************** ******************************************************************************** MOTIF CGGAAVCGGAG MEME-3 width = 11 sites = 7 llr = 75 E-value = 1.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGGAAVCGGAG MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::19a41::7: pos.-specific C a::1:391:3: probability G :99::3:9a:a matrix T :1::::::::: bits 2.9 * 2.6 * 2.3 * 2.0 ** Relative 1.7 * ** * Entropy 1.4 * ** *** (15.4 bits) 1.1 * *** * *** 0.9 ***** ***** 0.6 *********** 0.3 *********** 0.0 ----------- Multilevel CGGAAACGGAG consensus C C sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGAAVCGGAG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------- 22 76 3.31e-07 GCCGGTCCGC CGGAAACGGAG TCACCACCCA 7 53 3.31e-07 CACCGGCATT CGGAAACGGAG TCCGGTGACG 21 60 3.68e-06 GCGAACGGGC CGGAAACGGCG CGTGAACGTT 18 30 8.94e-06 CATCCGCCGC CTGAACAGGAG ACGCAGGCGC 24 82 1.17e-05 GCGCCGCAGG CGGAAGCCGAG CGGTTGCG 2 72 2.13e-05 GGCGTCGAGC CGGCACCGGAG GACTGACCGG 6 74 2.41e-05 CCACTCGTTG CGAAAGCGGCG AGAACAACAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGAAVCGGAG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 22 3.3e-07 75_[+3]_14 7 3.3e-07 52_[+3]_37 21 3.7e-06 59_[+3]_30 18 8.9e-06 29_[+3]_60 24 1.2e-05 81_[+3]_8 2 2.1e-05 71_[+3]_18 6 2.4e-05 73_[+3]_16 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGAAVCGGAG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CGGAAVCGGAG width=11 seqs=7 22 ( 76) CGGAAACGGAG 1 7 ( 53) CGGAAACGGAG 1 21 ( 60) CGGAAACGGCG 1 18 ( 30) CTGAACAGGAG 1 24 ( 82) CGGAAGCCGAG 1 2 ( 72) CGGCACCGGAG 1 6 ( 74) CGAAAGCGGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGAAVCGGAG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 2160 bayes= 8.87211 E= 1.0e+002 -945 157 -945 -945 -945 -945 117 -1 5 -945 117 -945 263 -123 -945 -945 285 -945 -945 -945 163 -24 -42 -945 5 135 -945 -945 -945 -123 117 -945 -945 -945 139 -945 237 -24 -945 -945 -945 -945 139 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGAAVCGGAG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 7 E= 1.0e+002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.857143 0.142857 0.142857 0.000000 0.857143 0.000000 0.857143 0.142857 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.428571 0.285714 0.285714 0.000000 0.142857 0.857143 0.000000 0.000000 0.000000 0.142857 0.857143 0.000000 0.000000 0.000000 1.000000 0.000000 0.714286 0.285714 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGAAVCGGAG MEME-3 regular expression -------------------------------------------------------------------------------- CGGAA[ACG]CGG[AC]G -------------------------------------------------------------------------------- Time 1.52 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1 1.21e-06 47_[+1(2.92e-10)]_31 2 3.77e-02 71_[+3(2.13e-05)]_18 3 5.16e-02 100 4 4.16e-01 100 5 2.90e-01 100 6 5.68e-10 19_[+2(8.29e-05)]_20_[+1(1.12e-09)]_\ 1_[+3(2.41e-05)]_16 7 1.18e-04 52_[+3(3.31e-07)]_37 8 5.09e-03 49_[+2(2.63e-06)]_40 9 4.44e-06 54_[+1(2.03e-09)]_24 10 5.14e-03 52_[+2(2.63e-06)]_37 11 6.30e-06 55_[+1(6.34e-09)]_23 12 1.61e-01 100 13 4.62e-01 100 14 1.07e-06 47_[+1(7.76e-10)]_31 15 7.18e-04 62_[+2(1.02e-06)]_27 16 5.65e-08 8_[+1(1.72e-09)]_31_[+2(1.99e-05)]_\ 28 17 4.66e-08 4_[+1(4.24e-11)]_74 18 3.78e-03 29_[+3(8.94e-06)]_60 19 4.73e-02 79_[+2(2.14e-05)]_10 20 3.27e-01 100 21 1.48e-06 23_[+2(8.23e-06)]_25_[+3(3.68e-06)]_\ 30 22 6.28e-04 75_[+3(3.31e-07)]_14 23 2.54e-02 64_[+2(3.64e-05)]_25 24 6.85e-05 56_[+2(7.47e-06)]_14_[+3(1.17e-05)]_\ 8 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kodomo ********************************************************************************