******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.3.3 (Release date: Sun Feb 7 15:39:52 2021 -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= ../result/final_prediction/worm/fasta/RankLinear2.0_40/nhr-28.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrM:13135-13215 1.0000 80 chrV:1627390-1627470 1.0000 80 chrIII:13779071-13779151 1.0000 80 chrM:196-276 1.0000 80 chrM:7860-7940 1.0000 80 chrIV:2162406-2162486 1.0000 80 chrIII:10225211-10225291 1.0000 80 chrM:1510-1590 1.0000 80 chrM:849-929 1.0000 80 chrV:777451-777531 1.0000 80 chrM:2926-3006 1.0000 80 chrM:11513-11593 1.0000 80 chrII:10950190-10950270 1.0000 80 chrV:15880862-15880942 1.0000 80 chrM:10361-10441 1.0000 80 chrM:8542-8622 1.0000 80 chrM:3575-3655 1.0000 80 chrM:9906-9986 1.0000 80 chrI:7056965-7057045 1.0000 80 chrM:9431-9511 1.0000 80 chrM:10152-10232 1.0000 80 chrM:8143-8223 1.0000 80 chrV:4844777-4844857 1.0000 80 chrI:13500550-13500630 1.0000 80 chrII:9586947-9587027 1.0000 80 chrIV:1624546-1624626 1.0000 80 chrM:7113-7193 1.0000 80 chrV:265144-265224 1.0000 80 chrM:6370-6450 1.0000 80 chrM:11240-11320 1.0000 80 chrM:1048-1128 1.0000 80 chrII:7771085-7771165 1.0000 80 chrIII:11444969-11445049 1.0000 80 chrI:13626332-13626412 1.0000 80 chrV:1743624-1743704 1.0000 80 chrM:2086-2166 1.0000 80 chrV:4908765-4908845 1.0000 80 chrM:4638-4718 1.0000 80 chrM:11020-11100 1.0000 80 chrX:15607728-15607808 1.0000 80 chrV:12413925-12414005 1.0000 80 chrM:6127-6207 1.0000 80 chrX:4142258-4142338 1.0000 80 chrV:12409116-12409196 1.0000 80 chrII:9112922-9113002 1.0000 80 chrI:12893170-12893250 1.0000 80 chrV:10709596-10709676 1.0000 80 chrM:12414-12494 1.0000 80 chrII:7060992-7061072 1.0000 80 chrIV:5656105-5656185 1.0000 80 chrII:7280842-7280922 1.0000 80 chrM:9214-9294 1.0000 80 chrI:13475708-13475788 1.0000 80 chrX:6255731-6255811 1.0000 80 chrI:14651864-14651944 1.0000 80 chrM:12619-12699 1.0000 80 chrII:14822612-14822692 1.0000 80 chrV:14200166-14200246 1.0000 80 chrII:13494952-13495032 1.0000 80 chrV:13463110-13463190 1.0000 80 chrX:12523184-12523264 1.0000 80 chrIV:6083789-6083869 1.0000 80 chrIII:4237907-4237987 1.0000 80 chrI:9275283-9275363 1.0000 80 chrII:11290414-11290494 1.0000 80 chrV:11764554-11764634 1.0000 80 chrV:773381-773461 1.0000 80 chrII:156049-156129 1.0000 80 chrIII:835678-835758 1.0000 80 chrI:8245718-8245798 1.0000 80 chrIII:3279254-3279334 1.0000 80 chrX:4222948-4223028 1.0000 80 chrI:4701212-4701292 1.0000 80 chrI:7595655-7595735 1.0000 80 chrX:2364972-2365052 1.0000 80 chrIV:2602133-2602213 1.0000 80 chrII:10552066-10552146 1.0000 80 chrX:6750326-6750406 1.0000 80 chrV:15766316-15766396 1.0000 80 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme -oc ../result/final_prediction/worm/inference_raw/MEME/RankLinear2.0_40_nhr-28/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/nhr-28.fasta model: mod= zoops nmotifs= 5 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + width: minw= 8 maxw= 8 nsites: minsites= 2 maxsites= 79 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= 6320 N= 79 sample: seed= 0 hsfrac= 0 searchsize= 6320 norand= no csites= 1000 Letter frequencies in dataset: A 0.329 C 0.153 G 0.175 T 0.344 Background letter frequencies (from file dataset with add-one prior applied): A 0.329 C 0.153 G 0.175 T 0.344 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AGACRCAG MEME-1 width = 8 sites = 11 llr = 105 E-value = 3.5e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGACRCAG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 7:7:4:9: pos.-specific C 313a:7:: probability G :9::631a matrix T :::::::: bits 2.7 * 2.4 * * 2.2 * * * 1.9 * * * * Relative 1.6 * * * * Entropy 1.4 * ***** (13.7 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel AGACGCAG consensus C C AG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGACRCAG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIV:6083789-6083869 38 4.47e-06 AGAGAGTTTT AGACGCAG ACTGCATAAG chrII:9586947-9587027 42 4.47e-06 TTGTAAGAAG AGACGCAG AGAATAAAGA chrV:777451-777531 20 4.47e-06 TCGCATGAAG AGACGCAG ACATAAAAAC chrV:1627390-1627470 44 4.47e-06 TAGTATGCCG AGACGCAG GCATAGAAAT chrX:4222948-4223028 20 1.47e-05 AGTGATCGAG AGACGGAG ACAGGTGACA chrI:7595655-7595735 17 2.31e-05 TGTTTTCTAT AGACACAG AGATCGGCTA chrI:13475708-13475788 42 3.57e-05 TGTAGTTTGT AGCCACAG CCTCAACCAT chrIV:2162406-2162486 6 3.91e-05 AACGC CGCCGGAG GTTTAGAGAA chrX:2364972-2365052 1 6.08e-05 . ccacgcag tggttggaaa chrV:15766316-15766396 58 7.99e-05 TCGAGAGATG CGCCAGAG GGGCTGCTGG chrV:265144-265224 31 7.99e-05 TCATAGCTAC AGACACGG TTGTACACTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGACRCAG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIV:6083789-6083869 4.5e-06 37_[+1]_35 chrII:9586947-9587027 4.5e-06 41_[+1]_31 chrV:777451-777531 4.5e-06 19_[+1]_53 chrV:1627390-1627470 4.5e-06 43_[+1]_29 chrX:4222948-4223028 1.5e-05 19_[+1]_53 chrI:7595655-7595735 2.3e-05 16_[+1]_56 chrI:13475708-13475788 3.6e-05 41_[+1]_31 chrIV:2162406-2162486 3.9e-05 5_[+1]_67 chrX:2364972-2365052 6.1e-05 [+1]_72 chrV:15766316-15766396 8e-05 57_[+1]_15 chrV:265144-265224 8e-05 30_[+1]_42 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGACRCAG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AGACRCAG width=8 seqs=11 chrIV:6083789-6083869 ( 38) AGACGCAG 1 chrII:9586947-9587027 ( 42) AGACGCAG 1 chrV:777451-777531 ( 20) AGACGCAG 1 chrV:1627390-1627470 ( 44) AGACGCAG 1 chrX:4222948-4223028 ( 20) AGACGGAG 1 chrI:7595655-7595735 ( 17) AGACACAG 1 chrI:13475708-13475788 ( 42) AGCCACAG 1 chrIV:2162406-2162486 ( 6) CGCCGGAG 1 chrX:2364972-2365052 ( 1) CCACGCAG 1 chrV:15766316-15766396 ( 58) CGCCAGAG 1 chrV:265144-265224 ( 31) AGACACGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGACRCAG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 5767 bayes= 10.0593 E= 3.5e+000 115 84 -1010 -1010 -1010 -75 238 -1010 115 84 -1010 -1010 -1010 271 -1010 -1010 15 -1010 186 -1010 -1010 225 64 -1010 147 -1010 -94 -1010 -1010 -1010 251 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGACRCAG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 11 E= 3.5e+000 0.727273 0.272727 0.000000 0.000000 0.000000 0.090909 0.909091 0.000000 0.727273 0.272727 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.363636 0.000000 0.636364 0.000000 0.000000 0.727273 0.272727 0.000000 0.909091 0.000000 0.090909 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGACRCAG MEME-1 regular expression -------------------------------------------------------------------------------- [AC]G[AC]C[GA][CG]AG -------------------------------------------------------------------------------- Time 1.09 secs. ******************************************************************************** ******************************************************************************** MOTIF AGWGAKCG MEME-2 width = 8 sites = 11 llr = 101 E-value = 1.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGWGAKCG MEME-2 Description -------------------------------------------------------------------------------- Simplified A 9:6:a12: pos.-specific C 1::::18: probability G :a:a:3:a matrix T ::4::5:: bits 2.7 2.4 * * * 2.2 * * * 1.9 * * ** Relative 1.6 * ** ** Entropy 1.4 ** ** ** (13.2 bits) 1.1 ** ** ** 0.8 ** ** ** 0.5 ***** ** 0.3 ******** 0.0 -------- Multilevel AGAGATCG consensus T G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGWGAKCG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:6750326-6750406 63 1.52e-05 TTGTATTTTC AGAGATCG CAGACATTTT chrII:10552066-10552146 70 1.52e-05 AGTGGTCAGT AGAGAGCG ATG chrV:4844777-4844857 49 1.52e-05 GTGCAGTTTG AGAGAGCG CAGTCACATG chrV:777451-777531 5 1.52e-05 AATT AGAGATCG CATGAAGAGA chrX:4222948-4223028 10 3.10e-05 CTTAAGATG AGTGATCG AGAGACGGAG chrX:6255731-6255811 17 3.10e-05 GATAACAAGA AGTGATCG GGGCACGTGG chrV:1627390-1627470 72 4.72e-05 TTGTGTCCAA AGTGACCG A chrV:12409116-12409196 25 5.68e-05 AAGTTTTATT AGAGAACG TGTGTAGTTG chrV:13463110-13463190 37 6.42e-05 TGACTCGTCG CGTGATCG GCGTCCCTCT chrII:14822612-14822692 63 9.68e-05 AATTAGCGCT AGAGATAG CAAACAGTCA chrII:9586947-9587027 15 9.68e-05 AAAGAATAAA AGAGAGAG AATGATAACT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGWGAKCG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:6750326-6750406 1.5e-05 62_[+2]_10 chrII:10552066-10552146 1.5e-05 69_[+2]_3 chrV:4844777-4844857 1.5e-05 48_[+2]_24 chrV:777451-777531 1.5e-05 4_[+2]_68 chrX:4222948-4223028 3.1e-05 9_[+2]_63 chrX:6255731-6255811 3.1e-05 16_[+2]_56 chrV:1627390-1627470 4.7e-05 71_[+2]_1 chrV:12409116-12409196 5.7e-05 24_[+2]_48 chrV:13463110-13463190 6.4e-05 36_[+2]_36 chrII:14822612-14822692 9.7e-05 62_[+2]_10 chrII:9586947-9587027 9.7e-05 14_[+2]_58 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGWGAKCG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AGWGAKCG width=8 seqs=11 chrX:6750326-6750406 ( 63) AGAGATCG 1 chrII:10552066-10552146 ( 70) AGAGAGCG 1 chrV:4844777-4844857 ( 49) AGAGAGCG 1 chrV:777451-777531 ( 5) AGAGATCG 1 chrX:4222948-4223028 ( 10) AGTGATCG 1 chrX:6255731-6255811 ( 17) AGTGATCG 1 chrV:1627390-1627470 ( 72) AGTGACCG 1 chrV:12409116-12409196 ( 25) AGAGAACG 1 chrV:13463110-13463190 ( 37) CGTGATCG 1 chrII:14822612-14822692 ( 63) AGAGATAG 1 chrII:9586947-9587027 ( 15) AGAGAGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGWGAKCG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 5767 bayes= 8.58296 E= 1.7e+002 147 -75 -1010 -1010 -1010 -1010 251 -1010 95 -1010 -1010 8 -1010 -1010 251 -1010 160 -1010 -1010 -1010 -185 -75 64 66 -85 242 -1010 -1010 -1010 -1010 251 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGWGAKCG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 11 E= 1.7e+002 0.909091 0.090909 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.636364 0.000000 0.000000 0.363636 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.090909 0.090909 0.272727 0.545455 0.181818 0.818182 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGWGAKCG MEME-2 regular expression -------------------------------------------------------------------------------- AG[AT]GA[TG]CG -------------------------------------------------------------------------------- Time 1.90 secs. ******************************************************************************** ******************************************************************************** MOTIF CGTCYCTC MEME-3 width = 8 sites = 7 llr = 71 E-value = 2.6e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGTCYCTC MEME-3 Description -------------------------------------------------------------------------------- Simplified A :::1:11: pos.-specific C a11969:a probability G :9:::::: matrix T ::9:4:9: bits 2.7 * * 2.4 * * 2.2 * * 1.9 ** * * * Relative 1.6 ** * * * Entropy 1.4 ** *** * (14.6 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel CGTCCCTC consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGTCYCTC MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:13463110-13463190 46 1.74e-06 GCGTGATCGG CGTCCCTC TTTCGCAATA chrV:773381-773461 40 6.41e-06 ATTTTCTCTG CGTCTCTC TCCTTCGCAC chrV:14200166-14200246 68 6.41e-06 ATTTCGCAAT CGTCTCTC ACACT chrX:15607728-15607808 5 7.93e-06 CGGT CCTCCCTC TAGTCATCTA chrX:4142258-4142338 65 1.88e-05 TGCACGCACA CGTACCTC CACGGGAG chrIV:2602133-2602213 18 2.74e-05 TTGATGTCTG CGTCTCAC CAGTGTCTCT chrX:12523184-12523264 48 3.21e-05 AGATTCCATT CGCCCATC TTCCTGTGAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGTCYCTC MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:13463110-13463190 1.7e-06 45_[+3]_27 chrV:773381-773461 6.4e-06 39_[+3]_33 chrV:14200166-14200246 6.4e-06 67_[+3]_5 chrX:15607728-15607808 7.9e-06 4_[+3]_68 chrX:4142258-4142338 1.9e-05 64_[+3]_8 chrIV:2602133-2602213 2.7e-05 17_[+3]_55 chrX:12523184-12523264 3.2e-05 47_[+3]_25 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGTCYCTC MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CGTCYCTC width=8 seqs=7 chrV:13463110-13463190 ( 46) CGTCCCTC 1 chrV:773381-773461 ( 40) CGTCTCTC 1 chrV:14200166-14200246 ( 68) CGTCTCTC 1 chrX:15607728-15607808 ( 5) CCTCCCTC 1 chrX:4142258-4142338 ( 65) CGTACCTC 1 chrIV:2602133-2602213 ( 18) CGTCTCAC 1 chrX:12523184-12523264 ( 48) CGCCCATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGTCYCTC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 5767 bayes= 10.2908 E= 2.6e+002 -945 271 -945 -945 -945 -9 229 -945 -945 -9 -945 132 -120 249 -945 -945 -945 190 -945 32 -120 249 -945 -945 -120 -945 -945 132 -945 271 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGTCYCTC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 2.6e+002 0.000000 1.000000 0.000000 0.000000 0.000000 0.142857 0.857143 0.000000 0.000000 0.142857 0.000000 0.857143 0.142857 0.857143 0.000000 0.000000 0.000000 0.571429 0.000000 0.428571 0.142857 0.857143 0.000000 0.000000 0.142857 0.000000 0.000000 0.857143 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGTCYCTC MEME-3 regular expression -------------------------------------------------------------------------------- CGTC[CT]CTC -------------------------------------------------------------------------------- Time 2.68 secs. ******************************************************************************** ******************************************************************************** MOTIF CTACAAAC MEME-4 width = 8 sites = 8 llr = 78 E-value = 2.1e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTACAAAC MEME-4 Description -------------------------------------------------------------------------------- Simplified A ::a:a89: pos.-specific C 9::a:1:a probability G :::::1:: matrix T 1a::::1: bits 2.7 * * 2.4 * * 2.2 * * 1.9 * * * Relative 1.6 ***** * Entropy 1.4 ***** * (14.0 bits) 1.1 ***** ** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel CTACAAAC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTACAAAC MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrI:12893170-12893250 52 1.44e-05 AAACTACAAA CTACAAAC TATGAAAACT chrV:4908765-4908845 16 1.44e-05 ACTCAAAATA CTACAAAC TACACTGACG chrII:7771085-7771165 58 1.44e-05 GTAGTCTTGA CTACAAAC TATTGTTTAT chrIV:1624546-1624626 57 1.44e-05 acactacaca ctacaaac tacaAATCAT chrI:13500550-13500630 64 1.44e-05 aaactacaaa ctacaaac tacaaGTAA chrIV:5656105-5656185 53 2.88e-05 TTTTCACTCA CTACAGAC TGATTTTCGA chrII:11290414-11290494 27 7.64e-05 TAAAACACAT TTACAAAC GTATATTTGT chrV:13463110-13463190 4 8.34e-05 TCT CTACACTC CATTCGTTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTACAAAC MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrI:12893170-12893250 1.4e-05 51_[+4]_21 chrV:4908765-4908845 1.4e-05 15_[+4]_57 chrII:7771085-7771165 1.4e-05 57_[+4]_15 chrIV:1624546-1624626 1.4e-05 56_[+4]_16 chrI:13500550-13500630 1.4e-05 63_[+4]_9 chrIV:5656105-5656185 2.9e-05 52_[+4]_20 chrII:11290414-11290494 7.6e-05 26_[+4]_46 chrV:13463110-13463190 8.3e-05 3_[+4]_69 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTACAAAC MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTACAAAC width=8 seqs=8 chrI:12893170-12893250 ( 52) CTACAAAC 1 chrV:4908765-4908845 ( 16) CTACAAAC 1 chrII:7771085-7771165 ( 58) CTACAAAC 1 chrIV:1624546-1624626 ( 57) CTACAAAC 1 chrI:13500550-13500630 ( 64) CTACAAAC 1 chrIV:5656105-5656185 ( 53) CTACAGAC 1 chrII:11290414-11290494 ( 27) TTACAAAC 1 chrV:13463110-13463190 ( 4) CTACACTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTACAAAC MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 5767 bayes= 9.4916 E= 2.1e+003 -965 252 -965 -146 -965 -965 -965 154 160 -965 -965 -965 -965 271 -965 -965 160 -965 -965 -965 119 -29 -48 -965 141 -965 -965 -146 -965 271 -965 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTACAAAC MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 8 E= 2.1e+003 0.000000 0.875000 0.000000 0.125000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.125000 0.125000 0.000000 0.875000 0.000000 0.000000 0.125000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTACAAAC MEME-4 regular expression -------------------------------------------------------------------------------- CTACAAAC -------------------------------------------------------------------------------- Time 3.47 secs. ******************************************************************************** ******************************************************************************** MOTIF CACSCCWC MEME-5 width = 8 sites = 3 llr = 36 E-value = 2.9e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CACSCCWC MEME-5 Description -------------------------------------------------------------------------------- Simplified A :a::::3: pos.-specific C a:a7aa:a probability G :::3:::: matrix T ::::::7: bits 2.7 * * ** * 2.4 * * ** * 2.2 * * ** * 1.9 * * ** * Relative 1.6 ****** * Entropy 1.4 ****** * (17.5 bits) 1.1 ****** * 0.8 ****** * 0.5 ******** 0.3 ******** 0.0 -------- Multilevel CACCCCTC consensus G A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACSCCWC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:13463110-13463190 68 1.45e-06 GCAATACCAA CACCCCTC AAGAC chrI:7056965-7057045 70 2.84e-06 GAAACTTAGT CACCCCAC CAT chrII:7771085-7771165 30 4.50e-06 CTCATAGATA CACGCCTC TTGTAGACGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACSCCWC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:13463110-13463190 1.5e-06 67_[+5]_5 chrI:7056965-7057045 2.8e-06 69_[+5]_3 chrII:7771085-7771165 4.5e-06 29_[+5]_43 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACSCCWC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CACSCCWC width=8 seqs=3 chrV:13463110-13463190 ( 68) CACCCCTC 1 chrI:7056965-7057045 ( 70) CACCCCAC 1 chrII:7771085-7771165 ( 30) CACGCCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACSCCWC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 5767 bayes= 11.3556 E= 2.9e+002 -823 271 -823 -823 160 -823 -823 -823 -823 271 -823 -823 -823 212 93 -823 -823 271 -823 -823 -823 271 -823 -823 2 -823 -823 95 -823 271 -823 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACSCCWC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 2.9e+002 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.666667 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CACSCCWC MEME-5 regular expression -------------------------------------------------------------------------------- CAC[CG]CC[TA]C -------------------------------------------------------------------------------- Time 4.25 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrM:13135-13215 9.49e-01 80 chrV:1627390-1627470 9.68e-04 43_[+1(4.47e-06)]_20_[+2(4.72e-05)]_\ 1 chrIII:13779071-13779151 9.92e-01 80 chrM:196-276 9.70e-01 80 chrM:7860-7940 5.33e-01 80 chrIV:2162406-2162486 1.75e-02 5_[+1(3.91e-05)]_67 chrIII:10225211-10225291 9.47e-01 80 chrM:1510-1590 8.00e-02 80 chrM:849-929 9.85e-01 80 chrV:777451-777531 4.35e-04 4_[+2(1.52e-05)]_7_[+1(4.47e-06)]_\ 53 chrM:2926-3006 4.61e-01 80 chrM:11513-11593 9.89e-01 80 chrII:10950190-10950270 2.57e-01 80 chrV:15880862-15880942 1.60e-01 80 chrM:10361-10441 9.69e-01 80 chrM:8542-8622 9.70e-01 80 chrM:3575-3655 8.06e-01 80 chrM:9906-9986 8.75e-01 80 chrI:7056965-7057045 1.37e-03 69_[+5(2.84e-06)]_3 chrM:9431-9511 9.97e-01 80 chrM:10152-10232 7.21e-01 80 chrM:8143-8223 3.51e-01 80 chrV:4844777-4844857 6.73e-02 48_[+2(1.52e-05)]_24 chrI:13500550-13500630 2.82e-02 1_[+4(1.44e-05)]_13_[+4(1.44e-05)]_\ 5_[+4(1.44e-05)]_6_[+4(1.44e-05)]_6_[+4(1.44e-05)]_9 chrII:9586947-9587027 4.70e-04 14_[+2(9.68e-05)]_19_[+1(4.47e-06)]_\ 31 chrIV:1624546-1624626 2.96e-02 [+4(2.11e-05)]_6_[+4(2.11e-05)]_13_\ [+4(1.44e-05)]_13_[+4(1.44e-05)]_16 chrM:7113-7193 9.40e-01 80 chrV:265144-265224 4.22e-03 26_[+4(2.88e-05)]_46 chrM:6370-6450 9.99e-01 80 chrM:11240-11320 8.07e-01 80 chrM:1048-1128 1.00e+00 80 chrII:7771085-7771165 4.78e-05 29_[+5(4.50e-06)]_20_[+4(1.44e-05)]_\ 15 chrIII:11444969-11445049 7.42e-01 80 chrI:13626332-13626412 6.25e-01 80 chrV:1743624-1743704 5.52e-02 80 chrM:2086-2166 9.98e-01 80 chrV:4908765-4908845 1.20e-02 15_[+4(1.44e-05)]_57 chrM:4638-4718 8.93e-01 80 chrM:11020-11100 1.00e+00 80 chrX:15607728-15607808 1.06e-03 4_[+3(7.93e-06)]_68 chrV:12413925-12414005 9.69e-01 80 chrM:6127-6207 1.00e+00 80 chrX:4142258-4142338 1.36e-02 64_[+3(1.88e-05)]_8 chrV:12409116-12409196 1.19e-01 24_[+2(5.68e-05)]_48 chrII:9112922-9113002 5.30e-01 80 chrI:12893170-12893250 1.44e-01 5_[+4(1.44e-05)]_8_[+4(1.44e-05)]_\ 15_[+4(1.44e-05)]_15_[+4(1.44e-05)]_5 chrV:10709596-10709676 2.73e-01 80 chrM:12414-12494 9.36e-01 80 chrII:7060992-7061072 9.99e-01 80 chrIV:5656105-5656185 1.89e-02 52_[+4(2.88e-05)]_20 chrII:7280842-7280922 1.62e-01 80 chrM:9214-9294 6.71e-01 80 chrI:13475708-13475788 4.92e-02 41_[+1(3.57e-05)]_31 chrX:6255731-6255811 9.38e-02 16_[+2(3.10e-05)]_56 chrI:14651864-14651944 9.96e-01 80 chrM:12619-12699 7.87e-01 80 chrII:14822612-14822692 3.68e-02 62_[+2(9.68e-05)]_10 chrV:14200166-14200246 1.32e-02 67_[+3(6.41e-06)]_5 chrII:13494952-13495032 5.97e-01 80 chrV:13463110-13463190 6.54e-09 3_[+4(8.34e-05)]_25_[+2(6.42e-05)]_\ 1_[+3(1.74e-06)]_14_[+5(1.45e-06)]_5 chrX:12523184-12523264 1.61e-02 47_[+3(3.21e-05)]_25 chrIV:6083789-6083869 2.95e-03 5_[+1(2.31e-05)]_24_[+1(4.47e-06)]_\ 35 chrIII:4237907-4237987 3.06e-01 80 chrI:9275283-9275363 4.99e-01 80 chrII:11290414-11290494 7.83e-02 26_[+4(7.64e-05)]_46 chrV:11764554-11764634 9.51e-01 80 chrV:773381-773461 1.50e-02 39_[+3(6.41e-06)]_33 chrII:156049-156129 7.29e-01 80 chrIII:835678-835758 4.98e-01 80 chrI:8245718-8245798 8.60e-01 80 chrIII:3279254-3279334 9.63e-01 80 chrX:4222948-4223028 7.19e-04 9_[+2(3.10e-05)]_2_[+1(1.47e-05)]_\ 53 chrI:4701212-4701292 1.07e-01 80 chrI:7595655-7595735 2.63e-05 22_[+2(1.52e-05)]_50 chrX:2364972-2365052 8.90e-02 [+1(6.08e-05)]_72 chrIV:2602133-2602213 6.39e-02 17_[+3(2.74e-05)]_55 chrII:10552066-10552146 4.66e-02 69_[+2(1.52e-05)]_3 chrX:6750326-6750406 1.39e-01 62_[+2(1.52e-05)]_10 chrV:15766316-15766396 5.81e-02 57_[+1(7.99e-05)]_15 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n07.farnam.hpc.yale.internal ********************************************************************************