******************************************************************************** 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/fly/fasta/RankLinear8.0_60/fru.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr3L:8107185-8107305 1.0000 120 chrM:18115-18235 1.0000 120 chrM:15653-15773 1.0000 120 chrM:16649-16769 1.0000 120 chrX:11563725-11563845 1.0000 120 chrM:9143-9263 1.0000 120 chrM:8002-8122 1.0000 120 chrX:5793607-5793727 1.0000 120 chr2L:8675667-8675787 1.0000 120 chrX:1656608-1656728 1.0000 120 chrX:1655993-1656113 1.0000 120 chrM:17644-17764 1.0000 120 chr2R:23073985-23074105 1.0000 120 chrM:5686-5806 1.0000 120 chr2L:3152784-3152904 1.0000 120 chrX:16094238-16094358 1.0000 120 chr3R:16533903-16534023 1.0000 120 chr2L:16787781-16787901 1.0000 120 chrM:16025-16145 1.0000 120 chrM:19296-19416 1.0000 120 chr3L:10771976-10772096 1.0000 120 chrX:5596661-5596781 1.0000 120 chrM:17208-17328 1.0000 120 chrM:13791-13911 1.0000 120 chrM:14771-14891 1.0000 120 chrM:8227-8347 1.0000 120 chrX:9684530-9684650 1.0000 120 chrM:4093-4213 1.0000 120 chr2R:13189338-13189458 1.0000 120 chr3L:11765774-11765894 1.0000 120 chrM:1289-1409 1.0000 120 chrM:944-1064 1.0000 120 chr2R:13028313-13028433 1.0000 120 chr2L:1556880-1557000 1.0000 120 chrM:15254-15374 1.0000 120 chrM:9548-9668 1.0000 120 chr3R:29457296-29457416 1.0000 120 chr2L:3772001-3772121 1.0000 120 chr2L:7419876-7419996 1.0000 120 chrM:10077-10197 1.0000 120 chr2L:19054486-19054606 1.0000 120 chrM:582-702 1.0000 120 chrM:4448-4568 1.0000 120 chr2R:15890897-15891017 1.0000 120 chr3L:21025855-21025975 1.0000 120 chrM:2364-2484 1.0000 120 chrM:168-288 1.0000 120 chr3L:19896567-19896687 1.0000 120 chrX:7097254-7097374 1.0000 120 chr2L:16485813-16485933 1.0000 120 chrM:11931-12051 1.0000 120 chr3L:5360246-5360366 1.0000 120 chr3R:27281492-27281612 1.0000 120 chr2L:6089110-6089230 1.0000 120 chrM:12831-12951 1.0000 120 chr2R:14275302-14275422 1.0000 120 chrM:5997-6117 1.0000 120 chr2R:6236188-6236308 1.0000 120 chrM:6861-6981 1.0000 120 chrM:4827-4947 1.0000 120 chr2R:22689151-22689271 1.0000 120 chrX:3780183-3780303 1.0000 120 chrX:19697493-19697613 1.0000 120 chrM:12506-12626 1.0000 120 chr2L:9494611-9494731 1.0000 120 ******************************************************************************** ******************************************************************************** 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/fly/inference_raw/MEME/RankLinear8.0_60_fru/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/fly/fasta/RankLinear8.0_60/fru.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= 65 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= 7800 N= 65 sample: seed= 0 hsfrac= 0 searchsize= 7800 norand= no csites= 1000 Letter frequencies in dataset: A 0.331 C 0.18 G 0.164 T 0.326 Background letter frequencies (from file dataset with add-one prior applied): A 0.331 C 0.18 G 0.164 T 0.326 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF ACTCGCYG MEME-1 width = 8 sites = 18 llr = 166 E-value = 1.8e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif ACTCGCYG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 9::::::2 pos.-specific C :928:a31 probability G :1:1a::7 matrix T 1:81::7: bits 2.6 * 2.3 ** 2.1 * ** 1.8 * ** Relative 1.6 * *** Entropy 1.3 ** *** * (13.3 bits) 1.0 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel ACTCGCTG consensus C CA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACTCGCYG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:19697493-19697613 112 5.52e-06 AAGCTGCCGT ACTCGCTG C chr2R:6236188-6236308 45 5.52e-06 GCACCAAGTC ACTCGCTG CTTTTGTTTT chr2L:6089110-6089230 105 5.52e-06 TAACTGTAAT ACTCGCTG CCTGCCTG chr3R:29457296-29457416 84 5.52e-06 ATTTCCCCCT ACTCGCTG GGATCAAAAA chr2L:16787781-16787901 74 5.52e-06 TCACCGCGCC ACTCGCTG GCACTACAAA chr3L:8107185-8107305 31 5.52e-06 GTTTCTCGCC ACTCGCTG CATTTGTGCC chr3L:11765774-11765894 86 8.56e-06 ACCTTCAAGC ACTCGCCG CTAGCTTACA chr2R:13189338-13189458 103 2.44e-05 GGCAGGATAT ACTCGCTA CAGAGGAGAT chrX:1656608-1656728 30 2.44e-05 ttcgttttct actcgcta tatctTATTC chr2L:7419876-7419996 79 3.84e-05 TTAAAGTTGA AGTCGCCG TCCCCTATTG chrM:4448-4568 15 4.45e-05 CTCAAGGAAC ACCCGCTA TTCTTATACC chr2L:9494611-9494731 79 6.90e-05 CGCCCTTTTC ACTTGCTG CGACGTTCGA chrX:3780183-3780303 85 6.90e-05 GAATAGTTAC ACTCGCTC TTTTGCTCGT chr2R:13028313-13028433 62 6.90e-05 ccgtccatcc acccGCCA AACAGCCTAG chr3L:19896567-19896687 30 8.34e-05 GCCTTGTATC ACTTGCCG TATAATTCGT chr3L:10771976-10772096 24 9.04e-05 TCAATAATCA AGCCGCCG TGAGAGGGAg chr2R:23073985-23074105 56 9.34e-05 GAGATGCGCT TCTCGCCG TAGACTTCGG chr2R:15890897-15891017 26 1.05e-04 AACTGAGCGG ACCGGCTG AGCAGATGTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACTCGCYG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:19697493-19697613 5.5e-06 111_[+1]_1 chr2R:6236188-6236308 5.5e-06 44_[+1]_68 chr2L:6089110-6089230 5.5e-06 104_[+1]_8 chr3R:29457296-29457416 5.5e-06 83_[+1]_29 chr2L:16787781-16787901 5.5e-06 73_[+1]_39 chr3L:8107185-8107305 5.5e-06 30_[+1]_82 chr3L:11765774-11765894 8.6e-06 85_[+1]_27 chr2R:13189338-13189458 2.4e-05 102_[+1]_10 chrX:1656608-1656728 2.4e-05 29_[+1]_83 chr2L:7419876-7419996 3.8e-05 78_[+1]_34 chrM:4448-4568 4.5e-05 14_[+1]_98 chr2L:9494611-9494731 6.9e-05 78_[+1]_34 chrX:3780183-3780303 6.9e-05 84_[+1]_28 chr2R:13028313-13028433 6.9e-05 61_[+1]_51 chr3L:19896567-19896687 8.3e-05 29_[+1]_83 chr3L:10771976-10772096 9e-05 23_[+1]_89 chr2R:23073985-23074105 9.3e-05 55_[+1]_57 chr2R:15890897-15891017 0.00011 25_[+1]_87 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACTCGCYG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ACTCGCYG width=8 seqs=18 chrX:19697493-19697613 ( 112) ACTCGCTG 1 chr2R:6236188-6236308 ( 45) ACTCGCTG 1 chr2L:6089110-6089230 ( 105) ACTCGCTG 1 chr3R:29457296-29457416 ( 84) ACTCGCTG 1 chr2L:16787781-16787901 ( 74) ACTCGCTG 1 chr3L:8107185-8107305 ( 31) ACTCGCTG 1 chr3L:11765774-11765894 ( 86) ACTCGCCG 1 chr2R:13189338-13189458 ( 103) ACTCGCTA 1 chrX:1656608-1656728 ( 30) ACTCGCTA 1 chr2L:7419876-7419996 ( 79) AGTCGCCG 1 chrM:4448-4568 ( 15) ACCCGCTA 1 chr2L:9494611-9494731 ( 79) ACTTGCTG 1 chrX:3780183-3780303 ( 85) ACTCGCTC 1 chr2R:13028313-13028433 ( 62) ACCCGCCA 1 chr3L:19896567-19896687 ( 30) ACTTGCCG 1 chr3L:10771976-10772096 ( 24) AGCCGCCG 1 chr2R:23073985-23074105 ( 56) TCTCGCCG 1 chr2R:15890897-15891017 ( 26) ACCGGCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACTCGCYG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 7345 bayes= 7.9689 E= 1.8e-005 151 -1081 -1081 -255 -1081 231 -56 -1081 -1081 31 -1081 126 -1081 221 -156 -155 -1081 -1081 261 -1081 -1081 248 -1081 -1081 -1081 89 -1081 103 -57 -169 214 -1081 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACTCGCYG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 18 E= 1.8e-005 0.944444 0.000000 0.000000 0.055556 0.000000 0.888889 0.111111 0.000000 0.000000 0.222222 0.000000 0.777778 0.000000 0.833333 0.055556 0.111111 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.666667 0.222222 0.055556 0.722222 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACTCGCYG MEME-1 regular expression -------------------------------------------------------------------------------- AC[TC]CGC[TC][GA] -------------------------------------------------------------------------------- Time 1.12 secs. ******************************************************************************** ******************************************************************************** MOTIF GSRGCGAG MEME-2 width = 8 sites = 16 llr = 149 E-value = 3.2e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GSRGCGAG MEME-2 Description -------------------------------------------------------------------------------- Simplified A 3:4:::9: pos.-specific C :621a1:1 probability G 8349:919 matrix T :1:::::: bits 2.6 2.3 * * 2.1 *** * 1.8 *** * Relative 1.6 * *** * Entropy 1.3 ** ***** (13.5 bits) 1.0 ** ***** 0.8 ** ***** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel GCAGCGAG consensus AGG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSRGCGAG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:11563725-11563845 41 1.27e-06 GGCGAGTGCT GCGGCGAG CTGGGCGAGT chr2R:15890897-15891017 99 3.84e-06 cgagtagcaa gcagcgag agagtatcgg chr2L:8675667-8675787 27 3.84e-06 GACTGCGTCA GCAGCGAG AGCAAGAAGA chr2L:1556880-1557000 103 5.00e-06 GGAATTGCGG GGGGCGAG TATGGCGAAG chr2L:16485813-16485933 4 1.06e-05 gac ggcgcgag gcgacgactg chr2R:14275302-14275422 85 1.45e-05 TCCTGTTTGT GCAGCGGG AGCGGACAAA chrX:5793607-5793727 83 1.45e-05 GAGAAATACA ACGGCGAG TAAATGGGGA chrX:19697493-19697613 2 1.85e-05 G GCGGCCAG TCCCGTGACC chr2L:3152784-3152904 13 1.85e-05 CAAACTGAGT GCGCCGAG TGTTGATtga chrX:9684530-9684650 48 4.33e-05 ATTTCATTTT GCCGCCAG TCCCCTAAAA chr2R:6236188-6236308 2 5.16e-05 g agagcgag aACCCATTGT chrX:7097254-7097374 48 5.16e-05 aaggagtggg agagcgag CAAAAACGGC chr3R:29457296-29457416 102 5.16e-05 GGATCAAAAA GTGGCGAG TTCGAGGTGC chr2R:13189338-13189458 79 5.16e-05 TATGGTGGGA AGAGCGAG TGAGCGGGCA chr3L:5360246-5360366 97 6.35e-05 GGCCACCATG GCAGCGAC ATTGCGAAGA chr2L:19054486-19054606 77 9.74e-05 AATTAACAGT GCCCCGGG AAGCTGGGCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSRGCGAG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:11563725-11563845 1.3e-06 40_[+2]_72 chr2R:15890897-15891017 3.8e-06 98_[+2]_14 chr2L:8675667-8675787 3.8e-06 26_[+2]_86 chr2L:1556880-1557000 5e-06 102_[+2]_10 chr2L:16485813-16485933 1.1e-05 3_[+2]_109 chr2R:14275302-14275422 1.4e-05 84_[+2]_28 chrX:5793607-5793727 1.4e-05 82_[+2]_30 chrX:19697493-19697613 1.9e-05 1_[+2]_111 chr2L:3152784-3152904 1.9e-05 12_[+2]_100 chrX:9684530-9684650 4.3e-05 47_[+2]_65 chr2R:6236188-6236308 5.2e-05 1_[+2]_111 chrX:7097254-7097374 5.2e-05 47_[+2]_65 chr3R:29457296-29457416 5.2e-05 101_[+2]_11 chr2R:13189338-13189458 5.2e-05 78_[+2]_34 chr3L:5360246-5360366 6.4e-05 96_[+2]_16 chr2L:19054486-19054606 9.7e-05 76_[+2]_36 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSRGCGAG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GSRGCGAG width=8 seqs=16 chrX:11563725-11563845 ( 41) GCGGCGAG 1 chr2R:15890897-15891017 ( 99) GCAGCGAG 1 chr2L:8675667-8675787 ( 27) GCAGCGAG 1 chr2L:1556880-1557000 ( 103) GGGGCGAG 1 chr2L:16485813-16485933 ( 4) GGCGCGAG 1 chr2R:14275302-14275422 ( 85) GCAGCGGG 1 chrX:5793607-5793727 ( 83) ACGGCGAG 1 chrX:19697493-19697613 ( 2) GCGGCCAG 1 chr2L:3152784-3152904 ( 13) GCGCCGAG 1 chrX:9684530-9684650 ( 48) GCCGCCAG 1 chr2R:6236188-6236308 ( 2) AGAGCGAG 1 chrX:7097254-7097374 ( 48) AGAGCGAG 1 chr3R:29457296-29457416 ( 102) GTGGCGAG 1 chr2R:13189338-13189458 ( 79) AGAGCGAG 1 chr3L:5360246-5360366 ( 97) GCAGCGAC 1 chr2L:19054486-19054606 ( 77) GCCCCGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSRGCGAG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 7345 bayes= 9.57763 E= 3.2e-004 -40 -1064 219 -1064 -1064 180 93 -238 40 6 119 -1064 -1064 -52 242 -1064 -1064 248 -1064 -1064 -1064 -52 242 -1064 140 -1064 -39 -1064 -1064 -152 252 -1064 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSRGCGAG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 16 E= 3.2e-004 0.250000 0.000000 0.750000 0.000000 0.000000 0.625000 0.312500 0.062500 0.437500 0.187500 0.375000 0.000000 0.000000 0.125000 0.875000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.125000 0.875000 0.000000 0.875000 0.000000 0.125000 0.000000 0.000000 0.062500 0.937500 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSRGCGAG MEME-2 regular expression -------------------------------------------------------------------------------- [GA][CG][AG]GCGAG -------------------------------------------------------------------------------- Time 2.16 secs. ******************************************************************************** ******************************************************************************** MOTIF RCGAGTGC MEME-3 width = 8 sites = 14 llr = 121 E-value = 6.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif RCGAGTGC MEME-3 Description -------------------------------------------------------------------------------- Simplified A 5:1a:::: pos.-specific C 19::22:8 probability G 319:6:a2 matrix T 1:::18:: bits 2.6 * 2.3 * 2.1 * * 1.8 ** ** Relative 1.6 *** ** Entropy 1.3 *** ** (12.5 bits) 1.0 ******* 0.8 ******* 0.5 ******* 0.3 ******** 0.0 -------- Multilevel ACGAGTGC consensus G CC G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCGAGTGC MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:11563725-11563845 32 2.53e-06 TGGTTTGAGG GCGAGTGC TGCGGCGAGC chr2L:16485813-16485933 47 7.63e-06 gcgggcgCTA ACGAGTGC TATTTTTTTA chr2R:13189338-13189458 25 7.63e-06 GGGGGAGCTG ACGAGTGC GCAAAACTAT chrX:7097254-7097374 13 2.72e-05 TGAAGTAACA ACGAGTGG ACGGgagaga chr2L:8675667-8675787 15 2.72e-05 AGCAGGAAGA ACGACTGC GTCAGCAGCG chr2L:16787781-16787901 101 3.73e-05 AACGTGTTCA GGGAGTGC TAGTCGTACT chr2L:19054486-19054606 102 5.04e-05 GCCGGTGTCC ACGAGCGG ATCTCAGCCA chr2R:13028313-13028433 103 5.04e-05 GAGAACGAGA ACGACCGC ATTGCATGAA chr2R:15890897-15891017 54 5.32e-05 TGTCTGTCCG TCGAGCGC TCGACAAAag chr2R:22689151-22689271 32 5.97e-05 TTCTTCCATT GCGATTGC ACTTGGAATT chr3R:16533903-16534023 93 9.70e-05 GTCTGCTGAC CCGACTGC AATTGTTTTG chrX:16094238-16094358 44 1.25e-04 CTATTCTCGT TGGAGTGC TCCTCGTTGG chr3L:5360246-5360366 28 1.59e-04 GATTCGATTG GCGATTGG CTGCCCGCAG chrX:9684530-9684650 76 1.59e-04 AATATGGAAA ACAAGTGC CGTCGTTGGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCGAGTGC MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:11563725-11563845 2.5e-06 31_[+3]_81 chr2L:16485813-16485933 7.6e-06 46_[+3]_66 chr2R:13189338-13189458 7.6e-06 24_[+3]_88 chrX:7097254-7097374 2.7e-05 12_[+3]_100 chr2L:8675667-8675787 2.7e-05 14_[+3]_98 chr2L:16787781-16787901 3.7e-05 100_[+3]_12 chr2L:19054486-19054606 5e-05 101_[+3]_11 chr2R:13028313-13028433 5e-05 102_[+3]_10 chr2R:15890897-15891017 5.3e-05 53_[+3]_59 chr2R:22689151-22689271 6e-05 31_[+3]_81 chr3R:16533903-16534023 9.7e-05 92_[+3]_20 chrX:16094238-16094358 0.00013 43_[+3]_69 chr3L:5360246-5360366 0.00016 27_[+3]_85 chrX:9684530-9684650 0.00016 75_[+3]_37 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCGAGTGC MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RCGAGTGC width=8 seqs=14 chrX:11563725-11563845 ( 32) GCGAGTGC 1 chr2L:16485813-16485933 ( 47) ACGAGTGC 1 chr2R:13189338-13189458 ( 25) ACGAGTGC 1 chrX:7097254-7097374 ( 13) ACGAGTGG 1 chr2L:8675667-8675787 ( 15) ACGACTGC 1 chr2L:16787781-16787901 ( 101) GGGAGTGC 1 chr2L:19054486-19054606 ( 102) ACGAGCGG 1 chr2R:13028313-13028433 ( 103) ACGACCGC 1 chr2R:15890897-15891017 ( 54) TCGAGCGC 1 chr2R:22689151-22689271 ( 32) GCGATTGC 1 chr3R:16533903-16534023 ( 93) CCGACTGC 1 chrX:16094238-16094358 ( 44) TGGAGTGC 1 chr3L:5360246-5360366 ( 28) GCGATTGG 1 chrX:9684530-9684650 ( 76) ACAAGTGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCGAGTGC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 7345 bayes= 8.87601 E= 6.5e+002 60 -133 80 -119 -1045 225 -20 -1045 -221 -1045 250 -1045 160 -1045 -1045 -1045 -1045 25 197 -119 -1045 25 -1045 127 -1045 -1045 261 -1045 -1045 213 39 -1045 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCGAGTGC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 14 E= 6.5e+002 0.500000 0.071429 0.285714 0.142857 0.000000 0.857143 0.142857 0.000000 0.071429 0.000000 0.928571 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.214286 0.642857 0.142857 0.000000 0.214286 0.000000 0.785714 0.000000 0.000000 1.000000 0.000000 0.000000 0.785714 0.214286 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCGAGTGC MEME-3 regular expression -------------------------------------------------------------------------------- [AG]CGA[GC][TC]G[CG] -------------------------------------------------------------------------------- Time 3.18 secs. ******************************************************************************** ******************************************************************************** MOTIF SKGWGMKG MEME-4 width = 8 sites = 12 llr = 112 E-value = 9.4e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif SKGWGMKG MEME-4 Description -------------------------------------------------------------------------------- Simplified A :::6:3:: pos.-specific C 3::1:6:: probability G 77a:a:7a matrix T :3:3:13: bits 2.6 * * * 2.3 * * * 2.1 * * * 1.8 * * * Relative 1.6 * * * * Entropy 1.3 *** * ** (13.4 bits) 1.0 *** * ** 0.8 *** **** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel GGGAGCGG consensus CT T AT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SKGWGMKG MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2L:16485813-16485933 33 1.22e-05 gagtgagcga gtgagcgg gcgCTAACGA chr2L:19054486-19054606 30 1.22e-05 cTCTGCCTTT GTGAGCGG ATTAGTGGCG chr2R:13189338-13189458 17 1.22e-05 ACTGAGAGGG GGGAGCTG ACGAGTGCGC chrX:5596661-5596781 112 1.22e-05 TGACCTTTCC GGGAGCTG C chr2L:1556880-1557000 79 1.43e-05 atgaatgcct gggtgagg gaatgaGGAA chr2R:22689151-22689271 6 2.12e-05 CCCGT GTGTGCGG TTCGGTCGTT chr2R:14275302-14275422 41 2.69e-05 AAGTGCTCTT CGGCGCGG CGATTCATTC chr2R:15890897-15891017 18 2.69e-05 CTTGACCAAA CTGAGCGG ACCGGCTGAG chrX:11563725-11563845 63 2.92e-05 GCGAGTACAG CGGTGAGG TCGGCGAGTA chr3L:10771976-10772096 37 3.89e-05 CGCCGTGAGA GGGAgatg ggttgctgga chr2R:13028313-13028433 86 6.34e-05 CTAGGTGAAG GGGTGTGG AGAACGAGAA chr2R:23073985-23074105 44 7.85e-05 CAAACCTCAA CGGAGATG CGCTTCTCGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SKGWGMKG MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2L:16485813-16485933 1.2e-05 32_[+4]_80 chr2L:19054486-19054606 1.2e-05 29_[+4]_83 chr2R:13189338-13189458 1.2e-05 16_[+4]_96 chrX:5596661-5596781 1.2e-05 111_[+4]_1 chr2L:1556880-1557000 1.4e-05 78_[+4]_34 chr2R:22689151-22689271 2.1e-05 5_[+4]_107 chr2R:14275302-14275422 2.7e-05 40_[+4]_72 chr2R:15890897-15891017 2.7e-05 17_[+4]_95 chrX:11563725-11563845 2.9e-05 62_[+4]_50 chr3L:10771976-10772096 3.9e-05 36_[+4]_76 chr2R:13028313-13028433 6.3e-05 85_[+4]_27 chr2R:23073985-23074105 7.9e-05 43_[+4]_69 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SKGWGMKG MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF SKGWGMKG width=8 seqs=12 chr2L:16485813-16485933 ( 33) GTGAGCGG 1 chr2L:19054486-19054606 ( 30) GTGAGCGG 1 chr2R:13189338-13189458 ( 17) GGGAGCTG 1 chrX:5596661-5596781 ( 112) GGGAGCTG 1 chr2L:1556880-1557000 ( 79) GGGTGAGG 1 chr2R:22689151-22689271 ( 6) GTGTGCGG 1 chr2R:14275302-14275422 ( 41) CGGCGCGG 1 chr2R:15890897-15891017 ( 18) CTGAGCGG 1 chrX:11563725-11563845 ( 63) CGGTGAGG 1 chr3L:10771976-10772096 ( 37) GGGAGATG 1 chr2R:13028313-13028433 ( 86) GGGTGTGG 1 chr2R:23073985-23074105 ( 44) CGGAGATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SKGWGMKG MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 7345 bayes= 10.356 E= 9.4e+000 -1023 89 202 -1023 -1023 -1023 202 3 -1023 -1023 261 -1023 82 -111 -1023 3 -1023 -1023 261 -1023 1 170 -1023 -196 -1023 -1023 202 3 -1023 -1023 261 -1023 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SKGWGMKG MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 12 E= 9.4e+000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 1.000000 0.000000 0.583333 0.083333 0.000000 0.333333 0.000000 0.000000 1.000000 0.000000 0.333333 0.583333 0.000000 0.083333 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SKGWGMKG MEME-4 regular expression -------------------------------------------------------------------------------- [GC][GT]G[AT]G[CA][GT]G -------------------------------------------------------------------------------- Time 4.15 secs. ******************************************************************************** ******************************************************************************** MOTIF TTCCCCCT MEME-5 width = 8 sites = 4 llr = 46 E-value = 3.3e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTCCCCCT MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C ::a8aaa: probability G :::3:::: matrix T aa:::::a bits 2.6 2.3 * *** 2.1 * *** 1.8 ***** Relative 1.6 ******** Entropy 1.3 ******** (16.5 bits) 1.0 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel TTCCCCCT consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCCCCT MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3R:29457296-29457416 76 6.55e-06 AAGGTCGAAT TTCCCCCT ACTCGCTGGG chrM:16649-16769 74 6.55e-06 AATAAATTTA TTCCCCCT ATTCATAAAT chrM:15653-15773 21 6.55e-06 AATAAATTTA TTCCCCCT ATTTATAAAT chr2L:9494611-9494731 67 1.25e-05 TTATCCGGTT TTCGCCCT TTTCACTTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCCCCT MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3R:29457296-29457416 6.5e-06 75_[+5]_37 chrM:16649-16769 6.5e-06 73_[+5]_39 chrM:15653-15773 6.5e-06 20_[+5]_92 chr2L:9494611-9494731 1.3e-05 66_[+5]_46 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCCCCT MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTCCCCCT width=8 seqs=4 chr3R:29457296-29457416 ( 76) TTCCCCCT 1 chrM:16649-16769 ( 74) TTCCCCCT 1 chrM:15653-15773 ( 21) TTCCCCCT 1 chr2L:9494611-9494731 ( 67) TTCGCCCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCCCCT MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 7345 bayes= 10.8418 E= 3.3e+003 -865 -865 -865 162 -865 -865 -865 162 -865 247 -865 -865 -865 206 61 -865 -865 247 -865 -865 -865 247 -865 -865 -865 247 -865 -865 -865 -865 -865 162 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCCCCT MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 3.3e+003 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCCCCT MEME-5 regular expression -------------------------------------------------------------------------------- TTC[CG]CCCT -------------------------------------------------------------------------------- Time 5.10 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3L:8107185-8107305 8.29e-03 30_[+1(5.52e-06)]_82 chrM:18115-18235 1.00e+00 120 chrM:15653-15773 1.08e-01 20_[+5(6.55e-06)]_92 chrM:16649-16769 1.07e-01 73_[+5(6.55e-06)]_39 chrX:11563725-11563845 1.12e-06 31_[+3(2.53e-06)]_1_[+2(1.27e-06)]_\ 14_[+4(2.92e-05)]_50 chrM:9143-9263 9.99e-01 120 chrM:8002-8122 9.11e-01 120 chrX:5793607-5793727 7.33e-03 82_[+2(1.45e-05)]_30 chr2L:8675667-8675787 1.10e-03 14_[+3(2.72e-05)]_4_[+2(3.84e-06)]_\ 22_[+2(3.84e-06)]_56 chrX:1656608-1656728 2.52e-02 29_[+1(2.44e-05)]_83 chrX:1655993-1656113 9.47e-02 120 chrM:17644-17764 1.00e+00 120 chr2R:23073985-23074105 2.82e-03 43_[+4(7.85e-05)]_4_[+1(9.34e-05)]_\ 57 chrM:5686-5806 4.54e-01 120 chr2L:3152784-3152904 9.19e-03 12_[+2(1.85e-05)]_100 chrX:16094238-16094358 2.34e-01 120 chr3R:16533903-16534023 1.88e-02 92_[+3(9.70e-05)]_20 chr2L:16787781-16787901 3.14e-04 73_[+1(5.52e-06)]_19_[+3(3.73e-05)]_\ 12 chrM:16025-16145 1.00e+00 120 chrM:19296-19416 1.00e+00 120 chr3L:10771976-10772096 7.15e-04 30_[+4(3.89e-05)]_82 chrX:5596661-5596781 3.11e-02 111_[+4(1.22e-05)]_1 chrM:17208-17328 1.00e+00 120 chrM:13791-13911 1.00e+00 120 chrM:14771-14891 1.00e+00 120 chrM:8227-8347 9.40e-01 120 chrX:9684530-9684650 2.29e-03 47_[+2(4.33e-05)]_65 chrM:4093-4213 9.93e-01 120 chr2R:13189338-13189458 2.35e-07 7_[+4(7.85e-05)]_1_[+4(1.22e-05)]_\ [+3(7.63e-06)]_53_[+4(1.22e-05)]_9_[+1(2.44e-05)]_10 chr3L:11765774-11765894 2.62e-03 85_[+1(8.56e-06)]_27 chrM:1289-1409 8.82e-01 120 chrM:944-1064 9.78e-01 120 chr2R:13028313-13028433 1.17e-04 61_[+1(6.90e-05)]_16_[+4(6.34e-05)]_\ 9_[+3(5.04e-05)]_10 chr2L:1556880-1557000 1.22e-04 78_[+4(1.43e-05)]_16_[+2(5.00e-06)]_\ 10 chrM:15254-15374 1.00e+00 120 chrM:9548-9668 9.96e-01 120 chr3R:29457296-29457416 1.13e-06 75_[+5(6.55e-06)]_[+1(5.52e-06)]_10_\ [+2(5.16e-05)]_11 chr2L:3772001-3772121 1.57e-01 120 chr2L:7419876-7419996 1.70e-02 78_[+1(3.84e-05)]_34 chrM:10077-10197 9.85e-01 120 chr2L:19054486-19054606 5.58e-05 29_[+4(1.22e-05)]_39_[+2(9.74e-05)]_\ 17_[+3(5.04e-05)]_11 chrM:582-702 8.51e-01 120 chrM:4448-4568 9.35e-03 14_[+1(4.45e-05)]_98 chr2R:15890897-15891017 1.32e-06 17_[+4(2.69e-05)]_28_[+3(5.32e-05)]_\ 23_[+2(3.84e-06)]_6_[+2(3.84e-06)]_14 chr3L:21025855-21025975 6.97e-01 120 chrM:2364-2484 7.97e-01 120 chrM:168-288 6.33e-01 120 chr3L:19896567-19896687 2.54e-01 29_[+1(8.34e-05)]_83 chrX:7097254-7097374 1.00e-03 12_[+3(2.72e-05)]_27_[+2(5.16e-05)]_\ 65 chr2L:16485813-16485933 2.84e-06 3_[+2(1.06e-05)]_3_[+3(2.72e-05)]_\ 10_[+4(1.22e-05)]_6_[+3(7.63e-06)]_66 chrM:11931-12051 4.87e-01 120 chr3L:5360246-5360366 3.52e-03 96_[+2(6.35e-05)]_16 chr3R:27281492-27281612 6.89e-01 120 chr2L:6089110-6089230 8.18e-03 104_[+1(5.52e-06)]_8 chrM:12831-12951 5.24e-01 120 chr2R:14275302-14275422 1.36e-05 40_[+4(2.69e-05)]_41_[+4(1.16e-06)]_\ 23 chrM:5997-6117 4.12e-01 120 chr2R:6236188-6236308 5.09e-04 1_[+2(5.16e-05)]_35_[+1(5.52e-06)]_\ 68 chrM:6861-6981 8.97e-01 120 chrM:4827-4947 9.76e-01 120 chr2R:22689151-22689271 6.87e-04 5_[+4(2.12e-05)]_18_[+3(5.97e-05)]_\ 81 chrX:3780183-3780303 6.34e-02 84_[+1(6.90e-05)]_28 chrX:19697493-19697613 1.10e-04 1_[+2(1.85e-05)]_102_[+1(5.52e-06)]_\ 1 chrM:12506-12626 9.24e-01 120 chr2L:9494611-9494731 1.20e-04 66_[+5(1.25e-05)]_4_[+1(6.90e-05)]_\ 34 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c22n05.farnam.hpc.yale.internal ********************************************************************************