******************************************************************************** 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/tbx-9.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrIII:10335276-10335356 1.0000 80 chrIII:10362877-10362957 1.0000 80 chrIII:10357246-10357326 1.0000 80 chrIII:10328989-10329069 1.0000 80 chrIII:10355475-10355555 1.0000 80 chrIII:13780512-13780592 1.0000 80 chrIII:10344698-10344778 1.0000 80 chrIII:10331515-10331595 1.0000 80 chrIII:9825366-9825446 1.0000 80 chrIV:3032117-3032197 1.0000 80 chrII:11917743-11917823 1.0000 80 chrIII:10337734-10337814 1.0000 80 chrIII:1625834-1625914 1.0000 80 chrIII:12607504-12607584 1.0000 80 chrIII:7495021-7495101 1.0000 80 chrI:4645434-4645514 1.0000 80 chrIII:10327958-10328038 1.0000 80 chrII:13522408-13522488 1.0000 80 chrV:7198487-7198567 1.0000 80 chrI:7868998-7869078 1.0000 80 chrIII:10339121-10339201 1.0000 80 chrIII:10332400-10332480 1.0000 80 chrIV:8377610-8377690 1.0000 80 chrIV:9739053-9739133 1.0000 80 chrIV:419817-419897 1.0000 80 chrV:7432912-7432992 1.0000 80 chrI:13953308-13953388 1.0000 80 chrIII:10353166-10353246 1.0000 80 chrII:8441668-8441748 1.0000 80 chrII:11651088-11651168 1.0000 80 chrII:8747989-8748069 1.0000 80 chrV:20848027-20848107 1.0000 80 chrV:8513315-8513395 1.0000 80 chrI:6219774-6219854 1.0000 80 chrI:5620779-5620859 1.0000 80 chrIII:9462775-9462855 1.0000 80 chrIV:13319009-13319089 1.0000 80 chrIII:5025341-5025421 1.0000 80 chrIII:10340023-10340103 1.0000 80 chrV:6655545-6655625 1.0000 80 chrI:1157616-1157696 1.0000 80 chrIV:6325952-6326032 1.0000 80 chrIII:10360547-10360627 1.0000 80 chrIV:3297015-3297095 1.0000 80 chrIII:10332923-10333003 1.0000 80 chrV:2664671-2664751 1.0000 80 chrII:14350903-14350983 1.0000 80 chrIII:11921730-11921810 1.0000 80 chrIV:427237-427317 1.0000 80 chrII:7900254-7900334 1.0000 80 chrIV:17281345-17281425 1.0000 80 chrII:11376655-11376735 1.0000 80 chrV:6015803-6015883 1.0000 80 chrIV:396678-396758 1.0000 80 chrIII:4491488-4491568 1.0000 80 chrX:8623903-8623983 1.0000 80 chrIII:835941-836021 1.0000 80 chrX:4148381-4148461 1.0000 80 chrI:7079491-7079571 1.0000 80 chrI:7656727-7656807 1.0000 80 chrIV:7789779-7789859 1.0000 80 chrIII:13464667-13464747 1.0000 80 chrIV:7962106-7962186 1.0000 80 chrIV:11026098-11026178 1.0000 80 chrII:11759428-11759508 1.0000 80 chrIV:16400862-16400942 1.0000 80 chrIV:9440961-9441041 1.0000 80 chrIV:1711227-1711307 1.0000 80 chrIII:1616854-1616934 1.0000 80 chrII:14155766-14155846 1.0000 80 chrI:5372648-5372728 1.0000 80 chrIV:15693439-15693519 1.0000 80 chrX:9237851-9237931 1.0000 80 chrI:1698076-1698156 1.0000 80 chrII:11545467-11545547 1.0000 80 chrI:2514262-2514342 1.0000 80 chrV:14833315-14833395 1.0000 80 chrIV:16776115-16776195 1.0000 80 chrIII:10746468-10746548 1.0000 80 chrIV:12086651-12086731 1.0000 80 chrV:12510126-12510206 1.0000 80 chrV:1875703-1875783 1.0000 80 chrIII:5230657-5230737 1.0000 80 chrIV:9477710-9477790 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_tbx-9/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/tbx-9.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= 84 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= 6720 N= 84 sample: seed= 0 hsfrac= 0 searchsize= 6720 norand= no csites= 1000 Letter frequencies in dataset: A 0.272 C 0.212 G 0.214 T 0.302 Background letter frequencies (from file dataset with add-one prior applied): A 0.272 C 0.212 G 0.214 T 0.302 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TGHGGCAG MEME-1 width = 8 sites = 11 llr = 99 E-value = 2.7e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGHGGCAG MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::4::2a: pos.-specific C ::4::5:: probability G 1a:aa2:a matrix T 9:3::1:: bits 2.2 * ** * 2.0 * ** * 1.8 * ** ** 1.6 * ** ** Relative 1.3 ** ** ** Entropy 1.1 ** ** ** (12.9 bits) 0.9 ** ** ** 0.7 ** ** ** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TGAGGCAG consensus C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGHGGCAG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrI:5620779-5620859 59 7.74e-06 TTTTGCACAT TGCGGCAG AAAGGTGAAC chrIII:9825366-9825446 19 7.74e-06 TTTGCTCGAA TGCGGCAG CCATTTCTTC chrIII:5230657-5230737 44 1.77e-05 TAAGCTCTGT TGAGGCAG CGAACTCTAG chrIV:7962106-7962186 10 2.87e-05 ATGAATTTT TGTGGCAG ATTTTATTCA chrV:8513315-8513395 32 2.87e-05 ATTCGATACA TGTGGCAG GCTACAGTTT chrIV:1711227-1711307 35 3.65e-05 TCGCATATTC TGCGGGAG CCTCGAACAA chrIII:1625834-1625914 15 5.65e-05 CTTTTTGCTG TGAGGGAG GTCGCCATGG chrV:20848027-20848107 67 6.92e-05 TAGTATTGGA TGAGGAAG GAATCC chrI:2514262-2514342 71 1.00e-04 TGGTGTTGCG GGCGGCAG GC chrIII:10332400-10332480 25 1.00e-04 TCGGAAGTCG TGTGGAAG TCGTTGCACA chrII:13522408-13522488 67 1.32e-04 TTCCTTCATT TGAGGTAG AAAACT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGHGGCAG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrI:5620779-5620859 7.7e-06 58_[+1]_14 chrIII:9825366-9825446 7.7e-06 18_[+1]_54 chrIII:5230657-5230737 1.8e-05 43_[+1]_29 chrIV:7962106-7962186 2.9e-05 9_[+1]_63 chrV:8513315-8513395 2.9e-05 31_[+1]_41 chrIV:1711227-1711307 3.7e-05 34_[+1]_38 chrIII:1625834-1625914 5.6e-05 14_[+1]_58 chrV:20848027-20848107 6.9e-05 66_[+1]_6 chrI:2514262-2514342 0.0001 70_[+1]_2 chrIII:10332400-10332480 0.0001 24_[+1]_48 chrII:13522408-13522488 0.00013 66_[+1]_6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGHGGCAG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGHGGCAG width=8 seqs=11 chrI:5620779-5620859 ( 59) TGCGGCAG 1 chrIII:9825366-9825446 ( 19) TGCGGCAG 1 chrIII:5230657-5230737 ( 44) TGAGGCAG 1 chrIV:7962106-7962186 ( 10) TGTGGCAG 1 chrV:8513315-8513395 ( 32) TGTGGCAG 1 chrIV:1711227-1711307 ( 35) TGCGGGAG 1 chrIII:1625834-1625914 ( 15) TGAGGGAG 1 chrV:20848027-20848107 ( 67) TGAGGAAG 1 chrI:2514262-2514342 ( 71) GGCGGCAG 1 chrIII:10332400-10332480 ( 25) TGTGGAAG 1 chrII:13522408-13522488 ( 67) TGAGGTAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGHGGCAG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 6132 bayes= 9.47578 E= 2.7e+003 -1010 -1010 -123 159 -1010 -1010 222 -1010 42 78 -1010 -15 -1010 -1010 222 -1010 -1010 -1010 222 -1010 -58 137 -24 -173 188 -1010 -1010 -1010 -1010 -1010 222 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGHGGCAG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 11 E= 2.7e+003 0.000000 0.000000 0.090909 0.909091 0.000000 0.000000 1.000000 0.000000 0.363636 0.363636 0.000000 0.272727 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.181818 0.545455 0.181818 0.090909 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGHGGCAG MEME-1 regular expression -------------------------------------------------------------------------------- TG[ACT]GGCAG -------------------------------------------------------------------------------- Time 1.56 secs. ******************************************************************************** ******************************************************************************** MOTIF TTCSYSCA MEME-2 width = 8 sites = 20 llr = 154 E-value = 1.2e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTCSYSCA MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::::1:7 pos.-specific C :1a555a2 probability G :::6:3:2 matrix T aa::52:: bits 2.2 * * 2.0 * * 1.8 * * * 1.6 *** * Relative 1.3 **** * Entropy 1.1 **** * (11.1 bits) 0.9 ***** ** 0.7 ***** ** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TTCGCCCA consensus CTG sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCSYSCA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:5230657-5230737 2 1.07e-05 C TTCGCCCA AAAGTAATTC chrV:6015803-6015883 56 2.13e-05 GCTACTGAAA TTCCCCCA ACTTTCCGTT chrIV:9739053-9739133 58 3.66e-05 AGTTATCGAG TTCGTCCA GGAGATACTG chrV:14833315-14833395 50 4.74e-05 CCCGTCTATT TTCGCGCA TCGTATCGAC chrIV:15693439-15693519 39 4.74e-05 GGCGCCGGGC TTCGCGCA TTTGTTTTGA chrII:14155766-14155846 28 7.33e-05 AGAATGGGAG TTCCCGCA TTCTTCAGAT chrIII:11921730-11921810 45 1.04e-04 AAGCTCACGA TTCCTGCA CACAAGTCGA chrII:11651088-11651168 25 1.04e-04 TTTCGGCCTG TTCCTGCA TAGCTTCTTC chrIII:4491488-4491568 16 1.19e-04 ATTTGATATA TTCGCTCA AAAGTCAGTT chrIV:6325952-6326032 35 1.51e-04 GTCTGTATGC TTCGCCCC CAATTTTTGT chrI:1698076-1698156 24 1.73e-04 ACAATGTCGC TTCGTTCA gtgtgtgtgt chrIV:9440961-9441041 41 1.73e-04 AATGCACAAA TTCGTTCA CGCGCGAATT chrIV:16776115-16776195 30 1.90e-04 GGGGGTTCGA TTCCCCCC GAACGCAGAT chrIII:9462775-9462855 37 1.90e-04 AGATCATCTT TTCCCCCC ATTTCTTTTT chrII:13522408-13522488 57 2.35e-04 AATTTAAAAT TTCCTTCA TTTGAGGTAG chrIV:3032117-3032197 29 2.35e-04 ATGTTTCCGG TTCGTCCG CCCGAGAGCA chrIII:10332400-10332480 64 2.76e-04 TCGCCAATTG TTCCTCCG AGAGCATCT chrIII:10331515-10331595 58 3.41e-04 GGATTTATTA TTCCTGCG GATTCACTGC chrI:5620779-5620859 1 4.77e-04 . TTCGTACA ATGATTCGCA chrIII:10337734-10337814 63 4.77e-04 TCAGATAGGC TCCGCCCA TTTTGATTCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCSYSCA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:5230657-5230737 1.1e-05 1_[+2]_71 chrV:6015803-6015883 2.1e-05 55_[+2]_17 chrIV:9739053-9739133 3.7e-05 57_[+2]_15 chrV:14833315-14833395 4.7e-05 49_[+2]_23 chrIV:15693439-15693519 4.7e-05 38_[+2]_34 chrII:14155766-14155846 7.3e-05 27_[+2]_45 chrIII:11921730-11921810 0.0001 44_[+2]_28 chrII:11651088-11651168 0.0001 24_[+2]_48 chrIII:4491488-4491568 0.00012 15_[+2]_57 chrIV:6325952-6326032 0.00015 34_[+2]_38 chrI:1698076-1698156 0.00017 23_[+2]_49 chrIV:9440961-9441041 0.00017 40_[+2]_32 chrIV:16776115-16776195 0.00019 29_[+2]_43 chrIII:9462775-9462855 0.00019 36_[+2]_36 chrII:13522408-13522488 0.00024 56_[+2]_16 chrIV:3032117-3032197 0.00024 28_[+2]_44 chrIII:10332400-10332480 0.00028 63_[+2]_9 chrIII:10331515-10331595 0.00034 57_[+2]_15 chrI:5620779-5620859 0.00048 [+2]_72 chrIII:10337734-10337814 0.00048 62_[+2]_10 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCSYSCA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTCSYSCA width=8 seqs=20 chrIII:5230657-5230737 ( 2) TTCGCCCA 1 chrV:6015803-6015883 ( 56) TTCCCCCA 1 chrIV:9739053-9739133 ( 58) TTCGTCCA 1 chrV:14833315-14833395 ( 50) TTCGCGCA 1 chrIV:15693439-15693519 ( 39) TTCGCGCA 1 chrII:14155766-14155846 ( 28) TTCCCGCA 1 chrIII:11921730-11921810 ( 45) TTCCTGCA 1 chrII:11651088-11651168 ( 25) TTCCTGCA 1 chrIII:4491488-4491568 ( 16) TTCGCTCA 1 chrIV:6325952-6326032 ( 35) TTCGCCCC 1 chrI:1698076-1698156 ( 24) TTCGTTCA 1 chrIV:9440961-9441041 ( 41) TTCGTTCA 1 chrIV:16776115-16776195 ( 30) TTCCCCCC 1 chrIII:9462775-9462855 ( 37) TTCCCCCC 1 chrII:13522408-13522488 ( 57) TTCCTTCA 1 chrIV:3032117-3032197 ( 29) TTCGTCCG 1 chrIII:10332400-10332480 ( 64) TTCCTCCG 1 chrIII:10331515-10331595 ( 58) TTCCTGCG 1 chrI:5620779-5620859 ( 1) TTCGTACA 1 chrIII:10337734-10337814 ( 63) TCCGCCCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCSYSCA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 6132 bayes= 10.0954 E= 1.2e+004 -1097 -1097 -1097 173 -1097 -208 -1097 165 -1097 224 -1097 -1097 -1097 109 136 -1097 -1097 124 -1097 73 -244 109 49 -60 -1097 224 -1097 -1097 136 -50 -51 -1097 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCSYSCA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 1.2e+004 0.000000 0.000000 0.000000 1.000000 0.000000 0.050000 0.000000 0.950000 0.000000 1.000000 0.000000 0.000000 0.000000 0.450000 0.550000 0.000000 0.000000 0.500000 0.000000 0.500000 0.050000 0.450000 0.300000 0.200000 0.000000 1.000000 0.000000 0.000000 0.700000 0.150000 0.150000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCSYSCA MEME-2 regular expression -------------------------------------------------------------------------------- TTC[GC][CT][CGT]CA -------------------------------------------------------------------------------- Time 2.42 secs. ******************************************************************************** ******************************************************************************** MOTIF ACCACGCC MEME-3 width = 8 sites = 2 llr = 24 E-value = 4.6e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif ACCACGCC MEME-3 Description -------------------------------------------------------------------------------- Simplified A a::a:::: pos.-specific C :aa:a:aa probability G :::::a:: matrix T :::::::: bits 2.2 ** **** 2.0 ** **** 1.8 ******** 1.6 ******** Relative 1.3 ******** Entropy 1.1 ******** (17.2 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel ACCACGCC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACCACGCC MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrV:14833315-14833395 7 6.78e-06 GTGACC ACCACGCC GGCCATCTGC chrII:14350903-14350983 27 6.78e-06 CAACCGACGG ACCACGCC TGGGCAGCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACCACGCC MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:14833315-14833395 6.8e-06 6_[+3]_66 chrII:14350903-14350983 6.8e-06 26_[+3]_46 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACCACGCC MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ACCACGCC width=8 seqs=2 chrV:14833315-14833395 ( 7) ACCACGCC 1 chrII:14350903-14350983 ( 27) ACCACGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACCACGCC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 6132 bayes= 11.5817 E= 4.6e+003 187 -765 -765 -765 -765 223 -765 -765 -765 223 -765 -765 187 -765 -765 -765 -765 223 -765 -765 -765 -765 222 -765 -765 223 -765 -765 -765 223 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACCACGCC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 4.6e+003 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACCACGCC MEME-3 regular expression -------------------------------------------------------------------------------- ACCACGCC -------------------------------------------------------------------------------- Time 3.26 secs. ******************************************************************************** ******************************************************************************** MOTIF GCAGMAGC MEME-4 width = 8 sites = 2 llr = 22 E-value = 5.2e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCAGMAGC MEME-4 Description -------------------------------------------------------------------------------- Simplified A ::a:5a:: pos.-specific C :a::5::a probability G a::a::a: matrix T :::::::: bits 2.2 ** * ** 2.0 ** * ** 1.8 **** *** 1.6 **** *** Relative 1.3 **** *** Entropy 1.1 ******** (16.0 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GCAGAAGC consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCAGMAGC MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:1625834-1625914 52 6.91e-06 GCGGCTCTCT GCAGCAGC TTtttctcac chrI:6219774-6219854 1 1.58e-05 . GCAGAAGC GAGTCACAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCAGMAGC MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:1625834-1625914 6.9e-06 51_[+4]_21 chrI:6219774-6219854 1.6e-05 [+4]_72 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCAGMAGC MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCAGMAGC width=8 seqs=2 chrIII:1625834-1625914 ( 52) GCAGCAGC 1 chrI:6219774-6219854 ( 1) GCAGAAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCAGMAGC MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 6132 bayes= 10.7333 E= 5.2e+004 -765 -765 222 -765 -765 223 -765 -765 187 -765 -765 -765 -765 -765 222 -765 87 124 -765 -765 187 -765 -765 -765 -765 -765 222 -765 -765 223 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCAGMAGC MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 5.2e+004 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCAGMAGC MEME-4 regular expression -------------------------------------------------------------------------------- GCAG[AC]AGC -------------------------------------------------------------------------------- Time 4.13 secs. ******************************************************************************** ******************************************************************************** MOTIF CAGGAACT MEME-5 width = 8 sites = 4 llr = 43 E-value = 2.2e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CAGGAACT MEME-5 Description -------------------------------------------------------------------------------- Simplified A :a3:aa:: pos.-specific C a:::::a: probability G ::8a:::: matrix T :::::::a bits 2.2 * * * 2.0 * * * 1.8 ** ***** 1.6 ** ***** Relative 1.3 ******** Entropy 1.1 ******** (15.4 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CAGGAACT consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGGAACT MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:9237851-9237931 30 1.25e-05 CCCATACCTC CAGGAACT TTTTTTCGAA chrIV:13319009-13319089 64 1.25e-05 AGGCGTTTTG CAGGAACT TATTTAGTA chrV:8513315-8513395 56 1.25e-05 GTTTCTGGTT CAGGAACT CCACATTTTA chrIV:9739053-9739133 15 2.84e-05 TTTTATAGGT CAAGAACT CTGGATACCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGGAACT MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:9237851-9237931 1.3e-05 29_[+5]_43 chrIV:13319009-13319089 1.3e-05 63_[+5]_9 chrV:8513315-8513395 1.3e-05 55_[+5]_17 chrIV:9739053-9739133 2.8e-05 14_[+5]_58 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGGAACT MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CAGGAACT width=8 seqs=4 chrX:9237851-9237931 ( 30) CAGGAACT 1 chrIV:13319009-13319089 ( 64) CAGGAACT 1 chrV:8513315-8513395 ( 56) CAGGAACT 1 chrIV:9739053-9739133 ( 15) CAAGAACT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGGAACT MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 6132 bayes= 10.5812 E= 2.2e+004 -865 224 -865 -865 188 -865 -865 -865 -12 -865 181 -865 -865 -865 222 -865 188 -865 -865 -865 188 -865 -865 -865 -865 224 -865 -865 -865 -865 -865 172 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGGAACT MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 2.2e+004 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGGAACT MEME-5 regular expression -------------------------------------------------------------------------------- CA[GA]GAACT -------------------------------------------------------------------------------- Time 5.07 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:10335276-10335356 5.77e-01 80 chrIII:10362877-10362957 9.87e-01 80 chrIII:10357246-10357326 1.01e-01 21_[+4(6.96e-05)]_51 chrIII:10328989-10329069 3.80e-01 80 chrIII:10355475-10355555 9.46e-01 80 chrIII:13780512-13780592 9.95e-01 80 chrIII:10344698-10344778 5.65e-01 80 chrIII:10331515-10331595 3.96e-01 80 chrIII:9825366-9825446 4.32e-04 18_[+1(7.74e-06)]_54 chrIV:3032117-3032197 5.01e-01 80 chrII:11917743-11917823 9.13e-01 80 chrIII:10337734-10337814 1.14e-01 80 chrIII:1625834-1625914 1.42e-04 14_[+1(5.65e-05)]_29_[+4(6.91e-06)]_\ 21 chrIII:12607504-12607584 7.57e-01 80 chrIII:7495021-7495101 2.73e-01 80 chrI:4645434-4645514 6.21e-01 80 chrIII:10327958-10328038 4.99e-01 80 chrII:13522408-13522488 5.80e-02 80 chrV:7198487-7198567 9.05e-01 80 chrI:7868998-7869078 4.89e-01 80 chrIII:10339121-10339201 5.76e-01 80 chrIII:10332400-10332480 1.67e-02 80 chrIV:8377610-8377690 1.30e-01 80 chrIV:9739053-9739133 1.84e-03 14_[+5(2.84e-05)]_35_[+2(3.66e-05)]_\ 15 chrIV:419817-419897 9.17e-01 80 chrV:7432912-7432992 3.25e-01 80 chrI:13953308-13953388 6.55e-01 80 chrIII:10353166-10353246 3.73e-01 80 chrII:8441668-8441748 7.92e-01 80 chrII:11651088-11651168 3.17e-01 80 chrII:8747989-8748069 3.07e-01 80 chrV:20848027-20848107 3.46e-02 66_[+1(6.92e-05)]_6 chrV:8513315-8513395 2.07e-04 31_[+1(2.87e-05)]_16_[+5(1.25e-05)]_\ 17 chrI:6219774-6219854 2.02e-03 [+4(1.58e-05)]_72 chrI:5620779-5620859 2.34e-03 58_[+1(7.74e-06)]_14 chrIII:9462775-9462855 3.74e-01 80 chrIV:13319009-13319089 1.97e-02 63_[+5(1.25e-05)]_9 chrIII:5025341-5025421 9.73e-01 80 chrIII:10340023-10340103 8.80e-01 80 chrV:6655545-6655625 9.29e-01 80 chrI:1157616-1157696 3.91e-01 80 chrIV:6325952-6326032 2.83e-01 80 chrIII:10360547-10360627 3.07e-01 80 chrIV:3297015-3297095 1.76e-02 7_[+4(6.91e-06)]_65 chrIII:10332923-10333003 4.85e-01 80 chrV:2664671-2664751 2.71e-01 80 chrII:14350903-14350983 1.79e-02 26_[+3(6.78e-06)]_46 chrIII:11921730-11921810 3.51e-02 80 chrIV:427237-427317 6.57e-01 80 chrII:7900254-7900334 9.93e-01 80 chrIV:17281345-17281425 1.44e-01 80 chrII:11376655-11376735 8.72e-01 80 chrV:6015803-6015883 1.09e-01 55_[+2(2.13e-05)]_17 chrIV:396678-396758 7.87e-01 80 chrIII:4491488-4491568 3.02e-01 80 chrX:8623903-8623983 6.34e-01 80 chrIII:835941-836021 7.91e-01 80 chrX:4148381-4148461 9.76e-01 80 chrI:7079491-7079571 7.92e-01 80 chrI:7656727-7656807 8.70e-01 80 chrIV:7789779-7789859 8.74e-01 80 chrIII:13464667-13464747 6.88e-01 80 chrIV:7962106-7962186 4.14e-02 9_[+1(2.87e-05)]_63 chrIV:11026098-11026178 8.41e-01 80 chrII:11759428-11759508 6.34e-01 80 chrIV:16400862-16400942 3.92e-01 80 chrIV:9440961-9441041 1.12e-01 80 chrIV:1711227-1711307 7.11e-03 34_[+1(3.65e-05)]_38 chrIII:1616854-1616934 7.62e-01 80 chrII:14155766-14155846 1.40e-01 27_[+2(7.33e-05)]_45 chrI:5372648-5372728 8.56e-01 80 chrIV:15693439-15693519 2.39e-02 38_[+2(4.74e-05)]_34 chrX:9237851-9237931 1.71e-02 29_[+5(1.25e-05)]_43 chrI:1698076-1698156 3.81e-01 80 chrII:11545467-11545547 4.60e-01 80 chrI:2514262-2514342 3.91e-02 80 chrV:14833315-14833395 2.07e-03 6_[+3(6.78e-06)]_35_[+2(4.74e-05)]_\ 23 chrIV:16776115-16776195 2.55e-01 80 chrIII:10746468-10746548 7.72e-01 80 chrIV:12086651-12086731 5.44e-01 80 chrV:12510126-12510206 1.00e+00 80 chrV:1875703-1875783 1.70e-01 80 chrIII:5230657-5230737 9.31e-05 1_[+2(1.07e-05)]_34_[+1(1.77e-05)]_\ 29 chrIV:9477710-9477790 1.45e-01 80 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n12.farnam.hpc.yale.internal ********************************************************************************