******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.12.0 (Release date: Tue Jun 27 16:22:50 2017 -0700) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme-suite.org . This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://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 ******************************************************************************** DATAFILE= /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--RPD3/seqs-sampled ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrXVI:770738-771111 1.0000 100 chrVIII:388768-389030 1.0000 100 chrXVI:453913-454409 1.0000 100 chrIX:386653-386905 1.0000 100 chrIV:1194557-1195053 1.0000 100 chrXIV:297676-298211 1.0000 100 chrXI:258579-258959 1.0000 100 chrVII:558160-558656 1.0000 100 chrIV:969766-970262 1.0000 100 chrXV:977982-978207 1.0000 100 chrIV:1269877-1270378 1.0000 100 chrIII:224812-225308 1.0000 100 chrXIII:420067-420831 1.0000 100 chrII:266239-266614 1.0000 100 chrVII:398610-399633 1.0000 100 chrXV:274513-274889 1.0000 100 chrXV:619891-620328 1.0000 100 chrIV:579405-580667 1.0000 100 chrXII:904018-904142 1.0000 100 chrXV:282015-282336 1.0000 100 chrVI:220887-221383 1.0000 100 chrV:61035-62113 1.0000 100 chrXV:288012-288400 1.0000 100 chrVII:559363-559859 1.0000 100 chrVII:480671-483006 1.0000 100 chrV:106598-106825 1.0000 100 chrXIII:20131-20627 1.0000 100 chrXII:795762-796258 1.0000 100 chrIV:491581-492048 1.0000 100 chrVII:784768-785264 1.0000 100 chrV:138514-140452 1.0000 100 chrXIII:372349-372608 1.0000 100 chrXII:1012064-1012523 1.0000 100 chrVIII:237706-238093 1.0000 100 chrII:405708-406154 1.0000 100 chrX:526497-526597 1.0000 100 chrIII:68374-68684 1.0000 100 chrIII:57859-58355 1.0000 100 chrVIII:75379-75990 1.0000 100 chrXV:967130-967626 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chrIV:1461581-1461884 1.0000 100 chrX:123456-123556 1.0000 100 chrXVI:645625-645865 1.0000 100 chrIV:216426-216922 1.0000 100 chrVII:878522-878963 1.0000 100 chrXIII:162182-162486 1.0000 100 chrXV:29710-29931 1.0000 100 chrXVI:435772-436119 1.0000 100 chrII:477400-477847 1.0000 100 chrIII:142607-142925 1.0000 100 chrXII:656802-657129 1.0000 100 chrXV:779911-781003 1.0000 100 chrXI:141618-142114 1.0000 100 chrVII:533980-534467 1.0000 100 chrXIV:104660-105030 1.0000 100 chrX:227790-227890 1.0000 100 chrIII:23690-24186 1.0000 100 chrXVI:901633-902206 1.0000 100 chrXVI:286360-286585 1.0000 100 chrXI:519892-520057 1.0000 100 chrV:237599-238095 1.0000 100 chrXV:624051-624547 1.0000 100 chrIV:1360108-1360684 1.0000 100 chrXVI:433770-434266 1.0000 100 chrXV:479273-479769 1.0000 100 chrXVI:692909-693405 1.0000 100 chrIV:1080559-1080888 1.0000 100 chrXV:87375-87980 1.0000 100 chrXII:80746-80948 1.0000 100 chrXV:903892-904236 1.0000 100 chrII:466617-466906 1.0000 100 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--RPD3/seqs-sampled -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--RPD3/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--RPD3/background -dna -revcomp -nostatus model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 6 maxw= 30 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 545 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 54500 N= 545 shuffle= -1 strands: + - sample: seed= 0 ctfrac= -1 maxwords= -1 Letter frequencies in dataset: A 0.301 C 0.199 G 0.199 T 0.301 Background letter frequencies (from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--RPD3/background): A 0.309 C 0.191 G 0.191 T 0.309 ******************************************************************************** ******************************************************************************** MOTIF YAATCDDRAGGTCVBGGGTTCGABYCCCV MEME-1 width = 29 sites = 46 llr = 970 E-value = 8.2e-182 ******************************************************************************** -------------------------------------------------------------------------------- Motif YAATCDDRAGGTCVBGGGTTCGABYCCCV MEME-1 Description -------------------------------------------------------------------------------- Simplified A 178::3258131:3:12::::2a1::1:3 pos.-specific C 32:2811::1:17432::::a::35a773 probability G :1:22444287::2377a:::8:2:::33 matrix T 5117:231:1:8313:1:aa:::45:21: bits 2.4 * * * 2.1 * * * 1.9 * * * 1.7 * **** * * Relative 1.4 * * ****** * Entropy 1.2 * ** * ****** * * (30.4 bits) 1.0 * * *** * ******** **** 0.7 * * ***** ******** **** 0.5 **** ****** ******** ***** 0.2 ***************************** 0.0 ----------------------------- Multilevel TAATCGGAAGGTCCTGGGTTCGATCCCCC consensus C ATGG A TACC A CT GA sequence TA GG G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YAATCDDRAGGTCVBGGGTTCGABYCCCV MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ----------------------------- chrVI:226563-226912 - 10 4.98e-14 GTATGACTCT TAATCATAAGGTTAGGGGTTCGAGCCCCC TACAGGGCT chrV:435639-435979 - 2 4.98e-14 GTATGACTCT TAATCATAAGGTTAGGGGTTCGAGCCCCC T chrVII:185590-185910 - 23 4.98e-14 GTATGACTCT TAATCATAAGGTTAGGGGTTCGAGCCCCC TACAGGGCTA chrVII:876249-876641 + 34 4.98e-14 GTATGACTCT TAATCATAAGGTTAGGGGTTCGAGCCCCC TACAGGGCTT chrVII:122111-122482 + 58 4.98e-14 GTATGACTCT TAATCATAAGGTTAGGGGTTCGAGCCCCC TACAGGGCTA chrIV:1201591-1201956 + 62 4.98e-14 GTATGACTCT TAATCATAAGGTTAGGGGTTCGAGCCCCC TACAGGGCTA chrVII:828564-828960 - 20 4.92e-13 GTCTGACTTC TAATCAGAAGATTATGGGTTCGACCCCCA TCGTGAGTGC chrIV:568741-569155 + 18 4.92e-13 GTCTGACTTC TAATCAGAAGATTATGGGTTCGACCCCCA TCGTGAGTGC chrXIII:747744-748127 - 16 4.92e-13 GTCTGACTTC TAATCAGAAGATTATGGGTTCGACCCCCA TCGTGAGTGT chrII:405708-406154 + 31 4.92e-13 GTCTGACTTC TAATCAGAAGATTATGGGTTCGACCCCCA TCGTGAGTGC chrXIV:631742-632026 - 21 6.66e-12 TCTCGCTTAG GGTGCGGGAGGTCCCGGGTTCGAGTCCCG GCTCGCCCCC chrI:166169-166431 + 52 1.23e-11 GCTTCCCTTG CAAGGAAGAGGTCATCGGTTCGATTCCGG TTGCGTCCAA chrVII:328447-328812 + 38 2.20e-11 CATCACGCTT TCACCGTGGAGACCGGGGTTCGACTCCCC GTATCGGAGT chrXII:797047-797362 + 58 2.20e-11 CATCACGCTT TCACCGTGGAGACCGGGGTTCGACTCCCC GTATCGGAGA chrVII:541702-542100 + 33 2.20e-11 CATCACGCTT TCACCGTGGAGACCGGGGTTCGACTCCCC GTATCGGAGT chrXIII:290645-290987 + 69 2.20e-11 CATCACGCTT TCACCGTGGAGACCGGGGTTCGACTCCCC GTA chrIV:992708-992995 + 64 5.94e-11 TCCAACGTTG CCATCGTTGGGCCCCCGGTTCGATTCCGG GCTTGCGC chrXII:875227-875602 + 70 5.94e-11 TTAAGCAAGG ATACCGAAATGTCAGGGGTTCGAGCCCCC TA chrXV:438515-438873 + 57 5.94e-11 TTAAGCAAGG ATACCGAAATGTCAGGGGTTCGAGCCCCC TATGAGGAGT chrXV:282015-282336 + 72 5.94e-11 TCCAACGTTG CCATCGTTGGGCCCCCGGTTCGATTCCGG chrX:422781-422881 + 72 6.60e-11 GTCAGTCTCA TAATCTGAAGGTCGAGAGTTCGAACCTCC chrIV:1175728-1176018 + 41 6.60e-11 GTCAGTCTCA TAATCTGAAGGTCGAGAGTTCGAACCTCC CCTGGAGCAT chrVIII:388768-389030 - 53 6.60e-11 GAAGACAAAG CATGCGAGAGGCCCTGGGTTCAATTCCCA GCTCGCCCCA chrVII:440453-441015 - 41 9.02e-11 TTCGGTCAAG TTATCTGGAGGTCCTGTGTTCGATCCACA GAATTCGCAT chrVIII:237706-238093 - 8 9.02e-11 TTCGGTCAAG TTATCTGGAGGTCCTGTGTTCGATCCACA GAATTCG chrXIV:102588-102924 + 46 1.11e-10 GTGCGACTGT TAATCGCAAGATCGTGAGTTCAACCCTCA CTGGGGTCGT chrVI:137313-137683 - 47 1.11e-10 GTGCGACTGT TAATCGCAAGATCGTGAGTTCAACCCTCA CTGGGGTCGT chrXVI:810561-810840 + 62 1.11e-10 GTGCGACTGT TAATCGCAAGATCGTGAGTTCAACCCTCA CTGGGGTCGT chrXII:656802-657129 - 28 1.81e-10 GCTCCCTTAG CATGGGAGAGGTCTCCGGTTCGATTCCGG ACTCGTCCAA chrVII:774206-774565 + 49 1.81e-10 GCTCCCTTAG CATGGGAGAGGTCTCCGGTTCGATTCCGG ACTCGTCCAA chrVIII:146110-146412 - 40 1.81e-10 GCTCCCTTAG CATGGGAGAGGTCTCCGGTTCGATTCCGG ACTCGTCCAA chrIV:1095253-1095599 - 3 3.51e-10 TTTGGTCAAG ATATCTGGAGGTCCTGTGTTCGATCCACA GA chrXIV:104660-105030 + 45 3.84e-10 GCCACACTAG TAATGTGGAGATCATCGGTTCAAATCCGA TTGGAAGCAT chrII:266239-266614 + 37 3.84e-10 GCCACACTAG TAATGTGGAGATCATCGGTTCAAATCCGA TTGGAAGCAT chrXIII:168678-169075 + 20 4.21e-10 TATCACTACG AAATCTTGAGATCGGGCGTTCGACTCGCC CCCGGGAGAT chrX:354115-354215 + 59 4.21e-10 TACCACTACG AAATCTTGAGATCGGGCGTTCGACTCGCC CCCGGGAGAT chrVII:878522-878963 - 27 1.09e-09 AATAAGATTG CAATCGAAGGGTTGCAGGTTCAATTCCTG TCCGTTTCAT chrXVI:56010-56419 - 14 1.09e-09 AATAAGATTG CAATCGAAGGGTTGCAGGTTCAATTCCTG TCCGTTTCAA chrVII:823328-823692 + 58 1.28e-09 ATCTGCTTAA CACGCAGAACGTCCCCAGTTCGATCCTGG GCGAAATCAT chrXIII:372349-372608 - 26 1.28e-09 ATCTGCTTAA CACGCAGAACGTCCCCAGTTCGATCCTGG GCGAAATCAT chrIV:645025-645398 - 1 2.06e-09 CTTTCGGTTT TGATCCGGACAACCCCGGTTCGAATCCGG chrXII:374203-374553 + 62 7.56e-09 GTCTGGCTAC GAACCAGAAGATTCCAGGTTCAAGTCCTG GCGGGGAAGA chrXVI:744132-744510 + 47 1.44e-08 GTTGCACTTG TAATGCAAAGGTCGTTAGTTCAATTCTGA CAGGTGGCAA chrXVI:435772-436119 - 7 2.06e-08 AGCAGATTGC AAATCTGTTGGTCCTTAGTTCGATCCTGA GTGCGA chrXII:818493-818794 + 50 3.07e-08 TGCATTCTTC CGGTGGCTGTGATCCGGGTTCGAGTCCCG GGAGGAGCTT chrXV:594244-594562 - 10 3.82e-08 TTTATGCTTC CCAAGCATGAGGCCCGGGTTCGATTCCCG GCTTGCGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YAATCDDRAGGTCVBGGGTTCGABYCCCV MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrVI:226563-226912 5e-14 9_[-1]_62 chrV:435639-435979 5e-14 1_[-1]_70 chrVII:185590-185910 5e-14 22_[-1]_49 chrVII:876249-876641 5e-14 33_[+1]_38 chrVII:122111-122482 5e-14 57_[+1]_14 chrIV:1201591-1201956 5e-14 61_[+1]_10 chrVII:828564-828960 4.9e-13 19_[-1]_52 chrIV:568741-569155 4.9e-13 17_[+1]_54 chrXIII:747744-748127 4.9e-13 15_[-1]_56 chrII:405708-406154 4.9e-13 30_[+1]_41 chrXIV:631742-632026 6.7e-12 20_[-1]_51 chrI:166169-166431 1.2e-11 51_[+1]_20 chrVII:328447-328812 2.2e-11 37_[+1]_34 chrXII:797047-797362 2.2e-11 57_[+1]_14 chrVII:541702-542100 2.2e-11 32_[+1]_39 chrXIII:290645-290987 2.2e-11 68_[+1]_3 chrIV:992708-992995 5.9e-11 63_[+1]_8 chrXII:875227-875602 5.9e-11 69_[+1]_2 chrXV:438515-438873 5.9e-11 56_[+1]_15 chrXV:282015-282336 5.9e-11 71_[+1] chrX:422781-422881 6.6e-11 71_[+1] chrIV:1175728-1176018 6.6e-11 40_[+1]_31 chrVIII:388768-389030 6.6e-11 52_[-1]_19 chrVII:440453-441015 9e-11 40_[-1]_31 chrVIII:237706-238093 9e-11 7_[-1]_64 chrXIV:102588-102924 1.1e-10 45_[+1]_26 chrVI:137313-137683 1.1e-10 46_[-1]_25 chrXVI:810561-810840 1.1e-10 61_[+1]_10 chrXII:656802-657129 1.8e-10 27_[-1]_44 chrVII:774206-774565 1.8e-10 48_[+1]_23 chrVIII:146110-146412 1.8e-10 39_[-1]_32 chrIV:1095253-1095599 3.5e-10 2_[-1]_69 chrXIV:104660-105030 3.8e-10 44_[+1]_27 chrII:266239-266614 3.8e-10 36_[+1]_35 chrXIII:168678-169075 4.2e-10 19_[+1]_52 chrX:354115-354215 4.2e-10 58_[+1]_13 chrVII:878522-878963 1.1e-09 26_[-1]_45 chrXVI:56010-56419 1.1e-09 13_[-1]_58 chrVII:823328-823692 1.3e-09 57_[+1]_14 chrXIII:372349-372608 1.3e-09 25_[-1]_46 chrIV:645025-645398 2.1e-09 [-1]_71 chrXII:374203-374553 7.6e-09 61_[+1]_10 chrXVI:744132-744510 1.4e-08 46_[+1]_25 chrXVI:435772-436119 2.1e-08 6_[-1]_65 chrXII:818493-818794 3.1e-08 49_[+1]_22 chrXV:594244-594562 3.8e-08 9_[-1]_62 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YAATCDDRAGGTCVBGGGTTCGABYCCCV MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF YAATCDDRAGGTCVBGGGTTCGABYCCCV width=29 seqs=46 chrVI:226563-226912 ( 10) TAATCATAAGGTTAGGGGTTCGAGCCCCC 1 chrV:435639-435979 ( 2) TAATCATAAGGTTAGGGGTTCGAGCCCCC 1 chrVII:185590-185910 ( 23) TAATCATAAGGTTAGGGGTTCGAGCCCCC 1 chrVII:876249-876641 ( 34) TAATCATAAGGTTAGGGGTTCGAGCCCCC 1 chrVII:122111-122482 ( 58) TAATCATAAGGTTAGGGGTTCGAGCCCCC 1 chrIV:1201591-1201956 ( 62) TAATCATAAGGTTAGGGGTTCGAGCCCCC 1 chrVII:828564-828960 ( 20) TAATCAGAAGATTATGGGTTCGACCCCCA 1 chrIV:568741-569155 ( 18) TAATCAGAAGATTATGGGTTCGACCCCCA 1 chrXIII:747744-748127 ( 16) TAATCAGAAGATTATGGGTTCGACCCCCA 1 chrII:405708-406154 ( 31) TAATCAGAAGATTATGGGTTCGACCCCCA 1 chrXIV:631742-632026 ( 21) GGTGCGGGAGGTCCCGGGTTCGAGTCCCG 1 chrI:166169-166431 ( 52) CAAGGAAGAGGTCATCGGTTCGATTCCGG 1 chrVII:328447-328812 ( 38) TCACCGTGGAGACCGGGGTTCGACTCCCC 1 chrXII:797047-797362 ( 58) TCACCGTGGAGACCGGGGTTCGACTCCCC 1 chrVII:541702-542100 ( 33) TCACCGTGGAGACCGGGGTTCGACTCCCC 1 chrXIII:290645-290987 ( 69) TCACCGTGGAGACCGGGGTTCGACTCCCC 1 chrIV:992708-992995 ( 64) CCATCGTTGGGCCCCCGGTTCGATTCCGG 1 chrXII:875227-875602 ( 70) ATACCGAAATGTCAGGGGTTCGAGCCCCC 1 chrXV:438515-438873 ( 57) ATACCGAAATGTCAGGGGTTCGAGCCCCC 1 chrXV:282015-282336 ( 72) CCATCGTTGGGCCCCCGGTTCGATTCCGG 1 chrX:422781-422881 ( 72) TAATCTGAAGGTCGAGAGTTCGAACCTCC 1 chrIV:1175728-1176018 ( 41) TAATCTGAAGGTCGAGAGTTCGAACCTCC 1 chrVIII:388768-389030 ( 53) CATGCGAGAGGCCCTGGGTTCAATTCCCA 1 chrVII:440453-441015 ( 41) TTATCTGGAGGTCCTGTGTTCGATCCACA 1 chrVIII:237706-238093 ( 8) TTATCTGGAGGTCCTGTGTTCGATCCACA 1 chrXIV:102588-102924 ( 46) TAATCGCAAGATCGTGAGTTCAACCCTCA 1 chrVI:137313-137683 ( 47) TAATCGCAAGATCGTGAGTTCAACCCTCA 1 chrXVI:810561-810840 ( 62) TAATCGCAAGATCGTGAGTTCAACCCTCA 1 chrXII:656802-657129 ( 28) CATGGGAGAGGTCTCCGGTTCGATTCCGG 1 chrVII:774206-774565 ( 49) CATGGGAGAGGTCTCCGGTTCGATTCCGG 1 chrVIII:146110-146412 ( 40) CATGGGAGAGGTCTCCGGTTCGATTCCGG 1 chrIV:1095253-1095599 ( 3) ATATCTGGAGGTCCTGTGTTCGATCCACA 1 chrXIV:104660-105030 ( 45) TAATGTGGAGATCATCGGTTCAAATCCGA 1 chrII:266239-266614 ( 37) TAATGTGGAGATCATCGGTTCAAATCCGA 1 chrXIII:168678-169075 ( 20) AAATCTTGAGATCGGGCGTTCGACTCGCC 1 chrX:354115-354215 ( 59) AAATCTTGAGATCGGGCGTTCGACTCGCC 1 chrVII:878522-878963 ( 27) CAATCGAAGGGTTGCAGGTTCAATTCCTG 1 chrXVI:56010-56419 ( 14) CAATCGAAGGGTTGCAGGTTCAATTCCTG 1 chrVII:823328-823692 ( 58) CACGCAGAACGTCCCCAGTTCGATCCTGG 1 chrXIII:372349-372608 ( 26) CACGCAGAACGTCCCCAGTTCGATCCTGG 1 chrIV:645025-645398 ( 1) TGATCCGGACAACCCCGGTTCGAATCCGG 1 chrXII:374203-374553 ( 62) GAACCAGAAGATTCCAGGTTCAAGTCCTG 1 chrXVI:744132-744510 ( 47) TAATGCAAAGGTCGTTAGTTCAATTCTGA 1 chrXVI:435772-436119 ( 7) AAATCTGTTGGTCCTTAGTTCGATCCTGA 1 chrXII:818493-818794 ( 50) CGGTGGCTGTGATCCGGGTTCGAGTCCCG 1 chrXV:594244-594562 ( 10) CCAAGCATGAGGCCCGGGTTCGATTCCCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YAATCDDRAGGTCVBGGGTTCGABYCCCV MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 29 n= 39240 bayes= 11.296 E= 8.2e-182 -124 56 -214 82 113 -33 -155 -151 142 -214 -313 -151 -382 -33 -14 108 -1217 207 3 -1217 -2 -155 111 -51 -37 -114 95 -2 70 -1217 103 -151 130 -1217 19 -382 -151 -155 199 -224 -13 -1217 191 -1217 -124 -155 -313 134 -1217 186 -1217 -2 8 103 19 -224 -283 67 67 17 -224 32 177 -283 -66 -214 186 -224 -1217 -1217 239 -1217 -1217 -1217 -1217 170 -1217 -1217 -1217 170 -1217 239 -1217 -1217 -51 -1217 203 -1217 170 -1217 -1217 -1217 -151 56 32 26 -1217 139 -1217 70 -1217 239 -1217 -1217 -224 186 -214 -66 -1217 177 56 -224 8 86 77 -1217 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YAATCDDRAGGTCVBGGGTTCGABYCCCV MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 29 nsites= 46 E= 8.2e-182 0.130435 0.282609 0.043478 0.543478 0.673913 0.152174 0.065217 0.108696 0.826087 0.043478 0.021739 0.108696 0.021739 0.152174 0.173913 0.652174 0.000000 0.804348 0.195652 0.000000 0.304348 0.065217 0.413043 0.217391 0.239130 0.086957 0.369565 0.304348 0.500000 0.000000 0.391304 0.108696 0.760870 0.000000 0.217391 0.021739 0.108696 0.065217 0.760870 0.065217 0.282609 0.000000 0.717391 0.000000 0.130435 0.065217 0.021739 0.782609 0.000000 0.695652 0.000000 0.304348 0.326087 0.391304 0.217391 0.065217 0.043478 0.304348 0.304348 0.347826 0.065217 0.239130 0.652174 0.043478 0.195652 0.043478 0.695652 0.065217 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.217391 0.000000 0.782609 0.000000 1.000000 0.000000 0.000000 0.000000 0.108696 0.282609 0.239130 0.369565 0.000000 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.065217 0.695652 0.043478 0.195652 0.000000 0.652174 0.282609 0.065217 0.326087 0.347826 0.326087 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YAATCDDRAGGTCVBGGGTTCGABYCCCV MEME-1 regular expression -------------------------------------------------------------------------------- [TC]AATC[GAT][GTA][AG][AG]G[GA]T[CT][CAG][TCG][GC]GGTTC[GA]A[TCG][CT]CC[CG][CAG] -------------------------------------------------------------------------------- Time 286.64 secs. ******************************************************************************** ******************************************************************************** MOTIF GCBYTAMCVACTVVGCCAHNDRV MEME-2 width = 23 sites = 46 llr = 729 E-value = 2.0e-093 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCBYTAMCVACTVVGCCAHNDRV MEME-2 Description -------------------------------------------------------------------------------- Simplified A :11:383:49::232::a42453 pos.-specific C 3824::6a3:8:22:a7:431:2 probability G 7:2::1::3:::458::::3335 matrix T :14571::::2a2:::3:2222: bits 2.4 * 2.1 * * 1.9 * * 1.7 * ** * Relative 1.4 ** * ** **** Entropy 1.2 ** * *** **** (22.9 bits) 1.0 ** * ** *** **** 0.7 ** **** *** ***** * 0.5 ** ***** *** ****** * 0.2 ******************* *** 0.0 ----------------------- Multilevel GCTTTACCAACTGGGCCAACAAG consensus C CCA A C CA T CGGGA sequence G G AC TAT C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCBYTAMCVACTVVGCCAHNDRV MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ----------------------- chrXII:784181-784576 - 28 5.37e-11 AGCAGGCATC GCCTTAACCACTCGGCCACTGGG ACGGTTGAAC chrXV:274513-274889 - 24 5.37e-11 GCAGGGCATC GCCTTAACCACTCGGCCACTGGG ACACGATTAC chrXI:578798-579191 - 23 1.95e-10 AAAGCCGAAC GCTCTACCAACTGAGCTAACAAG GATGAGTTCT chrIV:359419-359801 - 19 1.95e-10 AAAGCCGAAC GCTCTACCAACTGAGCTAACAAG GATGAGTTCT chrXII:875227-875602 - 14 1.95e-10 AAAGCCGAAC GCTCTACCAACTGAGCTAACAAG GATGAGTTCT chrXV:438515-438873 - 1 1.95e-10 AAAGCCGAAC GCTCTACCAACTGAGCTAACAAG chrVI:226563-226912 + 49 2.32e-10 AGAGTCATAC GCGCTACCGATTGCGCCAACAAG GCATTTTAAT chrV:435639-435979 + 41 2.32e-10 AGAGTCATAC GCGCTACCGATTGCGCCAACAAG GCTCTTATTG chrVII:185590-185910 + 62 2.32e-10 AGAGTCATAC GCGCTACCGATTGCGCCAACAAG GCTATTTCGT chrVII:876249-876641 - 1 2.32e-10 AGAGTCATAC GCGCTACCGATTGCGCCAACAAG chrVII:122111-122482 - 25 2.32e-10 AGAGTCATAC GCGCTACCGATTGCGCCAACAAG GCTAATTCGT chrIV:1201591-1201956 - 29 2.32e-10 AGAGTCATAC GCGCTACCGATTGCGCCAACAAG GCTATTTATT chrI:166169-166431 - 19 3.21e-10 CAAGGGAAGC GCGCTACCAACTGCGCCATGTGC CCAACTCATT chrIX:183343-183665 + 35 6.96e-10 TAGCACGGTG CCTTAACCAACTGGGCCAAGAGA CCAGGAATTT chrX:523905-524005 + 42 6.96e-10 CTAATCTTTC GCCTTAACCACTCGGCCAAGTTG CCTTTAATCT chrXII:734654-734965 - 45 6.96e-10 TAGCACGGTG CCTTAACCAACTGGGCCAAGAGA CCAAACTTTG chrIV:1305527-1305823 - 7 6.96e-10 CTAATCTTTC GCCTTAACCACTCGGCCAAGTTG CCTTAA chrXIV:104660-105030 - 12 1.07e-09 CTAGTGTGGC GCCTTACCAACTTGGCCATAGAA GCTGAGAACT chrXVI:689380-689800 - 27 1.07e-09 CAAGTCTGTC GCCTTAACCACTCGGCCATAGTG CCCAAAATAA chrV:288301-288676 + 62 1.07e-09 CAAGTCTGTC GCCTTAACCACTCGGCCATAGTG CCTATCATTA chrIII:227769-228207 - 6 1.07e-09 CGAGTCTCTC GCCTTAACCACTCGGCCATAGTG CCATT chrII:266239-266614 - 4 1.07e-09 CTAGTGTGGC GCCTTACCAACTTGGCCATAGAA GCA chrXII:656802-657129 + 67 1.23e-09 CTAAGGGAGC GCGCTACCGACTACGCCACACGC CCAATTTTCT chrXIV:102588-102924 - 12 1.23e-09 CAGTCGCACG CCTTAACCAACTTGGCCATGGAG TCTTATAATA chrVII:774206-774565 - 16 1.23e-09 CTAAGGGAGC GCGCTACCGACTACGCCACACGC CCAATTAATT chrXVI:810561-810840 - 28 1.23e-09 CAGTCGCACG CCTTAACCAACTTGGCCATGGAG TCGCAAATAA chrXII:374203-374553 - 29 3.74e-08 GTAGCCAGAC GCCGTGACCATTGGGCCACGAGG AACAAGATTT chrXII:592426-592733 + 66 3.74e-08 AAATCTGACG CCTTAAACCACTCGGCCAAACTC CCATTGTATG chrV:469304-469614 - 50 5.92e-08 TAAGCAGATG CCATAACCGACTAGACCACGAAA CCAATTATTT chrVII:823328-823692 - 24 5.92e-08 TAAGCAGATG CCATAACCGACTAGACCACGAAA CCACTCTTAT chrV:438565-438845 - 47 5.92e-08 TAAGCAGATG CCATAACCGACTAGACCACGAAA CCTAATTTGT chrXIII:372349-372608 + 66 5.92e-08 TAAGCAGATG CCATAACCGACTAGACCACGAAA CCAGGTTTTA chrX:422781-422881 - 39 7.07e-08 TGAGACTGAC GCTCTTCCTACTGAGCTACTGAA GCATACAAAG chrIV:1175728-1176018 - 8 7.07e-08 TGAGACTGAC GCTCTTCCTACTGAGCTACTGAA GCTTTGT chrIV:1095253-1095599 + 61 1.27e-07 TCAGTCTGGC GCTCTCCCAACTGAGCTAAGTCC GCTAACATAA chrVIII:237706-238093 + 66 2.04e-07 TCAGTCTGGC GCTCTCCCAACTGAGCTAAATCC GCTTACTATT chrX:354115-354215 - 10 3.67e-07 AGTCTTGCGC CTTAAACCAACTTGGCTACCGAG AGTGATAAA chrXV:288012-288400 - 38 3.67e-07 AGTCTTGCGC CTTAAACCAACTTGGCTACCGAG AGAAGCTATT chrXII:628218-628609 - 22 1.11e-06 GAATCAGGCG CCTTAGACCGCTCGGCCAAACAA CCACTTATTT chrIII:142607-142925 + 31 1.25e-06 GGCAACGTTG GATTTTACCACTAAACCACTTGC GCTAGTAATC chrIV:992708-992995 - 33 1.25e-06 GGCAACGTTG GATTTTACCACTAAACCACTTGC GCTCACAATT chrVI:162069-162391 - 50 1.25e-06 GGCAACGTTG GATTTTACCACTAAACCACTTGC GCTTGTTTTC chrXV:282015-282336 - 41 1.25e-06 GGCAACGTTG GATTTTACCACTAAACCACTTGC GCGCTTTCAT chrXII:951113-951862 + 20 5.55e-06 TTGTCTAATG CTGCTAACACTTCAGCCACATTA TCATCTTTGA chrI:72928-73463 + 13 1.28e-05 GATGTTGAAG CCCGTATCAACTTCGGTATTGAA AAGGCTAAGG chrIV:330916-331395 - 60 1.87e-05 GATACTTACC GCGCTGACATTACCGCTATCGTC ACCGACGCCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCBYTAMCVACTVVGCCAHNDRV MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrXII:784181-784576 5.4e-11 27_[-2]_50 chrXV:274513-274889 5.4e-11 23_[-2]_54 chrXI:578798-579191 2e-10 22_[-2]_55 chrIV:359419-359801 2e-10 18_[-2]_59 chrXII:875227-875602 2e-10 13_[-2]_64 chrXV:438515-438873 2e-10 [-2]_77 chrVI:226563-226912 2.3e-10 48_[+2]_29 chrV:435639-435979 2.3e-10 40_[+2]_37 chrVII:185590-185910 2.3e-10 61_[+2]_16 chrVII:876249-876641 2.3e-10 [-2]_77 chrVII:122111-122482 2.3e-10 24_[-2]_53 chrIV:1201591-1201956 2.3e-10 28_[-2]_49 chrI:166169-166431 3.2e-10 18_[-2]_59 chrIX:183343-183665 7e-10 34_[+2]_43 chrX:523905-524005 7e-10 41_[+2]_36 chrXII:734654-734965 7e-10 44_[-2]_33 chrIV:1305527-1305823 7e-10 6_[-2]_71 chrXIV:104660-105030 1.1e-09 11_[-2]_66 chrXVI:689380-689800 1.1e-09 26_[-2]_51 chrV:288301-288676 1.1e-09 61_[+2]_16 chrIII:227769-228207 1.1e-09 5_[-2]_72 chrII:266239-266614 1.1e-09 3_[-2]_74 chrXII:656802-657129 1.2e-09 66_[+2]_11 chrXIV:102588-102924 1.2e-09 11_[-2]_66 chrVII:774206-774565 1.2e-09 15_[-2]_62 chrXVI:810561-810840 1.2e-09 27_[-2]_50 chrXII:374203-374553 3.7e-08 28_[-2]_49 chrXII:592426-592733 3.7e-08 65_[+2]_12 chrV:469304-469614 5.9e-08 49_[-2]_28 chrVII:823328-823692 5.9e-08 23_[-2]_54 chrV:438565-438845 5.9e-08 46_[-2]_31 chrXIII:372349-372608 5.9e-08 65_[+2]_12 chrX:422781-422881 7.1e-08 38_[-2]_39 chrIV:1175728-1176018 7.1e-08 7_[-2]_70 chrIV:1095253-1095599 1.3e-07 60_[+2]_17 chrVIII:237706-238093 2e-07 65_[+2]_12 chrX:354115-354215 3.7e-07 9_[-2]_68 chrXV:288012-288400 3.7e-07 37_[-2]_40 chrXII:628218-628609 1.1e-06 21_[-2]_56 chrIII:142607-142925 1.2e-06 30_[+2]_47 chrIV:992708-992995 1.2e-06 32_[-2]_45 chrVI:162069-162391 1.2e-06 49_[-2]_28 chrXV:282015-282336 1.2e-06 40_[-2]_37 chrXII:951113-951862 5.5e-06 19_[+2]_58 chrI:72928-73463 1.3e-05 12_[+2]_65 chrIV:330916-331395 1.9e-05 59_[-2]_18 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCBYTAMCVACTVVGCCAHNDRV MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCBYTAMCVACTVVGCCAHNDRV width=23 seqs=46 chrXII:784181-784576 ( 28) GCCTTAACCACTCGGCCACTGGG 1 chrXV:274513-274889 ( 24) GCCTTAACCACTCGGCCACTGGG 1 chrXI:578798-579191 ( 23) GCTCTACCAACTGAGCTAACAAG 1 chrIV:359419-359801 ( 19) GCTCTACCAACTGAGCTAACAAG 1 chrXII:875227-875602 ( 14) GCTCTACCAACTGAGCTAACAAG 1 chrXV:438515-438873 ( 1) GCTCTACCAACTGAGCTAACAAG 1 chrVI:226563-226912 ( 49) GCGCTACCGATTGCGCCAACAAG 1 chrV:435639-435979 ( 41) GCGCTACCGATTGCGCCAACAAG 1 chrVII:185590-185910 ( 62) GCGCTACCGATTGCGCCAACAAG 1 chrVII:876249-876641 ( 1) GCGCTACCGATTGCGCCAACAAG 1 chrVII:122111-122482 ( 25) GCGCTACCGATTGCGCCAACAAG 1 chrIV:1201591-1201956 ( 29) GCGCTACCGATTGCGCCAACAAG 1 chrI:166169-166431 ( 19) GCGCTACCAACTGCGCCATGTGC 1 chrIX:183343-183665 ( 35) CCTTAACCAACTGGGCCAAGAGA 1 chrX:523905-524005 ( 42) GCCTTAACCACTCGGCCAAGTTG 1 chrXII:734654-734965 ( 45) CCTTAACCAACTGGGCCAAGAGA 1 chrIV:1305527-1305823 ( 7) GCCTTAACCACTCGGCCAAGTTG 1 chrXIV:104660-105030 ( 12) GCCTTACCAACTTGGCCATAGAA 1 chrXVI:689380-689800 ( 27) GCCTTAACCACTCGGCCATAGTG 1 chrV:288301-288676 ( 62) GCCTTAACCACTCGGCCATAGTG 1 chrIII:227769-228207 ( 6) GCCTTAACCACTCGGCCATAGTG 1 chrII:266239-266614 ( 4) GCCTTACCAACTTGGCCATAGAA 1 chrXII:656802-657129 ( 67) GCGCTACCGACTACGCCACACGC 1 chrXIV:102588-102924 ( 12) CCTTAACCAACTTGGCCATGGAG 1 chrVII:774206-774565 ( 16) GCGCTACCGACTACGCCACACGC 1 chrXVI:810561-810840 ( 28) CCTTAACCAACTTGGCCATGGAG 1 chrXII:374203-374553 ( 29) GCCGTGACCATTGGGCCACGAGG 1 chrXII:592426-592733 ( 66) CCTTAAACCACTCGGCCAAACTC 1 chrV:469304-469614 ( 50) CCATAACCGACTAGACCACGAAA 1 chrVII:823328-823692 ( 24) CCATAACCGACTAGACCACGAAA 1 chrV:438565-438845 ( 47) CCATAACCGACTAGACCACGAAA 1 chrXIII:372349-372608 ( 66) CCATAACCGACTAGACCACGAAA 1 chrX:422781-422881 ( 39) GCTCTTCCTACTGAGCTACTGAA 1 chrIV:1175728-1176018 ( 8) GCTCTTCCTACTGAGCTACTGAA 1 chrIV:1095253-1095599 ( 61) GCTCTCCCAACTGAGCTAAGTCC 1 chrVIII:237706-238093 ( 66) GCTCTCCCAACTGAGCTAAATCC 1 chrX:354115-354215 ( 10) CTTAAACCAACTTGGCTACCGAG 1 chrXV:288012-288400 ( 38) CTTAAACCAACTTGGCTACCGAG 1 chrXII:628218-628609 ( 22) CCTTAGACCGCTCGGCCAAACAA 1 chrIII:142607-142925 ( 31) GATTTTACCACTAAACCACTTGC 1 chrIV:992708-992995 ( 33) GATTTTACCACTAAACCACTTGC 1 chrVI:162069-162391 ( 50) GATTTTACCACTAAACCACTTGC 1 chrXV:282015-282336 ( 41) GATTTTACCACTAAACCACTTGC 1 chrXII:951113-951862 ( 20) CTGCTAACACTTCAGCCACATTA 1 chrI:72928-73463 ( 13) CCCGTATCAACTTCGGTATTGAA 1 chrIV:330916-331395 ( 60) GCGCTGACATTACCGCTATCGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCBYTAMCVACTVVGCCAHNDRV MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 23 n= 42510 bayes= 11.9422 E= 2.0e-093 -1217 67 186 -1217 -183 215 -1217 -224 -183 32 32 49 -283 111 -214 70 -24 -1217 -1217 126 130 -214 -155 -124 17 172 -1217 -382 -1217 239 -1217 -1217 34 67 45 -283 160 -313 -313 -382 -1217 207 -1217 -66 -382 -1217 -1217 166 -51 32 103 -102 -13 32 132 -1217 -83 -1217 211 -1217 -1217 235 -313 -1217 -1217 195 -1217 -24 170 -1217 -1217 -1217 34 103 -1217 -51 -37 56 56 -66 26 -114 77 -51 76 -214 45 -83 -13 32 132 -1217 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCBYTAMCVACTVVGCCAHNDRV MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 23 nsites= 46 E= 2.0e-093 0.000000 0.304348 0.695652 0.000000 0.086957 0.847826 0.000000 0.065217 0.086957 0.239130 0.239130 0.434783 0.043478 0.413043 0.043478 0.500000 0.260870 0.000000 0.000000 0.739130 0.760870 0.043478 0.065217 0.130435 0.347826 0.630435 0.000000 0.021739 0.000000 1.000000 0.000000 0.000000 0.391304 0.304348 0.260870 0.043478 0.934783 0.021739 0.021739 0.021739 0.000000 0.804348 0.000000 0.195652 0.021739 0.000000 0.000000 0.978261 0.217391 0.239130 0.391304 0.152174 0.282609 0.239130 0.478261 0.000000 0.173913 0.000000 0.826087 0.000000 0.000000 0.978261 0.021739 0.000000 0.000000 0.739130 0.000000 0.260870 1.000000 0.000000 0.000000 0.000000 0.391304 0.391304 0.000000 0.217391 0.239130 0.282609 0.282609 0.195652 0.369565 0.086957 0.326087 0.217391 0.521739 0.043478 0.260870 0.173913 0.282609 0.239130 0.478261 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCBYTAMCVACTVVGCCAHNDRV MEME-2 regular expression -------------------------------------------------------------------------------- [GC]C[TCG][TC][TA]A[CA]C[ACG]ACT[GCA][GAC]GC[CT]A[ACT][CGA][AGT][AG][GAC] -------------------------------------------------------------------------------- Time 555.42 secs. ******************************************************************************** ******************************************************************************** MOTIF GRAGTCVRAMGCKYTRCCATTRMGCCACSS MEME-3 width = 30 sites = 10 llr = 306 E-value = 1.7e-038 ******************************************************************************** -------------------------------------------------------------------------------- Motif GRAGTCVRAMGCKYTRCCATTRMGCCACSS MEME-3 Description -------------------------------------------------------------------------------- Simplified A :5a1::4483:::::5::a::54:::a11: pos.-specific C 11::192:16:a:6::aa:3::6:a9:835 probability G 84:9:1351:a:6::4:::::5:a::::65 matrix T 1:::9:11:1::44a1:::7a::::1:1:: bits 2.4 ** ** ** 2.1 ** ** ** 1.9 * * ** ** *** 1.7 ** * ** * *** * **** Relative 1.4 * ** * ** * *** * ***** * Entropy 1.2 * **** ***** *** * ****** * (44.2 bits) 1.0 * **** * ***** ************** 0.7 ****** *********************** 0.5 ****** *********************** 0.2 ****************************** 0.0 ------------------------------ Multilevel GAAGTCAGACGCGCTACCATTACGCCACGC consensus G GA A TT G C GA CG sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRAGTCVRAMGCKYTRCCATTRMGCCACSS MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------------------------ chrVII:828564-828960 + 49 1.78e-17 CTTCTGATTA GAAGTCAGACGCGTTGCCATTACGCCACGC GAGCTACTGT chrX:374407-374507 + 23 1.78e-17 CTTCTGATTA GAAGTCAGACGCGTTGCCATTACGCCACGC GAGCTACTAT chrXIII:747744-748127 + 45 1.78e-17 CTTCTGATTA GAAGTCAGACGCGTTGCCATTACGCCACGC GAGCTAGTCA chrII:405708-406154 - 1 1.78e-17 CTTCTGATTA GAAGTCAGACGCGTTGCCATTACGCCACGC chrXIII:379211-379569 + 35 1.41e-15 AGATTTAATT GGAGTCGAAAGCTCTACCATTGAGCCACCG CTTCAACTTT chrVII:287217-287620 + 54 1.41e-15 AGATTTAATT GGAGTCGAAAGCTCTACCATTGAGCCACCG CTTCATCTTG chrX:415830-415930 + 47 1.41e-15 AGATTTAATT GGAGTCGAAAGCTCTACCATTGAGCCACCG CTTCAACTTT chrXVI:338740-339094 + 19 2.72e-13 ATCAGGGTTA TGAGCCCTGCGCGCTTCCACTGCGCCACGG CGCTGCTAAA chrXVI:744132-744510 - 17 1.56e-12 CTTTGCATTA CAAGTGCAACGCTCTACCACTAAGCTAAGG AGGCTTTTAC chrXVI:435772-436119 + 36 2.74e-12 CAACAGATTT GCAATCTGCTGCGCTACCACTGCGCCATAC GAGCTTTTGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRAGTCVRAMGCKYTRCCATTRMGCCACSS MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrVII:828564-828960 1.8e-17 48_[+3]_22 chrX:374407-374507 1.8e-17 22_[+3]_48 chrXIII:747744-748127 1.8e-17 44_[+3]_26 chrII:405708-406154 1.8e-17 [-3]_70 chrXIII:379211-379569 1.4e-15 34_[+3]_36 chrVII:287217-287620 1.4e-15 53_[+3]_17 chrX:415830-415930 1.4e-15 46_[+3]_24 chrXVI:338740-339094 2.7e-13 18_[+3]_52 chrXVI:744132-744510 1.6e-12 16_[-3]_54 chrXVI:435772-436119 2.7e-12 35_[+3]_35 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRAGTCVRAMGCKYTRCCATTRMGCCACSS MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GRAGTCVRAMGCKYTRCCATTRMGCCACSS width=30 seqs=10 chrVII:828564-828960 ( 49) GAAGTCAGACGCGTTGCCATTACGCCACGC 1 chrX:374407-374507 ( 23) GAAGTCAGACGCGTTGCCATTACGCCACGC 1 chrXIII:747744-748127 ( 45) GAAGTCAGACGCGTTGCCATTACGCCACGC 1 chrII:405708-406154 ( 1) GAAGTCAGACGCGTTGCCATTACGCCACGC 1 chrXIII:379211-379569 ( 35) GGAGTCGAAAGCTCTACCATTGAGCCACCG 1 chrVII:287217-287620 ( 54) GGAGTCGAAAGCTCTACCATTGAGCCACCG 1 chrX:415830-415930 ( 47) GGAGTCGAAAGCTCTACCATTGAGCCACCG 1 chrXVI:338740-339094 ( 19) TGAGCCCTGCGCGCTTCCACTGCGCCACGG 1 chrXVI:744132-744510 ( 17) CAAGTGCAACGCTCTACCACTAAGCTAAGG 1 chrXVI:435772-436119 ( 36) GCAATCTGCTGCGCTACCACTGCGCCATAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRAGTCVRAMGCKYTRCCATTRMGCCACSS MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 30 n= 38695 bayes= 12.8612 E= 1.7e-038 -997 -93 206 -162 69 -93 106 -997 169 -997 -997 -997 -162 -997 223 -997 -997 -93 -997 154 -997 223 -93 -997 37 6 65 -162 37 -997 139 -162 137 -93 -93 -997 -4 165 -997 -162 -997 -997 239 -997 -997 239 -997 -997 -997 -997 165 37 -997 165 -997 37 -997 -997 -997 169 69 -997 106 -162 -997 239 -997 -997 -997 239 -997 -997 169 -997 -997 -997 -997 65 -997 118 -997 -997 -997 169 69 -997 139 -997 37 165 -997 -997 -997 -997 239 -997 -997 239 -997 -997 -997 223 -997 -162 169 -997 -997 -997 -162 206 -997 -162 -162 65 165 -997 -997 139 139 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRAGTCVRAMGCKYTRCCATTRMGCCACSS MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 30 nsites= 10 E= 1.7e-038 0.000000 0.100000 0.800000 0.100000 0.500000 0.100000 0.400000 0.000000 1.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.900000 0.000000 0.000000 0.100000 0.000000 0.900000 0.000000 0.900000 0.100000 0.000000 0.400000 0.200000 0.300000 0.100000 0.400000 0.000000 0.500000 0.100000 0.800000 0.100000 0.100000 0.000000 0.300000 0.600000 0.000000 0.100000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.400000 0.000000 0.600000 0.000000 0.400000 0.000000 0.000000 0.000000 1.000000 0.500000 0.000000 0.400000 0.100000 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 0.300000 0.000000 0.700000 0.000000 0.000000 0.000000 1.000000 0.500000 0.000000 0.500000 0.000000 0.400000 0.600000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.900000 0.000000 0.100000 1.000000 0.000000 0.000000 0.000000 0.100000 0.800000 0.000000 0.100000 0.100000 0.300000 0.600000 0.000000 0.000000 0.500000 0.500000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRAGTCVRAMGCKYTRCCATTRMGCCACSS MEME-3 regular expression -------------------------------------------------------------------------------- G[AG]AGTC[AGC][GA]A[CA]GC[GT][CT]T[AG]CCA[TC]T[AG][CA]GCCAC[GC][CG] -------------------------------------------------------------------------------- Time 820.73 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrXVI:770738-771111 3.60e-01 100 chrVIII:388768-389030 5.97e-07 52_[-1(6.60e-11)]_19 chrXVI:453913-454409 8.57e-01 100 chrIX:386653-386905 2.96e-02 46_[+2(1.09e-05)]_31 chrIV:1194557-1195053 7.14e-01 100 chrXIV:297676-298211 1.88e-01 100 chrXI:258579-258959 1.62e-01 100 chrVII:558160-558656 9.67e-01 100 chrIV:969766-970262 3.54e-02 100 chrXV:977982-978207 9.65e-01 100 chrIV:1269877-1270378 3.18e-01 100 chrIII:224812-225308 9.49e-01 100 chrXIII:420067-420831 9.65e-01 100 chrII:266239-266614 3.04e-12 3_[-2(1.07e-09)]_10_[+1(3.84e-10)]_\ 35 chrVII:398610-399633 5.83e-01 100 chrXV:274513-274889 2.89e-08 23_[-2(5.37e-11)]_54 chrXV:619891-620328 4.44e-01 100 chrIV:579405-580667 7.98e-01 100 chrXII:904018-904142 2.46e-01 100 chrXV:282015-282336 9.04e-12 40_[-2(1.25e-06)]_8_[+1(5.94e-11)] chrVI:220887-221383 1.77e-01 100 chrV:61035-62113 5.65e-01 100 chrXV:288012-288400 5.82e-04 37_[-2(3.67e-07)]_40 chrVII:559363-559859 6.87e-01 100 chrVII:480671-483006 3.05e-01 100 chrV:106598-106825 7.65e-01 100 chrXIII:20131-20627 4.53e-01 100 chrXII:795762-796258 9.82e-01 100 chrIV:491581-492048 4.09e-01 100 chrVII:784768-785264 6.70e-01 100 chrV:138514-140452 4.77e-02 100 chrXIII:372349-372608 4.22e-10 25_[-1(1.28e-09)]_11_[+2(5.92e-08)]_\ 12 chrXII:1012064-1012523 1.96e-01 100 chrVIII:237706-238093 3.92e-11 7_[-1(9.02e-11)]_29_[+2(2.04e-07)]_\ 12 chrII:405708-406154 2.69e-22 [-3(1.78e-17)]_[+1(4.92e-13)]_41 chrX:526497-526597 6.39e-01 100 chrIII:68374-68684 7.71e-01 100 chrIII:57859-58355 7.26e-02 100 chrVIII:75379-75990 4.00e-02 100 chrXV:967130-967626 8.40e-01 100 chrXVI:696985-697169 1.29e-01 100 chrV:77967-78904 4.08e-01 100 chrXII:232110-234268 2.45e-02 46_[+1(2.84e-05)]_25 chrIX:257623-258119 9.08e-01 100 chrVIII:387271-387767 8.77e-01 100 chrXIII:891515-892011 8.75e-01 100 chrXVI:403677-404173 6.48e-01 100 chrXIV:415669-415911 3.41e-01 100 chrXII:794163-795324 4.41e-01 100 chrII:393264-393861 2.51e-01 100 chrIV:541266-541848 9.51e-01 100 chrX:354115-354215 8.60e-11 9_[-2(3.67e-07)]_26_[+1(4.21e-10)]_\ 13 chrXV:1015404-1015900 5.54e-02 100 chrII:159666-160162 6.13e-01 100 chrIV:322353-323356 9.11e-01 100 chrIX:69364-69622 5.09e-01 100 chrVIII:121309-121611 4.71e-03 55_[+2(3.64e-06)]_22 chrXII:636744-638320 1.04e-02 42_[-2(7.99e-05)]_35 chrVIII:34435-36187 2.56e-01 100 chrXIII:861174-861411 4.02e-01 100 chrIII:28878-29950 8.47e-01 100 chrXIV:568140-568636 8.86e-01 100 chrV:39380-39876 2.65e-01 100 chrVIII:451156-452870 6.42e-01 100 chrXV:571801-572127 3.59e-02 100 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chrIV:216426-216922 2.21e-01 100 chrVII:878522-878963 6.18e-06 26_[-1(1.09e-09)]_45 chrXIII:162182-162486 3.54e-01 100 chrXV:29710-29931 9.85e-01 100 chrXVI:435772-436119 1.36e-13 6_[-1(2.06e-08)]_[+3(2.74e-12)]_35 chrII:477400-477847 9.92e-01 100 chrIII:142607-142925 5.99e-05 30_[+2(1.25e-06)]_47 chrXII:656802-657129 2.29e-13 27_[-1(1.81e-10)]_10_[+2(1.23e-09)]_\ 11 chrXV:779911-781003 4.99e-01 100 chrXI:141618-142114 9.50e-01 100 chrVII:533980-534467 7.88e-01 100 chrXIV:104660-105030 3.04e-12 11_[-2(1.07e-09)]_10_[+1(3.84e-10)]_\ 27 chrX:227790-227890 9.49e-01 100 chrIII:23690-24186 7.22e-01 100 chrXVI:901633-902206 8.62e-01 100 chrXVI:286360-286585 5.47e-01 100 chrXI:519892-520057 1.11e-01 100 chrV:237599-238095 6.61e-01 100 chrXV:624051-624547 1.00e+00 100 chrIV:1360108-1360684 8.26e-01 100 chrXVI:433770-434266 1.97e-01 100 chrXV:479273-479769 7.67e-01 100 chrXVI:692909-693405 6.27e-01 100 chrIV:1080559-1080888 2.85e-01 100 chrXV:87375-87980 9.86e-01 100 chrXII:80746-80948 6.87e-01 100 chrXV:903892-904236 2.86e-01 100 chrII:466617-466906 9.73e-01 100 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kali.stanford.edu ********************************************************************************