******************************************************************************** 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/GM12878/fasta/RankLinear0.6_10/NFATC1.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr7:121635188-121635208 1.0000 20 chr4:37767483-37767503 1.0000 20 chrX:120442325-120442345 1.0000 20 chr7:2681226-2681246 1.0000 20 chr1:75805086-75805106 1.0000 20 chr1:53125232-53125252 1.0000 20 chr11:122614870-12261489 1.0000 20 chr7:144518361-144518381 1.0000 20 chr1:42107264-42107284 1.0000 20 chr12:95576775-95576795 1.0000 20 chr1:231147143-231147163 1.0000 20 chr1:235080861-235080881 1.0000 20 chr1:53744094-53744114 1.0000 20 chr7:100143212-100143232 1.0000 20 chr6:119671693-119671713 1.0000 20 chr11:102906922-10290694 1.0000 20 chr6:11139781-11139801 1.0000 20 chr14:55840732-55840752 1.0000 20 chr1:192775191-192775211 1.0000 20 chr2:233935527-233935547 1.0000 20 chr2:189843589-189843609 1.0000 20 chr15:59541714-59541734 1.0000 20 chr12:82832360-82832380 1.0000 20 chr17:65478185-65478205 1.0000 20 chr6:35270527-35270547 1.0000 20 chr10:5888319-5888339 1.0000 20 chr6:37207985-37208005 1.0000 20 chr1:185409463-185409483 1.0000 20 chr1:87799550-87799570 1.0000 20 chr1:181367915-181367935 1.0000 20 chr7:90242586-90242606 1.0000 20 chr19:3831010-3831030 1.0000 20 chr6:56271223-56271243 1.0000 20 chr17:65050944-65050964 1.0000 20 chr18:61575025-61575045 1.0000 20 chr15:101326484-10132650 1.0000 20 chr1:25096226-25096246 1.0000 20 chr3:144013630-144013650 1.0000 20 chr2:62533073-62533093 1.0000 20 chr6:46188632-46188652 1.0000 20 chr1:226837185-226837205 1.0000 20 chr6:2079371-2079391 1.0000 20 chr5:115412490-115412510 1.0000 20 chr12:76132401-76132421 1.0000 20 chr10:5670958-5670978 1.0000 20 chr6:412706-412726 1.0000 20 chr17:68523931-68523951 1.0000 20 chr21:37314818-37314838 1.0000 20 chr22:44542183-44542203 1.0000 20 chr1:183871331-183871351 1.0000 20 chr15:83761307-83761327 1.0000 20 chr17:72541409-72541429 1.0000 20 chr15:79399657-79399677 1.0000 20 chr2:223292541-223292561 1.0000 20 chr6:164056500-164056520 1.0000 20 chr5:88275272-88275292 1.0000 20 chr4:48249375-48249395 1.0000 20 chr2:231121594-231121614 1.0000 20 chr7:11653181-11653201 1.0000 20 chr5:171388313-171388333 1.0000 20 chr15:77306292-77306312 1.0000 20 chr17:74273772-74273792 1.0000 20 chr6:51766709-51766729 1.0000 20 chr7:1110385-1110405 1.0000 20 chr4:40562041-40562061 1.0000 20 chr15:41206410-41206430 1.0000 20 chr12:53811396-53811416 1.0000 20 chr12:95634517-95634537 1.0000 20 chr19:1389240-1389260 1.0000 20 chr4:178674859-178674879 1.0000 20 chr3:56722403-56722423 1.0000 20 chr12:111214624-11121464 1.0000 20 chr9:135280059-135280079 1.0000 20 chr12:123360516-12336053 1.0000 20 chr9:79191445-79191465 1.0000 20 chr13:111526489-11152650 1.0000 20 chr9:130628301-130628321 1.0000 20 chr17:21247817-21247837 1.0000 20 chr12:90103478-90103498 1.0000 20 chr21:44090390-44090410 1.0000 20 chr8:56757158-56757178 1.0000 20 chr10:35283709-35283729 1.0000 20 chr6:144569828-144569848 1.0000 20 chr12:10438706-10438726 1.0000 20 chr16:48192367-48192387 1.0000 20 chr17:79943032-79943052 1.0000 20 chr3:12602549-12602569 1.0000 20 chr8:129063105-129063125 1.0000 20 chr2:61126857-61126877 1.0000 20 chr6:135466819-135466839 1.0000 20 chr21:44011826-44011846 1.0000 20 chr1:38993143-38993163 1.0000 20 chr2:64328624-64328644 1.0000 20 chr11:65577998-65578018 1.0000 20 chr22:36029689-36029709 1.0000 20 chr2:12644714-12644734 1.0000 20 chr12:124963896-12496391 1.0000 20 chr20:61182477-61182497 1.0000 20 chr15:75397365-75397385 1.0000 20 chr5:176873492-176873512 1.0000 20 chr4:151953357-151953377 1.0000 20 chr22:39157850-39157870 1.0000 20 chr21:26955468-26955488 1.0000 20 chr4:3470571-3470591 1.0000 20 chr12:65271292-65271312 1.0000 20 chr14:69253517-69253537 1.0000 20 chr7:871502-871522 1.0000 20 chr21:26944147-26944167 1.0000 20 chr1:63091342-63091362 1.0000 20 chr8:144636681-144636701 1.0000 20 chr13:63098422-63098442 1.0000 20 chr13:73574368-73574388 1.0000 20 chr13:111288753-11128877 1.0000 20 chr4:68424351-68424371 1.0000 20 chr4:112852014-112852034 1.0000 20 chr6:106969158-106969178 1.0000 20 chr17:72094982-72095002 1.0000 20 chr5:1502038-1502058 1.0000 20 chr7:24795420-24795440 1.0000 20 chr5:82602633-82602653 1.0000 20 chr5:178977249-178977269 1.0000 20 chr7:155055635-155055655 1.0000 20 chr16:11188885-11188905 1.0000 20 chr16:87908909-87908929 1.0000 20 chr8:104090774-104090794 1.0000 20 chr9:140699673-140699693 1.0000 20 chr17:27052479-27052499 1.0000 20 chr2:218479374-218479394 1.0000 20 chr6:16690907-16690927 1.0000 20 chr2:240212379-240212399 1.0000 20 chr11:35412732-35412752 1.0000 20 chr15:93375011-93375031 1.0000 20 chr2:36473601-36473621 1.0000 20 chr17:8732784-8732804 1.0000 20 chr19:4053594-4053614 1.0000 20 chr16:17510976-17510996 1.0000 20 chr12:125000200-12500022 1.0000 20 chr1:97625108-97625128 1.0000 20 chr20:18620427-18620447 1.0000 20 chr21:26954704-26954724 1.0000 20 chr12:43672322-43672342 1.0000 20 chr17:31203434-31203454 1.0000 20 chr20:33153748-33153768 1.0000 20 chr11:71673821-71673841 1.0000 20 chr2:233807698-233807718 1.0000 20 chr12:114400413-11440043 1.0000 20 chr6:86171037-86171057 1.0000 20 chr9:115117814-115117834 1.0000 20 chr12:39861391-39861411 1.0000 20 chr12:6744707-6744727 1.0000 20 chr10:134502318-13450233 1.0000 20 chr2:177862016-177862036 1.0000 20 chr8:126447052-126447072 1.0000 20 chr18:28565928-28565948 1.0000 20 chr17:62077184-62077204 1.0000 20 chr3:143388512-143388532 1.0000 20 chr20:62478614-62478634 1.0000 20 chr7:124533353-124533373 1.0000 20 chr12:105064336-10506435 1.0000 20 chr2:765525-765545 1.0000 20 chr4:56428244-56428264 1.0000 20 chr17:74181480-74181500 1.0000 20 chr8:138918216-138918236 1.0000 20 chr2:238907334-238907354 1.0000 20 chr19:51298292-51298312 1.0000 20 chr6:135898522-135898542 1.0000 20 chr16:11676179-11676199 1.0000 20 chr19:6663520-6663540 1.0000 20 chr10:90923458-90923478 1.0000 20 chr3:105891821-105891841 1.0000 20 chr2:62826063-62826083 1.0000 20 chr21:35267819-35267839 1.0000 20 chr11:109960416-10996043 1.0000 20 chr12:97769174-97769194 1.0000 20 chr3:138609795-138609815 1.0000 20 chr9:138542356-138542376 1.0000 20 chr21:16810383-16810403 1.0000 20 chr6:143141278-143141298 1.0000 20 chr2:28114156-28114176 1.0000 20 chr2:25781384-25781404 1.0000 20 chr10:79260665-79260685 1.0000 20 chr19:46461765-46461785 1.0000 20 chr7:42909187-42909207 1.0000 20 chr15:58808141-58808161 1.0000 20 chr21:26938103-26938123 1.0000 20 chr10:134568758-13456877 1.0000 20 chr1:156786649-156786669 1.0000 20 chr4:106113095-106113115 1.0000 20 chr17:75878180-75878200 1.0000 20 chr19:2557178-2557198 1.0000 20 chr3:14730960-14730980 1.0000 20 chr13:105701300-10570132 1.0000 20 chr18:46546100-46546120 1.0000 20 chr18:11146028-11146048 1.0000 20 chr5:15432180-15432200 1.0000 20 chr19:10216538-10216558 1.0000 20 chr16:27450726-27450746 1.0000 20 chr2:38406379-38406399 1.0000 20 chr9:132779095-132779115 1.0000 20 chr3:188107965-188107985 1.0000 20 chr16:27419522-27419542 1.0000 20 chr3:98241903-98241923 1.0000 20 chr15:29601525-29601545 1.0000 20 chr1:27959131-27959151 1.0000 20 chr17:35174387-35174407 1.0000 20 chr3:9210184-9210204 1.0000 20 chr1:25227940-25227960 1.0000 20 chr9:36843042-36843062 1.0000 20 chr18:2959134-2959154 1.0000 20 chr11:60859922-60859942 1.0000 20 chr17:62493556-62493576 1.0000 20 chr7:5565991-5566011 1.0000 20 chr12:118473559-11847357 1.0000 20 chr17:57840068-57840088 1.0000 20 chr1:247569683-247569703 1.0000 20 chr1:40866271-40866291 1.0000 20 chr8:71042841-71042861 1.0000 20 chr2:48540889-48540909 1.0000 20 chr2:172174552-172174572 1.0000 20 chr2:237967984-237968004 1.0000 20 chr6:148525319-148525339 1.0000 20 chr7:102036727-102036747 1.0000 20 chr17:62631949-62631969 1.0000 20 chr5:33300703-33300723 1.0000 20 chr10:121462210-12146223 1.0000 20 chr5:172333631-172333651 1.0000 20 chr15:33162809-33162829 1.0000 20 chr13:21596413-21596433 1.0000 20 chr4:8421343-8421363 1.0000 20 chr21:26950805-26950825 1.0000 20 chr17:72508864-72508884 1.0000 20 chr9:79322578-79322598 1.0000 20 chr4:99404171-99404191 1.0000 20 chr20:4970401-4970421 1.0000 20 chr2:88315866-88315886 1.0000 20 chr6:43721757-43721777 1.0000 20 chr6:30582596-30582616 1.0000 20 chr22:24050640-24050660 1.0000 20 chr17:38309778-38309798 1.0000 20 chr1:219638785-219638805 1.0000 20 chr9:138899322-138899342 1.0000 20 chr19:42627181-42627201 1.0000 20 chr19:13030159-13030179 1.0000 20 chr9:90150848-90150868 1.0000 20 chr3:141515531-141515551 1.0000 20 chr21:26945386-26945406 1.0000 20 chr22:24830762-24830782 1.0000 20 chr21:45731246-45731266 1.0000 20 chr2:111807674-111807694 1.0000 20 chrX:12996454-12996474 1.0000 20 ******************************************************************************** ******************************************************************************** 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/GM12878/inference_raw/MEME/RankLinear0.6_10_NFATC1/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/GM12878/fasta/RankLinear0.6_10/NFATC1.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= 250 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= 5000 N= 250 sample: seed= 0 hsfrac= 0 searchsize= 5000 norand= no csites= 1000 Letter frequencies in dataset: A 0.278 C 0.216 G 0.218 T 0.288 Background letter frequencies (from file dataset with add-one prior applied): A 0.278 C 0.216 G 0.218 T 0.288 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF RTGTGTGH MEME-1 width = 8 sites = 52 llr = 359 E-value = 1.3e-025 ******************************************************************************** -------------------------------------------------------------------------------- Motif RTGTGTGH MEME-1 Description -------------------------------------------------------------------------------- Simplified A 3::3::14 pos.-specific C 2:1:::24 probability G 5:91a:7: matrix T 1a:7:a:2 bits 2.2 * 2.0 * 1.8 * ** 1.5 ** ** Relative 1.3 ** ** Entropy 1.1 ** *** (10.0 bits) 0.9 ** *** 0.7 ****** 0.4 ******* 0.2 ******** 0.0 -------- Multilevel GTGTGTGA consensus A A C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RTGTGTGH MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr6:43721757-43721777 5 1.17e-05 aggt gtgtgtgc gtatgtgt chr17:35174387-35174407 8 1.17e-05 cgtgtgt gtgtgtgc atgtg chr10:134568758-13456877 5 1.17e-05 GCAG Gtgtgtgc atgtgagc chr17:62077184-62077204 7 1.17e-05 gtgcac gtgtgtgC GAGCGG chr8:144636681-144636701 2 1.17e-05 c GTGTGTGC TCACGTGcac chr4:3470571-3470591 1 1.17e-05 . gtgtgtgc gcgtatgagt chr22:36029689-36029709 13 1.17e-05 gcgtgtgtca gtgtgtgc chr21:44011826-44011846 7 1.17e-05 gtgcgt gtgtgtgc gtgcat chr9:130628301-130628321 9 1.17e-05 gaatgagt gtgtgtgc aagt chr1:226837185-226837205 8 1.17e-05 tgcatca gtgtgtgc atgcg chr15:41206410-41206430 1 2.67e-05 . gtgtgtga gtgtacgact chr9:138542356-138542376 12 6.83e-05 gtgtgcgagt gtgtgtgt g chr21:35267819-35267839 12 6.83e-05 gtgtgcatgt gtgtgtgt c chr4:68424351-68424371 9 6.83e-05 AAAAgtgt gtgtgtgt gtgt chr18:46546100-46546120 4 1.02e-04 AGT GTGAGTGA ACGAGCAtg chr19:46461765-46461785 4 1.02e-04 agc atgtgtga caatgtgtg chr17:21247817-21247837 12 1.02e-04 aactatgagt atgtgtga c chr17:72541409-72541429 8 1.02e-04 tgtgtgc atgtgtga ctgtg chr18:28565928-28565948 4 1.13e-04 cat ctgtgtgc tcatttgtg chr22:39157850-39157870 9 1.13e-04 ttgtgtga ctgtgtgc aagt chr13:21596413-21596433 12 2.04e-04 ttgtatgtgc atgtgtgt g chr9:36843042-36843062 3 2.04e-04 gt gtgagtgt atcagtgtgt chr12:125000200-12500022 1 2.04e-04 . gtgagtgt gcatgtgagt chr7:155055635-155055655 1 2.04e-04 . atgtgtgt ctgagtgtta chr15:101326484-10132650 10 2.04e-04 agtgtgtat atgtgtgt atg chr21:16810383-16810403 1 2.38e-04 . TTGTGTGC ACGTTTCTGT chr10:5888319-5888339 3 2.38e-04 CT TTGTGTGC TGGAAAATGT chr10:134502318-13450233 8 2.84e-04 tgcatga ctgagtgc aagtg chr1:231147143-231147163 10 3.49e-04 ttgtgtaga ctgagtga tga chr7:121635188-121635208 9 3.49e-04 TGTTAGTT GTGGGTGC CCTC chr9:140699673-140699693 4 3.93e-04 TCC ATGTGTCA GTCCACATG chr12:6744707-6744727 11 4.72e-04 AGTGGAAAAA GTGTGTAA AC chr4:178674859-178674879 6 4.72e-04 aacag ctgtgtca aaatttc chr3:188107965-188107985 11 5.19e-04 CTTTCCATTG TTGTGTGT GG chr17:57840068-57840088 13 5.68e-04 GTCAGTTTAG TTGAGTGA chr12:76132401-76132421 10 6.40e-04 TCCACGGGA GTGGGTGT TAC chr15:93375011-93375031 5 6.73e-04 AACA ATGAGTCA TTCATGCT chr1:183871331-183871351 2 6.73e-04 T ATGAGTCA ATGACCATCT chr6:37207985-37208005 6 6.73e-04 tttcc atgagtca ggaatcc chrX:120442325-120442345 13 6.73e-04 CATGGAACAA ATGAGTCA chr11:60859922-60859942 6 7.96e-04 TCCTC TTGTGTCA TGGAAAG chr21:26954704-26954724 6 7.96e-04 atcaa atgtgtac acaaaga chr17:38309778-38309798 4 8.88e-04 ttg ctgagtca tgtggtaac chr15:33162809-33162829 11 8.88e-04 AACGTCACAG CTGAGTCA GA chr6:35270527-35270547 2 8.88e-04 t ctgagtca gtaggtctgg chr20:4970401-4970421 7 9.79e-04 catcct gtcagtgc tcaaaa chr2:765525-765545 3 9.79e-04 AC ATCTGTGC TGATATGTAC chr19:4053594-4053614 9 9.79e-04 gtgcatgt gtatgtga tgtg chr6:164056500-164056520 8 9.79e-04 tgaatga gtatgtga aagtg chr1:53744094-53744114 6 9.79e-04 ccaga gtctgtgt tttcact chr15:59541714-59541734 7 1.40e-03 GAAAAT ATGAGTAA GACTGA chr1:27959131-27959151 6 1.78e-03 TTCTT GTGGGTAA AAGTGGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RTGTGTGH MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:43721757-43721777 1.2e-05 4_[+1]_8 chr17:35174387-35174407 1.2e-05 7_[+1]_5 chr10:134568758-13456877 1.2e-05 4_[+1]_8 chr17:62077184-62077204 1.2e-05 6_[+1]_6 chr8:144636681-144636701 1.2e-05 1_[+1]_11 chr4:3470571-3470591 1.2e-05 [+1]_12 chr22:36029689-36029709 1.2e-05 12_[+1] chr21:44011826-44011846 1.2e-05 6_[+1]_6 chr9:130628301-130628321 1.2e-05 8_[+1]_4 chr1:226837185-226837205 1.2e-05 7_[+1]_5 chr15:41206410-41206430 2.7e-05 [+1]_12 chr9:138542356-138542376 6.8e-05 11_[+1]_1 chr21:35267819-35267839 6.8e-05 11_[+1]_1 chr4:68424351-68424371 6.8e-05 8_[+1]_4 chr18:46546100-46546120 0.0001 3_[+1]_9 chr19:46461765-46461785 0.0001 3_[+1]_9 chr17:21247817-21247837 0.0001 11_[+1]_1 chr17:72541409-72541429 0.0001 7_[+1]_5 chr18:28565928-28565948 0.00011 3_[+1]_9 chr22:39157850-39157870 0.00011 8_[+1]_4 chr13:21596413-21596433 0.0002 11_[+1]_1 chr9:36843042-36843062 0.0002 2_[+1]_10 chr12:125000200-12500022 0.0002 [+1]_12 chr7:155055635-155055655 0.0002 [+1]_12 chr15:101326484-10132650 0.0002 9_[+1]_3 chr21:16810383-16810403 0.00024 [+1]_12 chr10:5888319-5888339 0.00024 2_[+1]_10 chr10:134502318-13450233 0.00028 7_[+1]_5 chr1:231147143-231147163 0.00035 9_[+1]_3 chr7:121635188-121635208 0.00035 8_[+1]_4 chr9:140699673-140699693 0.00039 3_[+1]_9 chr12:6744707-6744727 0.00047 10_[+1]_2 chr4:178674859-178674879 0.00047 5_[+1]_7 chr3:188107965-188107985 0.00052 10_[+1]_2 chr17:57840068-57840088 0.00057 12_[+1] chr12:76132401-76132421 0.00064 9_[+1]_3 chr15:93375011-93375031 0.00067 4_[+1]_8 chr1:183871331-183871351 0.00067 1_[+1]_11 chr6:37207985-37208005 0.00067 5_[+1]_7 chrX:120442325-120442345 0.00067 12_[+1] chr11:60859922-60859942 0.0008 5_[+1]_7 chr21:26954704-26954724 0.0008 5_[+1]_7 chr17:38309778-38309798 0.00089 3_[+1]_9 chr15:33162809-33162829 0.00089 10_[+1]_2 chr6:35270527-35270547 0.00089 1_[+1]_11 chr20:4970401-4970421 0.00098 6_[+1]_6 chr2:765525-765545 0.00098 2_[+1]_10 chr19:4053594-4053614 0.00098 8_[+1]_4 chr6:164056500-164056520 0.00098 7_[+1]_5 chr1:53744094-53744114 0.00098 5_[+1]_7 chr15:59541714-59541734 0.0014 6_[+1]_6 chr1:27959131-27959151 0.0018 5_[+1]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RTGTGTGH MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RTGTGTGH width=8 seqs=52 chr6:43721757-43721777 ( 5) GTGTGTGC 1 chr17:35174387-35174407 ( 8) GTGTGTGC 1 chr10:134568758-13456877 ( 5) GTGTGTGC 1 chr17:62077184-62077204 ( 7) GTGTGTGC 1 chr8:144636681-144636701 ( 2) GTGTGTGC 1 chr4:3470571-3470591 ( 1) GTGTGTGC 1 chr22:36029689-36029709 ( 13) GTGTGTGC 1 chr21:44011826-44011846 ( 7) GTGTGTGC 1 chr9:130628301-130628321 ( 9) GTGTGTGC 1 chr1:226837185-226837205 ( 8) GTGTGTGC 1 chr15:41206410-41206430 ( 1) GTGTGTGA 1 chr9:138542356-138542376 ( 12) GTGTGTGT 1 chr21:35267819-35267839 ( 12) GTGTGTGT 1 chr4:68424351-68424371 ( 9) GTGTGTGT 1 chr18:46546100-46546120 ( 4) GTGAGTGA 1 chr19:46461765-46461785 ( 4) ATGTGTGA 1 chr17:21247817-21247837 ( 12) ATGTGTGA 1 chr17:72541409-72541429 ( 8) ATGTGTGA 1 chr18:28565928-28565948 ( 4) CTGTGTGC 1 chr22:39157850-39157870 ( 9) CTGTGTGC 1 chr13:21596413-21596433 ( 12) ATGTGTGT 1 chr9:36843042-36843062 ( 3) GTGAGTGT 1 chr12:125000200-12500022 ( 1) GTGAGTGT 1 chr7:155055635-155055655 ( 1) ATGTGTGT 1 chr15:101326484-10132650 ( 10) ATGTGTGT 1 chr21:16810383-16810403 ( 1) TTGTGTGC 1 chr10:5888319-5888339 ( 3) TTGTGTGC 1 chr10:134502318-13450233 ( 8) CTGAGTGC 1 chr1:231147143-231147163 ( 10) CTGAGTGA 1 chr7:121635188-121635208 ( 9) GTGGGTGC 1 chr9:140699673-140699693 ( 4) ATGTGTCA 1 chr12:6744707-6744727 ( 11) GTGTGTAA 1 chr4:178674859-178674879 ( 6) CTGTGTCA 1 chr3:188107965-188107985 ( 11) TTGTGTGT 1 chr17:57840068-57840088 ( 13) TTGAGTGA 1 chr12:76132401-76132421 ( 10) GTGGGTGT 1 chr15:93375011-93375031 ( 5) ATGAGTCA 1 chr1:183871331-183871351 ( 2) ATGAGTCA 1 chr6:37207985-37208005 ( 6) ATGAGTCA 1 chrX:120442325-120442345 ( 13) ATGAGTCA 1 chr11:60859922-60859942 ( 6) TTGTGTCA 1 chr21:26954704-26954724 ( 6) ATGTGTAC 1 chr17:38309778-38309798 ( 4) CTGAGTCA 1 chr15:33162809-33162829 ( 11) CTGAGTCA 1 chr6:35270527-35270547 ( 2) CTGAGTCA 1 chr20:4970401-4970421 ( 7) GTCAGTGC 1 chr2:765525-765545 ( 3) ATCTGTGC 1 chr19:4053594-4053614 ( 9) GTATGTGA 1 chr6:164056500-164056520 ( 8) GTATGTGA 1 chr1:53744094-53744114 ( 6) GTCTGTGT 1 chr15:59541714-59541734 ( 7) ATGAGTAA 1 chr1:27959131-27959151 ( 6) GTGGGTAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RTGTGTGH MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 7.11984 E= 1.3e-025 -5 -49 114 -158 -1234 -1234 -1234 179 -285 -190 205 -1234 5 -1234 -192 118 -1234 -1234 220 -1234 -1234 -1234 -1234 179 -185 -17 175 -1234 60 76 -1234 -45 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RTGTGTGH MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 52 E= 1.3e-025 0.269231 0.153846 0.480769 0.096154 0.000000 0.000000 0.000000 1.000000 0.038462 0.057692 0.903846 0.000000 0.288462 0.000000 0.057692 0.653846 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.076923 0.192308 0.730769 0.000000 0.423077 0.365385 0.000000 0.211538 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RTGTGTGH MEME-1 regular expression -------------------------------------------------------------------------------- [GA]TG[TA]GTG[ACT] -------------------------------------------------------------------------------- Time 3.08 secs. ******************************************************************************** ******************************************************************************** MOTIF RCACACAC MEME-2 width = 8 sites = 24 llr = 214 E-value = 1.6e-018 ******************************************************************************** -------------------------------------------------------------------------------- Motif RCACACAC MEME-2 Description -------------------------------------------------------------------------------- Simplified A 4:9:a:9: pos.-specific C :a:8:a:a probability G 5:1::::: matrix T 1::2::1: bits 2.2 * * 2.0 * * * 1.8 * ** * 1.5 * ** * Relative 1.3 ******* Entropy 1.1 ******* (12.9 bits) 0.9 ******* 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GCACACAC consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCACACAC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr9:138899322-138899342 3 1.02e-05 ac gcacacac gcacagacac chr19:2557178-2557198 11 1.02e-05 caAGACACGT GCACACAC AT chr2:240212379-240212399 6 1.02e-05 cgcat gcacacac acgcacg chr11:65577998-65578018 2 1.02e-05 c gcacacac atgcacacTC chr17:79943032-79943052 10 1.02e-05 cgcacacct gcacacac cca chr13:111526489-11152650 10 1.02e-05 tacacatct gcacacac gtc chr17:74273772-74273792 9 1.02e-05 tcatacat gcacacac atac chr20:62478614-62478634 11 2.32e-05 acaagcagag acacacac ac chr17:8732784-8732804 3 2.32e-05 tg acacacac tcatgcacgc chr17:72094982-72095002 12 2.32e-05 atgcacattc acacacac a chr17:65050944-65050964 2 2.32e-05 g acacacac tgacacacac chr21:45731246-45731266 13 5.83e-05 acacacagac gcgcacac chr21:44090390-44090410 13 5.83e-05 acatacacat tcacacac chr22:44542183-44542203 8 5.83e-05 cacgtgc tcacacac gcaca chr19:3831010-3831030 11 5.83e-05 aggcacacat gcgcacac at chr20:33153748-33153768 13 7.56e-05 tcacaggtac acatacac chr20:61182477-61182497 7 7.56e-05 cgtgac acatacac atccct chr7:1110385-1110405 10 7.56e-05 cgcacgcag acatacac atg chr21:37314818-37314838 11 7.56e-05 acatttgcac acatacac aT chr18:11146028-11146048 9 8.62e-05 acacatgt gcacactc acac chr12:124963896-12496391 13 8.62e-05 tgcaacacat gcacactc chr17:74181480-74181500 6 1.15e-04 ATAAA GCAGACAC AGTCATC chr12:105064336-10506435 7 1.38e-04 atacac acccacac atgcac chr17:75878180-75878200 10 1.64e-04 actgtatag gcacaaac gga -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCACACAC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr9:138899322-138899342 1e-05 2_[+2]_10 chr19:2557178-2557198 1e-05 10_[+2]_2 chr2:240212379-240212399 1e-05 5_[+2]_7 chr11:65577998-65578018 1e-05 1_[+2]_11 chr17:79943032-79943052 1e-05 9_[+2]_3 chr13:111526489-11152650 1e-05 9_[+2]_3 chr17:74273772-74273792 1e-05 8_[+2]_4 chr20:62478614-62478634 2.3e-05 10_[+2]_2 chr17:8732784-8732804 2.3e-05 2_[+2]_10 chr17:72094982-72095002 2.3e-05 11_[+2]_1 chr17:65050944-65050964 2.3e-05 1_[+2]_11 chr21:45731246-45731266 5.8e-05 12_[+2] chr21:44090390-44090410 5.8e-05 12_[+2] chr22:44542183-44542203 5.8e-05 7_[+2]_5 chr19:3831010-3831030 5.8e-05 10_[+2]_2 chr20:33153748-33153768 7.6e-05 12_[+2] chr20:61182477-61182497 7.6e-05 6_[+2]_6 chr7:1110385-1110405 7.6e-05 9_[+2]_3 chr21:37314818-37314838 7.6e-05 10_[+2]_2 chr18:11146028-11146048 8.6e-05 8_[+2]_4 chr12:124963896-12496391 8.6e-05 12_[+2] chr17:74181480-74181500 0.00011 5_[+2]_7 chr12:105064336-10506435 0.00014 6_[+2]_6 chr17:75878180-75878200 0.00016 9_[+2]_3 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCACACAC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RCACACAC width=8 seqs=24 chr9:138899322-138899342 ( 3) GCACACAC 1 chr19:2557178-2557198 ( 11) GCACACAC 1 chr2:240212379-240212399 ( 6) GCACACAC 1 chr11:65577998-65578018 ( 2) GCACACAC 1 chr17:79943032-79943052 ( 10) GCACACAC 1 chr13:111526489-11152650 ( 10) GCACACAC 1 chr17:74273772-74273792 ( 9) GCACACAC 1 chr20:62478614-62478634 ( 11) ACACACAC 1 chr17:8732784-8732804 ( 3) ACACACAC 1 chr17:72094982-72095002 ( 12) ACACACAC 1 chr17:65050944-65050964 ( 2) ACACACAC 1 chr21:45731246-45731266 ( 13) GCGCACAC 1 chr21:44090390-44090410 ( 13) TCACACAC 1 chr22:44542183-44542203 ( 8) TCACACAC 1 chr19:3831010-3831030 ( 11) GCGCACAC 1 chr20:33153748-33153768 ( 13) ACATACAC 1 chr20:61182477-61182497 ( 7) ACATACAC 1 chr7:1110385-1110405 ( 10) ACATACAC 1 chr21:37314818-37314838 ( 11) ACATACAC 1 chr18:11146028-11146048 ( 9) GCACACTC 1 chr12:124963896-12496391 ( 13) GCACACTC 1 chr17:74181480-74181500 ( 6) GCAGACAC 1 chr12:105064336-10506435 ( 7) ACCCACAC 1 chr17:75878180-75878200 ( 10) GCACAAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCACACAC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 8.66267 E= 1.6e-018 43 -1123 131 -179 -1123 221 -1123 -1123 165 -237 -139 -1123 -1123 187 -238 -79 185 -1123 -1123 -1123 -274 215 -1123 -1123 172 -1123 -1123 -179 -1123 221 -1123 -1123 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCACACAC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.6e-018 0.375000 0.000000 0.541667 0.083333 0.000000 1.000000 0.000000 0.000000 0.875000 0.041667 0.083333 0.000000 0.000000 0.791667 0.041667 0.166667 1.000000 0.000000 0.000000 0.000000 0.041667 0.958333 0.000000 0.000000 0.916667 0.000000 0.000000 0.083333 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCACACAC MEME-2 regular expression -------------------------------------------------------------------------------- [GA]CACACAC -------------------------------------------------------------------------------- Time 3.84 secs. ******************************************************************************** ******************************************************************************** MOTIF TTTTCCAT MEME-3 width = 8 sites = 24 llr = 199 E-value = 4.8e-012 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTTCCAT MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::::::8: pos.-specific C 2:::aa:1 probability G 3:::::21 matrix T 5aaa:::7 bits 2.2 ** 2.0 ** 1.8 **** 1.5 ***** Relative 1.3 ****** Entropy 1.1 ****** (12.0 bits) 0.9 ****** 0.7 ******* 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TTTTCCAT consensus G sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTCCAT MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr13:105701300-10570132 12 2.57e-05 TGCAAGCTTA TTTTCCAT T chr11:109960416-10996043 1 2.57e-05 . TTTTCCAT TAGTAATGCT chr2:233807698-233807718 10 2.57e-05 TGTCTCATT TTTTCCAT GCA chr2:61126857-61126877 11 2.57e-05 ATGTCATGGT TTTTCCAT GT chr12:95634517-95634537 8 2.57e-05 CAGCTAA TTTTCCAT TTTGG chr5:171388313-171388333 13 2.57e-05 ACGAGTGTTG TTTTCCAT chr1:42107264-42107284 1 2.57e-05 . TTTTCCAT AGAAAGTTTC chr19:10216538-10216558 10 4.52e-05 TGATGTGGA GTTTCCAT CCC chr17:31203434-31203454 2 4.52e-05 A GTTTCCAT GAGGTCACCG chr12:90103478-90103498 11 4.52e-05 TGACGTCCGT GTTTCCAT GA chr3:188107965-188107985 1 6.44e-05 . CTTTCCAT TGTTGTGTGT chr15:83761307-83761327 7 6.44e-05 cagttt ctttccat tagatc chr3:144013630-144013650 9 6.44e-05 CAGGCCAC CTTTCCAT TCTG chr8:126447052-126447072 8 8.46e-05 AGTCATA TTTTCCGT TTACA chr11:71673821-71673841 4 1.23e-04 ttg ttttccac agaagctgc chr13:73574368-73574388 8 1.23e-04 ACTCATG TTTTCCAC TTCCT chr2:62533073-62533093 7 1.23e-04 GTCATT TTTTCCAG ATGTGG chr2:48540889-48540909 5 1.39e-04 CTCC GTTTCCGT ATCTGTAA chr1:53125232-53125252 13 1.68e-04 atgactcaaa gtttccag chr2:28114156-28114176 3 1.83e-04 CC CTTTCCGT TCCATGACGT chr6:143141278-143141298 13 2.12e-04 CATTGTCATA CTTTCCAC chr8:56757158-56757178 10 2.42e-04 CATTCGCGG TTTTCCGG CCA chr8:104090774-104090794 7 2.86e-04 TTTCAT TTTTCCAA TATGTC chr6:412706-412726 9 3.43e-04 gtaagtgg gcttccat aaga -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTCCAT MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr13:105701300-10570132 2.6e-05 11_[+3]_1 chr11:109960416-10996043 2.6e-05 [+3]_12 chr2:233807698-233807718 2.6e-05 9_[+3]_3 chr2:61126857-61126877 2.6e-05 10_[+3]_2 chr12:95634517-95634537 2.6e-05 7_[+3]_5 chr5:171388313-171388333 2.6e-05 12_[+3] chr1:42107264-42107284 2.6e-05 [+3]_12 chr19:10216538-10216558 4.5e-05 9_[+3]_3 chr17:31203434-31203454 4.5e-05 1_[+3]_11 chr12:90103478-90103498 4.5e-05 10_[+3]_2 chr3:188107965-188107985 6.4e-05 [+3]_12 chr15:83761307-83761327 6.4e-05 6_[+3]_6 chr3:144013630-144013650 6.4e-05 8_[+3]_4 chr8:126447052-126447072 8.5e-05 7_[+3]_5 chr11:71673821-71673841 0.00012 3_[+3]_9 chr13:73574368-73574388 0.00012 7_[+3]_5 chr2:62533073-62533093 0.00012 6_[+3]_6 chr2:48540889-48540909 0.00014 4_[+3]_8 chr1:53125232-53125252 0.00017 12_[+3] chr2:28114156-28114176 0.00018 2_[+3]_10 chr6:143141278-143141298 0.00021 12_[+3] chr8:56757158-56757178 0.00024 9_[+3]_3 chr8:104090774-104090794 0.00029 6_[+3]_6 chr6:412706-412726 0.00034 8_[+3]_4 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTCCAT MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTTTCCAT width=8 seqs=24 chr13:105701300-10570132 ( 12) TTTTCCAT 1 chr11:109960416-10996043 ( 1) TTTTCCAT 1 chr2:233807698-233807718 ( 10) TTTTCCAT 1 chr2:61126857-61126877 ( 11) TTTTCCAT 1 chr12:95634517-95634537 ( 8) TTTTCCAT 1 chr5:171388313-171388333 ( 13) TTTTCCAT 1 chr1:42107264-42107284 ( 1) TTTTCCAT 1 chr19:10216538-10216558 ( 10) GTTTCCAT 1 chr17:31203434-31203454 ( 2) GTTTCCAT 1 chr12:90103478-90103498 ( 11) GTTTCCAT 1 chr3:188107965-188107985 ( 1) CTTTCCAT 1 chr15:83761307-83761327 ( 7) CTTTCCAT 1 chr3:144013630-144013650 ( 9) CTTTCCAT 1 chr8:126447052-126447072 ( 8) TTTTCCGT 1 chr11:71673821-71673841 ( 4) TTTTCCAC 1 chr13:73574368-73574388 ( 8) TTTTCCAC 1 chr2:62533073-62533093 ( 7) TTTTCCAG 1 chr2:48540889-48540909 ( 5) GTTTCCGT 1 chr1:53125232-53125252 ( 13) GTTTCCAG 1 chr2:28114156-28114176 ( 3) CTTTCCGT 1 chr6:143141278-143141298 ( 13) CTTTCCAC 1 chr8:56757158-56757178 ( 10) TTTTCCGG 1 chr8:104090774-104090794 ( 7) TTTTCCAA 1 chr6:412706-412726 ( 9) GCTTCCAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTCCAT MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 8.17582 E= 4.8e-012 -1123 -5 20 91 -1123 -237 -1123 173 -1123 -1123 -1123 179 -1123 -1123 -1123 179 -1123 221 -1123 -1123 -1123 221 -1123 -1123 158 -1123 -39 -1123 -274 -79 -80 130 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTCCAT MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 4.8e-012 0.000000 0.208333 0.250000 0.541667 0.000000 0.041667 0.000000 0.958333 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 1.000000 0.000000 0.000000 0.833333 0.000000 0.166667 0.000000 0.041667 0.125000 0.125000 0.708333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTCCAT MEME-3 regular expression -------------------------------------------------------------------------------- [TGC]TTTCCAT -------------------------------------------------------------------------------- Time 4.67 secs. ******************************************************************************** ******************************************************************************** MOTIF ARTGGAAA MEME-4 width = 8 sites = 19 llr = 164 E-value = 1.2e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif ARTGGAAA MEME-4 Description -------------------------------------------------------------------------------- Simplified A 751:1aa9 pos.-specific C 2::::::: probability G 15:a9::: matrix T ::9::::1 bits 2.2 * 2.0 * 1.8 **** 1.5 ****** Relative 1.3 ****** Entropy 1.1 ******* (12.5 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel AATGGAAA consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARTGGAAA MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr12:6744707-6744727 1 1.78e-05 . AGTGGAAA AAGTGTGTAA chr12:111214624-11121464 5 1.78e-05 TCAC AGTGGAAA ATAAGAGT chr1:87799550-87799570 6 1.78e-05 TTTGA AGTGGAAA AATTGAC chr1:185409463-185409483 5 1.78e-05 GGTC AGTGGAAA ATGTGATG chr7:144518361-144518381 13 1.78e-05 TTACCTGGCA AGTGGAAA chr2:25781384-25781404 13 4.05e-05 ACTTCTTTGT AATGGAAA chr20:18620427-18620447 9 4.05e-05 TTCTTTGT AATGGAAA GATC chr2:218479374-218479394 6 4.05e-05 GGTGT AATGgaaa gacctgt chr15:75397365-75397385 13 4.05e-05 GAGATGAGGA AATGGAAA chr14:55840732-55840752 7 4.05e-05 ATTCTC AATGGAAA ACCTGA chr3:141515531-141515551 8 5.44e-05 GAGGCAC CGTGGAAA GTATG chr1:156786649-156786669 7 7.21e-05 TCACGT CATGGAAA GCCTTA chr1:38993143-38993163 12 7.21e-05 aggctgatgt catggaaa g chr4:37767483-37767503 4 8.60e-05 GAG GGTGGAAA TTCTGACTC chr1:235080861-235080881 9 1.04e-04 agtttgtg gatggaaa ttat chr6:30582596-30582616 2 1.27e-04 A AGTGAAAA TAAAAACTGG chr5:178977249-178977269 11 1.56e-04 TAGACCATGA AATGAAAA TT chr7:871502-871522 6 1.73e-04 TAGCC AGAGGAAA GTATGAG chr17:62631949-62631969 9 2.37e-04 tacctagg aatggaat tgct -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARTGGAAA MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr12:6744707-6744727 1.8e-05 [+4]_12 chr12:111214624-11121464 1.8e-05 4_[+4]_8 chr1:87799550-87799570 1.8e-05 5_[+4]_7 chr1:185409463-185409483 1.8e-05 4_[+4]_8 chr7:144518361-144518381 1.8e-05 12_[+4] chr2:25781384-25781404 4.1e-05 12_[+4] chr20:18620427-18620447 4.1e-05 8_[+4]_4 chr2:218479374-218479394 4.1e-05 5_[+4]_7 chr15:75397365-75397385 4.1e-05 12_[+4] chr14:55840732-55840752 4.1e-05 6_[+4]_6 chr3:141515531-141515551 5.4e-05 7_[+4]_5 chr1:156786649-156786669 7.2e-05 6_[+4]_6 chr1:38993143-38993163 7.2e-05 11_[+4]_1 chr4:37767483-37767503 8.6e-05 3_[+4]_9 chr1:235080861-235080881 0.0001 8_[+4]_4 chr6:30582596-30582616 0.00013 1_[+4]_11 chr5:178977249-178977269 0.00016 10_[+4]_2 chr7:871502-871522 0.00017 5_[+4]_7 chr17:62631949-62631969 0.00024 8_[+4]_4 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARTGGAAA MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ARTGGAAA width=8 seqs=19 chr12:6744707-6744727 ( 1) AGTGGAAA 1 chr12:111214624-11121464 ( 5) AGTGGAAA 1 chr1:87799550-87799570 ( 6) AGTGGAAA 1 chr1:185409463-185409483 ( 5) AGTGGAAA 1 chr7:144518361-144518381 ( 13) AGTGGAAA 1 chr2:25781384-25781404 ( 13) AATGGAAA 1 chr20:18620427-18620447 ( 9) AATGGAAA 1 chr2:218479374-218479394 ( 6) AATGGAAA 1 chr15:75397365-75397385 ( 13) AATGGAAA 1 chr14:55840732-55840752 ( 7) AATGGAAA 1 chr3:141515531-141515551 ( 8) CGTGGAAA 1 chr1:156786649-156786669 ( 7) CATGGAAA 1 chr1:38993143-38993163 ( 12) CATGGAAA 1 chr4:37767483-37767503 ( 4) GGTGGAAA 1 chr1:235080861-235080881 ( 9) GATGGAAA 1 chr6:30582596-30582616 ( 2) AGTGAAAA 1 chr5:178977249-178977269 ( 11) AATGAAAA 1 chr7:871502-871522 ( 6) AGAGGAAA 1 chr17:62631949-62631969 ( 9) AATGGAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARTGGAAA MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 8.31119 E= 1.2e-007 140 -45 -105 -1089 92 -1089 112 -1089 -240 -1089 -1089 172 -1089 -1089 220 -1089 -140 -1089 204 -1089 185 -1089 -1089 -1089 185 -1089 -1089 -1089 177 -1089 -1089 -245 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARTGGAAA MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 1.2e-007 0.736842 0.157895 0.105263 0.000000 0.526316 0.000000 0.473684 0.000000 0.052632 0.000000 0.000000 0.947368 0.000000 0.000000 1.000000 0.000000 0.105263 0.000000 0.894737 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.947368 0.000000 0.000000 0.052632 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARTGGAAA MEME-4 regular expression -------------------------------------------------------------------------------- A[AG]TGGAAA -------------------------------------------------------------------------------- Time 5.37 secs. ******************************************************************************** ******************************************************************************** MOTIF TGACTCAT MEME-5 width = 8 sites = 8 llr = 75 E-value = 2.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGACTCAT MEME-5 Description -------------------------------------------------------------------------------- Simplified A 1:9:::a1 pos.-specific C :::a:a:: probability G :a:::::1 matrix T 9:1:a::8 bits 2.2 * * * 2.0 * * * 1.8 * **** 1.5 * **** Relative 1.3 ******* Entropy 1.1 ******* (13.6 bits) 0.9 ******** 0.7 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TGACTCAT consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGACTCAT MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr5:172333631-172333651 1 1.88e-05 . TGACTCAT TCTTTCCCTA chr7:124533353-124533373 9 1.88e-05 CTAAATTT TGACTCAT AACT chr5:82602633-82602653 1 1.88e-05 . TGACTCAT GTTTTTGTGG chr9:79191445-79191465 10 1.88e-05 TGGAACAGT TGACTCAT GGC chr4:48249375-48249395 6 3.30e-05 tcgta tgactcag catttcc chr1:53125232-53125252 4 5.11e-05 aga tgactcaa agtttccag chr1:219638785-219638805 6 6.92e-05 CATTC AGACTCAT AACAATA chr2:233807698-233807718 1 8.87e-05 . TGTCTCAT TTTTTCCATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGACTCAT MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr5:172333631-172333651 1.9e-05 [+5]_12 chr7:124533353-124533373 1.9e-05 8_[+5]_4 chr5:82602633-82602653 1.9e-05 [+5]_12 chr9:79191445-79191465 1.9e-05 9_[+5]_3 chr4:48249375-48249395 3.3e-05 5_[+5]_7 chr1:53125232-53125252 5.1e-05 3_[+5]_9 chr1:219638785-219638805 6.9e-05 5_[+5]_7 chr2:233807698-233807718 8.9e-05 [+5]_12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGACTCAT MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGACTCAT width=8 seqs=8 chr5:172333631-172333651 ( 1) TGACTCAT 1 chr7:124533353-124533373 ( 9) TGACTCAT 1 chr5:82602633-82602653 ( 1) TGACTCAT 1 chr9:79191445-79191465 ( 10) TGACTCAT 1 chr4:48249375-48249395 ( 6) TGACTCAG 1 chr1:53125232-53125252 ( 4) TGACTCAA 1 chr1:219638785-219638805 ( 6) AGACTCAT 1 chr2:233807698-233807718 ( 1) TGTCTCAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGACTCAT MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 9.40106 E= 2.1e+002 -115 -965 -965 160 -965 -965 220 -965 165 -965 -965 -120 -965 221 -965 -965 -965 -965 -965 179 -965 221 -965 -965 184 -965 -965 -965 -115 -965 -80 138 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGACTCAT MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 8 E= 2.1e+002 0.125000 0.000000 0.000000 0.875000 0.000000 0.000000 1.000000 0.000000 0.875000 0.000000 0.000000 0.125000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.125000 0.000000 0.125000 0.750000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGACTCAT MEME-5 regular expression -------------------------------------------------------------------------------- TGACTCAT -------------------------------------------------------------------------------- Time 6.53 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:121635188-121635208 1.94e-01 20 chr4:37767483-37767503 3.03e-02 3_[+4(8.60e-05)]_9 chrX:120442325-120442345 2.77e-02 20 chr7:2681226-2681246 5.40e-01 20 chr1:75805086-75805106 4.31e-01 20 chr1:53125232-53125252 2.26e-04 3_[+5(5.11e-05)]_9 chr11:122614870-12261489 9.01e-01 20 chr7:144518361-144518381 2.57e-02 12_[+4(1.78e-05)] chr1:42107264-42107284 2.55e-03 [+3(2.57e-05)]_12 chr12:95576775-95576795 2.28e-01 20 chr1:231147143-231147163 1.34e-02 20 chr1:235080861-235080881 5.61e-02 20 chr1:53744094-53744114 3.72e-02 20 chr7:100143212-100143232 1.77e-01 20 chr6:119671693-119671713 5.58e-01 20 chr11:102906922-10290694 7.44e-01 20 chr6:11139781-11139801 4.45e-01 20 chr14:55840732-55840752 3.85e-03 6_[+4(4.05e-05)]_6 chr1:192775191-192775211 6.34e-01 20 chr2:233935527-233935547 7.40e-01 20 chr2:189843589-189843609 4.55e-01 20 chr15:59541714-59541734 2.14e-01 20 chr12:82832360-82832380 1.50e-01 20 chr17:65478185-65478205 4.93e-02 20 chr6:35270527-35270547 3.85e-02 20 chr10:5888319-5888339 1.50e-02 20 chr6:37207985-37208005 2.32e-02 20 chr1:185409463-185409483 1.70e-02 4_[+4(1.78e-05)]_8 chr1:87799550-87799570 4.38e-02 5_[+4(1.78e-05)]_7 chr1:181367915-181367935 5.05e-01 20 chr7:90242586-90242606 4.34e-01 20 chr19:3831010-3831030 5.92e-02 10_[+2(5.83e-05)]_2 chr6:56271223-56271243 3.35e-01 20 chr17:65050944-65050964 9.39e-03 1_[+2(2.32e-05)]_2_[+2(2.32e-05)]_1 chr18:61575025-61575045 1.80e-01 20 chr15:101326484-10132650 1.74e-01 20 chr1:25096226-25096246 5.73e-01 20 chr3:144013630-144013650 1.13e-01 8_[+3(6.44e-05)]_4 chr2:62533073-62533093 1.69e-01 20 chr6:46188632-46188652 4.45e-01 20 chr1:226837185-226837205 4.05e-03 7_[+1(1.17e-05)]_5 chr6:2079371-2079391 8.25e-01 20 chr5:115412490-115412510 7.10e-02 20 chr12:76132401-76132421 3.82e-01 20 chr10:5670958-5670978 7.17e-01 20 chr6:412706-412726 7.53e-02 20 chr17:68523931-68523951 5.81e-01 20 chr21:37314818-37314838 1.70e-02 10_[+2(7.56e-05)]_2 chr22:44542183-44542203 4.84e-02 7_[+2(5.83e-05)]_5 chr1:183871331-183871351 1.78e-02 20 chr15:83761307-83761327 3.32e-02 6_[+3(6.44e-05)]_6 chr17:72541409-72541429 2.10e-02 20 chr15:79399657-79399677 3.85e-01 20 chr2:223292541-223292561 6.09e-01 20 chr6:164056500-164056520 1.24e-01 20 chr5:88275272-88275292 6.43e-01 20 chr4:48249375-48249395 2.40e-02 5_[+5(3.30e-05)]_7 chr2:231121594-231121614 1.67e-01 20 chr7:11653181-11653201 1.36e-01 20 chr5:171388313-171388333 1.32e-02 12_[+3(2.57e-05)] chr15:77306292-77306312 3.40e-01 20 chr17:74273772-74273792 2.96e-03 8_[+2(1.02e-05)]_4 chr6:51766709-51766729 2.12e-01 20 chr7:1110385-1110405 4.73e-02 9_[+2(7.56e-05)]_3 chr4:40562041-40562061 7.76e-01 20 chr15:41206410-41206430 2.10e-02 [+1(2.67e-05)]_12 chr12:53811396-53811416 6.80e-01 20 chr12:95634517-95634537 6.58e-02 7_[+3(2.57e-05)]_5 chr19:1389240-1389260 7.56e-02 20 chr4:178674859-178674879 1.82e-02 20 chr3:56722403-56722423 1.99e-01 20 chr12:111214624-11121464 2.32e-02 4_[+4(1.78e-05)]_8 chr9:135280059-135280079 1.20e-01 20 chr12:123360516-12336053 2.80e-01 20 chr9:79191445-79191465 1.01e-02 9_[+5(1.88e-05)]_3 chr13:111526489-11152650 1.82e-02 9_[+2(1.02e-05)]_3 chr9:130628301-130628321 1.86e-02 8_[+1(1.17e-05)]_4 chr17:21247817-21247837 1.29e-01 20 chr12:90103478-90103498 1.36e-02 10_[+3(4.52e-05)]_2 chr21:44090390-44090410 3.71e-02 2_[+2(7.56e-05)]_2_[+2(5.83e-05)] chr8:56757158-56757178 2.63e-01 20 chr10:35283709-35283729 5.25e-01 20 chr6:144569828-144569848 3.94e-01 20 chr12:10438706-10438726 8.69e-01 20 chr16:48192367-48192387 6.99e-01 20 chr17:79943032-79943052 3.69e-02 9_[+2(1.02e-05)]_3 chr3:12602549-12602569 8.22e-01 20 chr8:129063105-129063125 5.72e-02 20 chr2:61126857-61126877 3.52e-02 10_[+3(2.57e-05)]_2 chr6:135466819-135466839 2.36e-01 20 chr21:44011826-44011846 1.36e-02 6_[+1(1.17e-05)]_6 chr1:38993143-38993163 2.34e-02 11_[+4(7.21e-05)]_1 chr2:64328624-64328644 8.61e-01 20 chr11:65577998-65578018 6.08e-03 1_[+2(1.02e-05)]_2_[+2(8.62e-05)]_1 chr22:36029689-36029709 2.80e-03 12_[+1(1.17e-05)] chr2:12644714-12644734 7.96e-01 20 chr12:124963896-12496391 4.04e-02 12_[+2(8.62e-05)] chr20:61182477-61182497 1.89e-03 6_[+2(7.56e-05)]_6 chr15:75397365-75397385 3.33e-02 12_[+4(4.05e-05)] chr5:176873492-176873512 8.27e-01 20 chr4:151953357-151953377 2.88e-01 20 chr22:39157850-39157870 2.99e-02 20 chr21:26955468-26955488 2.30e-02 20 chr4:3470571-3470591 2.75e-02 [+1(1.17e-05)]_12 chr12:65271292-65271312 5.74e-01 20 chr14:69253517-69253537 5.25e-01 20 chr7:871502-871522 8.57e-02 20 chr21:26944147-26944167 6.45e-01 20 chr1:63091342-63091362 5.31e-01 20 chr8:144636681-144636701 1.75e-03 1_[+1(1.17e-05)]_11 chr13:63098422-63098442 7.29e-01 20 chr13:73574368-73574388 1.27e-01 20 chr13:111288753-11128877 3.54e-01 20 chr4:68424351-68424371 1.34e-01 4_[+1(6.83e-05)]_[+1(6.83e-05)] chr4:112852014-112852034 1.22e-01 20 chr6:106969158-106969178 6.34e-01 20 chr17:72094982-72095002 1.54e-02 11_[+2(2.32e-05)]_1 chr5:1502038-1502058 1.49e-01 20 chr7:24795420-24795440 1.17e-01 20 chr5:82602633-82602653 1.36e-02 [+5(1.88e-05)]_12 chr5:178977249-178977269 1.58e-01 20 chr7:155055635-155055655 2.32e-02 20 chr16:11188885-11188905 6.87e-02 20 chr16:87908909-87908929 1.01e-01 20 chr8:104090774-104090794 2.16e-01 20 chr9:140699673-140699693 1.23e-02 20 chr17:27052479-27052499 8.14e-01 20 chr2:218479374-218479394 7.43e-02 5_[+4(4.05e-05)]_7 chr6:16690907-16690927 7.44e-01 20 chr2:240212379-240212399 9.17e-03 5_[+2(1.02e-05)]_7 chr11:35412732-35412752 2.08e-01 20 chr15:93375011-93375031 7.80e-03 20 chr2:36473601-36473621 6.54e-01 20 chr17:8732784-8732804 3.88e-03 2_[+2(2.32e-05)]_10 chr19:4053594-4053614 4.13e-01 20 chr16:17510976-17510996 5.26e-01 20 chr12:125000200-12500022 7.12e-02 20 chr1:97625108-97625128 5.40e-01 20 chr20:18620427-18620447 2.20e-02 8_[+4(4.05e-05)]_4 chr21:26954704-26954724 3.69e-02 20 chr12:43672322-43672342 1.41e-01 20 chr17:31203434-31203454 2.16e-02 1_[+3(4.52e-05)]_11 chr20:33153748-33153768 4.41e-02 12_[+2(7.56e-05)] chr11:71673821-71673841 3.00e-02 20 chr2:233807698-233807718 8.02e-04 [+5(8.87e-05)]_1_[+3(2.57e-05)]_3 chr12:114400413-11440043 2.66e-01 20 chr6:86171037-86171057 8.03e-02 20 chr9:115117814-115117834 5.80e-01 20 chr12:39861391-39861411 4.62e-01 20 chr12:6744707-6744727 2.25e-04 [+4(1.78e-05)]_12 chr10:134502318-13450233 8.76e-03 20 chr2:177862016-177862036 1.61e-01 20 chr8:126447052-126447072 4.15e-02 7_[+3(8.46e-05)]_5 chr18:28565928-28565948 7.70e-02 20 chr17:62077184-62077204 3.16e-02 6_[+1(1.17e-05)]_6 chr3:143388512-143388532 2.77e-01 20 chr20:62478614-62478634 1.01e-02 10_[+2(2.32e-05)]_2 chr7:124533353-124533373 1.77e-02 8_[+5(1.88e-05)]_4 chr12:105064336-10506435 1.35e-01 20 chr2:765525-765545 3.75e-01 20 chr4:56428244-56428264 5.28e-01 20 chr17:74181480-74181500 6.48e-03 20 chr8:138918216-138918236 4.97e-01 20 chr2:238907334-238907354 5.05e-01 20 chr19:51298292-51298312 9.60e-01 20 chr6:135898522-135898542 7.48e-01 20 chr16:11676179-11676199 9.06e-01 20 chr19:6663520-6663540 6.16e-01 20 chr10:90923458-90923478 6.75e-01 20 chr3:105891821-105891841 6.03e-01 20 chr2:62826063-62826083 5.24e-01 20 chr21:35267819-35267839 5.48e-02 9_[+1(6.83e-05)]_3 chr11:109960416-10996043 1.80e-02 [+3(2.57e-05)]_12 chr12:97769174-97769194 5.59e-01 20 chr3:138609795-138609815 5.61e-01 20 chr9:138542356-138542376 1.03e-01 9_[+1(6.83e-05)]_3 chr21:16810383-16810403 2.58e-02 20 chr6:143141278-143141298 3.29e-02 20 chr2:28114156-28114176 1.38e-01 20 chr2:25781384-25781404 2.39e-02 12_[+4(4.05e-05)] chr10:79260665-79260685 8.13e-01 20 chr19:46461765-46461785 2.98e-02 20 chr7:42909187-42909207 6.23e-01 20 chr15:58808141-58808161 2.82e-01 20 chr21:26938103-26938123 1.84e-01 20 chr10:134568758-13456877 1.53e-02 4_[+1(1.17e-05)]_8 chr1:156786649-156786669 1.23e-01 6_[+4(7.21e-05)]_6 chr4:106113095-106113115 2.58e-01 20 chr17:75878180-75878200 5.75e-02 20 chr19:2557178-2557198 3.85e-03 10_[+2(1.02e-05)]_2 chr3:14730960-14730980 4.25e-01 20 chr13:105701300-10570132 4.90e-02 11_[+3(2.57e-05)]_1 chr18:46546100-46546120 2.68e-02 20 chr18:11146028-11146048 1.18e-02 8_[+2(8.62e-05)]_4 chr5:15432180-15432200 4.10e-01 20 chr19:10216538-10216558 2.44e-02 9_[+3(4.52e-05)]_3 chr16:27450726-27450746 2.59e-01 20 chr2:38406379-38406399 9.91e-02 20 chr9:132779095-132779115 8.51e-01 20 chr3:188107965-188107985 5.89e-03 [+3(6.44e-05)]_12 chr16:27419522-27419542 9.04e-01 20 chr3:98241903-98241923 6.99e-01 20 chr15:29601525-29601545 5.71e-01 20 chr1:27959131-27959151 2.75e-01 20 chr17:35174387-35174407 1.76e-02 7_[+1(1.17e-05)]_5 chr3:9210184-9210204 3.09e-02 20 chr1:25227940-25227960 2.75e-01 20 chr9:36843042-36843062 1.61e-02 20 chr18:2959134-2959154 2.63e-01 20 chr11:60859922-60859942 3.42e-04 11_[+4(7.21e-05)]_1 chr17:62493556-62493576 5.87e-01 20 chr7:5565991-5566011 5.76e-01 20 chr12:118473559-11847357 9.15e-01 20 chr17:57840068-57840088 1.98e-01 20 chr1:247569683-247569703 6.13e-01 20 chr1:40866271-40866291 1.75e-02 20 chr8:71042841-71042861 4.55e-02 20 chr2:48540889-48540909 1.78e-02 20 chr2:172174552-172174572 7.32e-01 20 chr2:237967984-237968004 8.95e-01 20 chr6:148525319-148525339 5.99e-01 20 chr7:102036727-102036747 6.85e-01 20 chr17:62631949-62631969 2.15e-01 20 chr5:33300703-33300723 4.09e-01 20 chr10:121462210-12146223 8.93e-01 20 chr5:172333631-172333651 1.33e-03 [+5(1.88e-05)]_12 chr15:33162809-33162829 3.43e-02 20 chr13:21596413-21596433 1.98e-01 20 chr4:8421343-8421363 2.71e-01 20 chr21:26950805-26950825 5.73e-01 20 chr17:72508864-72508884 8.43e-01 20 chr9:79322578-79322598 1.92e-01 20 chr4:99404171-99404191 2.80e-01 20 chr20:4970401-4970421 9.38e-02 20 chr2:88315866-88315886 7.42e-01 20 chr6:43721757-43721777 2.35e-02 4_[+1(1.17e-05)]_8 chr6:30582596-30582616 9.94e-02 20 chr22:24050640-24050660 5.24e-01 20 chr17:38309778-38309798 7.85e-03 20 chr1:219638785-219638805 2.03e-03 5_[+5(6.92e-05)]_7 chr9:138899322-138899342 2.93e-02 2_[+2(1.02e-05)]_10 chr19:42627181-42627201 8.33e-01 20 chr19:13030159-13030179 1.16e-01 20 chr9:90150848-90150868 1.91e-01 20 chr3:141515531-141515551 5.89e-02 7_[+4(5.44e-05)]_5 chr21:26945386-26945406 6.12e-02 20 chr22:24830762-24830782 9.61e-01 20 chr21:45731246-45731266 3.11e-02 12_[+2(5.83e-05)] chr2:111807674-111807694 3.33e-01 20 chrX:12996454-12996474 5.31e-01 20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c22n04.farnam.hpc.yale.internal ********************************************************************************