******************************************************************************** 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/RB1.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr1:9555486-9555506 1.0000 20 chr19:46282717-46282737 1.0000 20 chr6:37137575-37137595 1.0000 20 chr15:44119229-44119249 1.0000 20 chr22:38966072-38966092 1.0000 20 chr16:3019249-3019269 1.0000 20 chr11:9595098-9595118 1.0000 20 chr6:35420211-35420231 1.0000 20 chr19:16222125-16222145 1.0000 20 chr17:60501152-60501172 1.0000 20 chr3:13461903-13461923 1.0000 20 chr16:30710236-30710256 1.0000 20 chr8:26435207-26435227 1.0000 20 chr10:70231632-70231652 1.0000 20 chr2:71503663-71503683 1.0000 20 chr12:7126208-7126228 1.0000 20 chr16:29984763-29984783 1.0000 20 chr11:58912291-58912311 1.0000 20 chr13:114238877-11423889 1.0000 20 chrX:153238342-153238362 1.0000 20 chr17:40897221-40897241 1.0000 20 chr14:50154903-50154923 1.0000 20 chr6:89855657-89855677 1.0000 20 chr21:37757765-37757785 1.0000 20 chr3:171515345-171515365 1.0000 20 chr10:43892071-43892091 1.0000 20 chr2:96822935-96822955 1.0000 20 chr1:16173936-16173956 1.0000 20 chr16:90074423-90074443 1.0000 20 chr14:105994777-10599479 1.0000 20 chr3:52058014-52058034 1.0000 20 chr16:19897713-19897733 1.0000 20 chr2:242823405-242823425 1.0000 20 chr2:153575194-153575214 1.0000 20 chr8:145669663-145669683 1.0000 20 chrX:153707449-153707469 1.0000 20 chr21:33104672-33104692 1.0000 20 chr14:23426333-23426353 1.0000 20 chr7:134671647-134671667 1.0000 20 chr1:91966514-91966534 1.0000 20 chr2:177005481-177005501 1.0000 20 chr3:197237108-197237128 1.0000 20 chr11:111472765-11147278 1.0000 20 chr7:2710774-2710794 1.0000 20 chr17:34838951-34838971 1.0000 20 chrX:19881777-19881797 1.0000 20 chr7:50517949-50517969 1.0000 20 chr1:211870875-211870895 1.0000 20 chr7:128116706-128116726 1.0000 20 chr5:150036131-150036151 1.0000 20 chr4:40058591-40058611 1.0000 20 chr2:48010307-48010327 1.0000 20 chr11:85565946-85565966 1.0000 20 chr22:18507323-18507343 1.0000 20 chr16:29937826-29937846 1.0000 20 chr1:24307179-24307199 1.0000 20 chr6:90539492-90539512 1.0000 20 chr6:36391145-36391165 1.0000 20 chr2:219432984-219433004 1.0000 20 chr22:42095523-42095543 1.0000 20 chr16:85722560-85722580 1.0000 20 chr1:8703807-8703827 1.0000 20 chr15:43663623-43663643 1.0000 20 chr16:57015452-57015472 1.0000 20 chr17:43117184-43117204 1.0000 20 chr19:15375085-15375105 1.0000 20 chr17:40333468-40333488 1.0000 20 chr7:155137661-155137681 1.0000 20 chr10:22292331-22292351 1.0000 20 chr15:41234168-41234188 1.0000 20 chr6:41473089-41473109 1.0000 20 chr13:98628451-98628471 1.0000 20 chr13:34117076-34117096 1.0000 20 chr17:48278112-48278132 1.0000 20 chr2:136743549-136743569 1.0000 20 chr2:174219421-174219441 1.0000 20 chr11:67723250-67723270 1.0000 20 chrX:15693364-15693384 1.0000 20 chrX:48659876-48659896 1.0000 20 chr1:59248110-59248130 1.0000 20 chr1:31867691-31867711 1.0000 20 chr3:47563764-47563784 1.0000 20 chr17:58677194-58677214 1.0000 20 chr16:15850166-15850186 1.0000 20 chr16:30103942-30103962 1.0000 20 chr7:102920437-102920457 1.0000 20 chr1:6844937-6844957 1.0000 20 chr11:74303674-74303694 1.0000 20 chr2:203103407-203103427 1.0000 20 chr19:50184120-50184140 1.0000 20 chr16:11837007-11837027 1.0000 20 chr17:71278279-71278299 1.0000 20 chr11:69458205-69458225 1.0000 20 chr4:156588729-156588749 1.0000 20 chr1:46050238-46050258 1.0000 20 chr15:75494378-75494398 1.0000 20 chr7:23513854-23513874 1.0000 20 chr21:37885896-37885916 1.0000 20 chr6:37467585-37467605 1.0000 20 chr6:31632917-31632937 1.0000 20 chr12:31226907-31226927 1.0000 20 chr13:41885434-41885454 1.0000 20 chr2:73404560-73404580 1.0000 20 chr9:123837085-123837105 1.0000 20 chr11:72525509-72525529 1.0000 20 chr19:56015141-56015161 1.0000 20 chr9:94860408-94860428 1.0000 20 chr11:75863380-75863400 1.0000 20 chr2:58468525-58468545 1.0000 20 chr12:49524573-49524593 1.0000 20 chr1:180502890-180502910 1.0000 20 chr8:128748416-128748436 1.0000 20 chr17:29159026-29159046 1.0000 20 chr12:57146074-57146094 1.0000 20 chr12:54673859-54673879 1.0000 20 chr19:797925-797945 1.0000 20 chr3:178764528-178764548 1.0000 20 chr11:68228394-68228414 1.0000 20 chr2:152882379-152882399 1.0000 20 chr16:58137092-58137112 1.0000 20 chr1:51434227-51434247 1.0000 20 chr6:27725255-27725275 1.0000 20 chr17:43463017-43463037 1.0000 20 chr2:128459422-128459442 1.0000 20 chr20:32274199-32274219 1.0000 20 chr2:132250620-132250640 1.0000 20 chr19:10305267-10305287 1.0000 20 chr12:56843078-56843098 1.0000 20 chr16:30006883-30006903 1.0000 20 chr18:61616674-61616694 1.0000 20 chr6:44355618-44355638 1.0000 20 chr16:11043477-11043497 1.0000 20 chr19:267484-267504 1.0000 20 chr12:15942407-15942427 1.0000 20 chr12:98910312-98910332 1.0000 20 chr1:937360-937380 1.0000 20 chr19:18281852-18281872 1.0000 20 chr7:35077576-35077596 1.0000 20 chr6:24775542-24775562 1.0000 20 chr5:174905593-174905613 1.0000 20 chr17:7819171-7819191 1.0000 20 chr4:39367958-39367978 1.0000 20 chr1:36235558-36235578 1.0000 20 chr2:166810663-166810683 1.0000 20 chr2:62081201-62081221 1.0000 20 chr15:48624420-48624440 1.0000 20 chr9:129933181-129933201 1.0000 20 chr11:46504839-46504859 1.0000 20 chr9:133569266-133569286 1.0000 20 chr5:134734868-134734888 1.0000 20 chr9:128508575-128508595 1.0000 20 chr19:59055933-59055953 1.0000 20 chr19:5978330-5978350 1.0000 20 chr1:59762235-59762255 1.0000 20 chr4:1872425-1872445 1.0000 20 chr16:67189339-67189359 1.0000 20 chr13:40634642-40634662 1.0000 20 chr19:48673554-48673574 1.0000 20 chr17:45266425-45266445 1.0000 20 chr19:14247524-14247544 1.0000 20 chr7:100797558-100797578 1.0000 20 chr19:17666634-17666654 1.0000 20 chr10:121632322-12163234 1.0000 20 chr6:33679409-33679429 1.0000 20 chr9:129622663-129622683 1.0000 20 chr12:123011803-12301182 1.0000 20 chr20:25388351-25388371 1.0000 20 chr7:148581683-148581703 1.0000 20 chr5:176560567-176560587 1.0000 20 chr16:85004282-85004302 1.0000 20 chr6:159125441-159125461 1.0000 20 chr17:46570064-46570084 1.0000 20 chr16:30064350-30064370 1.0000 20 chr19:49164379-49164399 1.0000 20 chr22:46546091-46546111 1.0000 20 chr1:155197584-155197604 1.0000 20 chr2:130939154-130939174 1.0000 20 chr12:69753768-69753788 1.0000 20 chr8:95907771-95907791 1.0000 20 chr8:22740564-22740584 1.0000 20 chr1:172413144-172413164 1.0000 20 chr3:196729965-196729985 1.0000 20 chr1:208042509-208042529 1.0000 20 chr10:115614015-11561403 1.0000 20 chr3:48129180-48129200 1.0000 20 chr22:50946683-50946703 1.0000 20 chr2:215674202-215674222 1.0000 20 chr10:62538105-62538125 1.0000 20 chr19:47777106-47777126 1.0000 20 chr17:38024400-38024420 1.0000 20 chr12:31479261-31479281 1.0000 20 chr19:36103720-36103740 1.0000 20 chr9:137000967-137000987 1.0000 20 chr8:143808537-143808557 1.0000 20 chr6:11094252-11094272 1.0000 20 chr12:53718734-53718754 1.0000 20 chr11:58874073-58874093 1.0000 20 chr12:76478404-76478424 1.0000 20 chr5:75699006-75699026 1.0000 20 chr17:40172034-40172054 1.0000 20 chr16:88870143-88870163 1.0000 20 chr16:75466996-75467016 1.0000 20 chr7:21985718-21985738 1.0000 20 chr12:122124971-12212499 1.0000 20 chr1:36348722-36348742 1.0000 20 chr3:156806746-156806766 1.0000 20 chr17:42287926-42287946 1.0000 20 chr1:151253865-151253885 1.0000 20 chr17:46048743-46048763 1.0000 20 chr19:45909491-45909511 1.0000 20 chr3:56717473-56717493 1.0000 20 chr17:58114575-58114595 1.0000 20 chr20:60982551-60982571 1.0000 20 chr8:120868102-120868122 1.0000 20 chr3:186524191-186524211 1.0000 20 chr11:65029443-65029463 1.0000 20 chr9:112891480-112891500 1.0000 20 chr12:94541996-94542016 1.0000 20 chr5:175843530-175843550 1.0000 20 chr19:54693211-54693231 1.0000 20 chr10:16859885-16859905 1.0000 20 chr3:38388463-38388483 1.0000 20 chr14:91526879-91526899 1.0000 20 chr12:96793227-96793247 1.0000 20 chr1:161410342-161410362 1.0000 20 chr13:33160503-33160523 1.0000 20 chr15:40397271-40397291 1.0000 20 chr13:25875819-25875839 1.0000 20 chr15:91473509-91473529 1.0000 20 chr5:137799928-137799948 1.0000 20 chr11:62494793-62494813 1.0000 20 chr1:46050481-46050501 1.0000 20 chr22:35795962-35795982 1.0000 20 chr2:220406517-220406537 1.0000 20 chr6:20534683-20534703 1.0000 20 chr22:42327977-42327997 1.0000 20 chr13:100018526-10001854 1.0000 20 chr15:42840983-42841003 1.0000 20 chr9:130830642-130830662 1.0000 20 chr12:54611026-54611046 1.0000 20 chr6:17706216-17706236 1.0000 20 chr5:139145336-139145356 1.0000 20 chr11:125495871-12549589 1.0000 20 chr13:61821980-61822000 1.0000 20 chr2:128145367-128145387 1.0000 20 chr20:42378619-42378639 1.0000 20 chr6:97731030-97731050 1.0000 20 chr2:75185742-75185762 1.0000 20 chr1:249200527-249200547 1.0000 20 chr3:196696848-196696868 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_RB1/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/GM12878/fasta/RankLinear0.6_10/RB1.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 0.163 C 0.329 G 0.333 T 0.175 Background letter frequencies (from file dataset with add-one prior applied): A 0.163 C 0.329 G 0.333 T 0.175 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF WMCTATTT MEME-1 width = 8 sites = 10 llr = 90 E-value = 1.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif WMCTATTT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 65:37::3 pos.-specific C :38::::: probability G :::::1:: matrix T 422739a7 bits 2.6 * 2.4 * 2.1 * 1.8 *** Relative 1.6 * ***** Entropy 1.3 * ***** (13.0 bits) 1.0 * ****** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel AACTATTT consensus TCTAT A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WMCTATTT MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr1:24307179-24307199 2 1.34e-06 A AACTATTT AGTTCAGAGA chr6:31632917-31632937 4 7.41e-06 TGG AACTTTTT CAATAGTAA chr9:112891480-112891500 8 8.84e-06 GGAGTTC ATCTATTT CTGAC chr6:17706216-17706236 11 1.50e-05 ATCATGGGCC TACAATTT CT chr9:137000967-137000987 3 4.10e-05 TG TATTATTA TACTTCAGTT chr17:58114575-58114595 2 6.58e-05 t atcaatta agcttcagag chr20:32274199-32274219 13 6.89e-05 ACGCGCCAAA TCCTTTTT chr2:242823405-242823425 11 7.76e-05 CAGGTGCCAC ACTTATTA TG chr6:90539492-90539512 1 8.08e-05 . AACTAGTT GTGGGCGCTG chr6:37137575-37137595 7 1.14e-04 TCCCCC TCCATTTT GGCGCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WMCTATTT MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:24307179-24307199 1.3e-06 1_[+1]_11 chr6:31632917-31632937 7.4e-06 3_[+1]_9 chr9:112891480-112891500 8.8e-06 7_[+1]_5 chr6:17706216-17706236 1.5e-05 10_[+1]_2 chr9:137000967-137000987 4.1e-05 2_[+1]_10 chr17:58114575-58114595 6.6e-05 1_[+1]_11 chr20:32274199-32274219 6.9e-05 12_[+1] chr2:242823405-242823425 7.8e-05 10_[+1]_2 chr6:90539492-90539512 8.1e-05 [+1]_12 chr6:37137575-37137595 0.00011 6_[+1]_6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WMCTATTT MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF WMCTATTT width=8 seqs=10 chr1:24307179-24307199 ( 2) AACTATTT 1 chr6:31632917-31632937 ( 4) AACTTTTT 1 chr9:112891480-112891500 ( 8) ATCTATTT 1 chr6:17706216-17706236 ( 11) TACAATTT 1 chr9:137000967-137000987 ( 3) TATTATTA 1 chr17:58114575-58114595 ( 2) ATCAATTA 1 chr20:32274199-32274219 ( 13) TCCTTTTT 1 chr2:242823405-242823425 ( 11) ACTTATTA 1 chr6:90539492-90539512 ( 1) AACTAGTT 1 chr6:37137575-37137595 ( 7) TCCATTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WMCTATTT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 9.2854 E= 1.6e+001 188 -997 -997 119 162 -13 -997 19 -997 128 -997 19 88 -997 -997 200 210 -997 -997 78 -997 -997 -173 236 -997 -997 -997 251 88 -997 -997 200 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WMCTATTT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 10 E= 1.6e+001 0.600000 0.000000 0.000000 0.400000 0.500000 0.300000 0.000000 0.200000 0.000000 0.800000 0.000000 0.200000 0.300000 0.000000 0.000000 0.700000 0.700000 0.000000 0.000000 0.300000 0.000000 0.000000 0.100000 0.900000 0.000000 0.000000 0.000000 1.000000 0.300000 0.000000 0.000000 0.700000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WMCTATTT MEME-1 regular expression -------------------------------------------------------------------------------- [AT][ACT][CT][TA][AT]TT[TA] -------------------------------------------------------------------------------- Time 3.35 secs. ******************************************************************************** ******************************************************************************** MOTIF WWTAAAYG MEME-2 width = 8 sites = 3 llr = 34 E-value = 6.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif WWTAAAYG MEME-2 Description -------------------------------------------------------------------------------- Simplified A 77:aaa:: pos.-specific C ::::::3: probability G :::::::a matrix T 33a:::7: bits 2.6 **** 2.4 **** 2.1 **** 1.8 **** Relative 1.6 ****** * Entropy 1.3 ******** (16.6 bits) 1.0 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel AATAAATG consensus TT C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWTAAAYG MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr17:43117184-43117204 1 1.17e-06 . AATAAATG CTCCCCTGGG chr6:20534683-20534703 6 5.90e-06 GCGCA AATAAACG TGGCGGG chr2:152882379-152882399 2 7.25e-06 T TTTAAATG TGATTACAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWTAAAYG MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr17:43117184-43117204 1.2e-06 [+2]_12 chr6:20534683-20534703 5.9e-06 5_[+2]_7 chr2:152882379-152882399 7.3e-06 1_[+2]_11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWTAAAYG MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF WWTAAAYG width=8 seqs=3 chr17:43117184-43117204 ( 1) AATAAATG 1 chr6:20534683-20534703 ( 6) AATAAACG 1 chr2:152882379-152882399 ( 2) TTTAAATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWTAAAYG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 9.73854 E= 6.5e+002 203 -823 -823 93 203 -823 -823 93 -823 -823 -823 251 261 -823 -823 -823 261 -823 -823 -823 261 -823 -823 -823 -823 2 -823 193 -823 -823 158 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWTAAAYG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 6.5e+002 0.666667 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWTAAAYG MEME-2 regular expression -------------------------------------------------------------------------------- [AT][AT]TAAA[TC]G -------------------------------------------------------------------------------- Time 4.34 secs. ******************************************************************************** ******************************************************************************** MOTIF AGAAGCTC MEME-3 width = 8 sites = 7 llr = 67 E-value = 4.9e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGAAGCTC MEME-3 Description -------------------------------------------------------------------------------- Simplified A 9:aa::31 pos.-specific C 1::::a:6 probability G :a::a::1 matrix T ::::::71 bits 2.6 ** 2.4 ** 2.1 ** 1.8 * ** Relative 1.6 ******* Entropy 1.3 ******* (13.8 bits) 1.0 ******* 0.8 ******* 0.5 ******* 0.3 ******** 0.0 -------- Multilevel AGAAGCTC consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAAGCTC MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr11:65029443-65029463 9 9.10e-06 CGTCACTG AGAAGCTC AGCG chr12:31479261-31479281 10 9.10e-06 TTTAAGGGG AGAAGCTC CGC chr16:30006883-30006903 1 1.36e-05 . AGAAGCTA CGGGTGAACT chr16:57015452-57015472 10 2.69e-05 CTATGAGAC AGAAGCAC TGG chr7:100797558-100797578 1 3.61e-05 . AGAAGCTG CAGTCAAGGA chr17:42287926-42287946 6 4.48e-05 CGGGC AGAAGCAT GGGCTGG chr17:29159026-29159046 1 7.18e-05 . CGAAGCTC TGTGGTCCGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAAGCTC MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr11:65029443-65029463 9.1e-06 8_[+3]_4 chr12:31479261-31479281 9.1e-06 9_[+3]_3 chr16:30006883-30006903 1.4e-05 [+3]_12 chr16:57015452-57015472 2.7e-05 9_[+3]_3 chr7:100797558-100797578 3.6e-05 [+3]_12 chr17:42287926-42287946 4.5e-05 5_[+3]_7 chr17:29159026-29159046 7.2e-05 [+3]_12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAAGCTC MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AGAAGCTC width=8 seqs=7 chr11:65029443-65029463 ( 9) AGAAGCTC 1 chr12:31479261-31479281 ( 10) AGAAGCTC 1 chr16:30006883-30006903 ( 1) AGAAGCTA 1 chr16:57015452-57015472 ( 10) AGAAGCAC 1 chr7:100797558-100797578 ( 1) AGAAGCTG 1 chr17:42287926-42287946 ( 6) AGAAGCAT 1 chr17:29159026-29159046 ( 1) CGAAGCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAAGCTC MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 8.69928 E= 4.9e+002 239 -120 -945 -945 -945 -945 159 -945 261 -945 -945 -945 261 -945 -945 -945 -945 -945 159 -945 -945 160 -945 -945 81 -945 -945 203 -19 79 -122 -29 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAAGCTC MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 4.9e+002 0.857143 0.142857 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.285714 0.000000 0.000000 0.714286 0.142857 0.571429 0.142857 0.142857 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGAAGCTC MEME-3 regular expression -------------------------------------------------------------------------------- AGAAGC[TA]C -------------------------------------------------------------------------------- Time 5.57 secs. ******************************************************************************** ******************************************************************************** MOTIF AGTGTKTG MEME-4 width = 8 sites = 8 llr = 75 E-value = 4.9e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGTGTKTG MEME-4 Description -------------------------------------------------------------------------------- Simplified A 81::::3: pos.-specific C :::::::: probability G :9:a:4:8 matrix T 3:a:a683 bits 2.6 * * 2.4 * * 2.1 * * 1.8 * * * * Relative 1.6 * *** * Entropy 1.3 * ***** (13.5 bits) 1.0 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel AGTGTTTG consensus T GAT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGTGTKTG MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr11:62494793-62494813 9 5.65e-06 CGCTGCGC AGTGTTTG CTTC chr7:21985718-21985738 7 3.07e-05 ATTACC AGTGTTAG GGCGCC chr10:115614015-11561403 10 3.07e-05 ACAAAACGC TGTGTTTG TGT chr16:85004282-85004302 10 3.07e-05 GGCCTGAGC AGTGTGTG GGT chr2:177005481-177005501 8 3.07e-05 CGCGCCA AGTGTGTG GGGCC chr13:100018526-10001854 13 4.50e-05 cagtctcttg tgtgtttt chr16:19897713-19897733 2 4.50e-05 A AGTGTGTT CCCGCCAGAC chr1:8703807-8703827 1 8.45e-05 . AATGTTAG CGTGTGCCTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGTGTKTG MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr11:62494793-62494813 5.6e-06 8_[+4]_4 chr7:21985718-21985738 3.1e-05 6_[+4]_6 chr10:115614015-11561403 3.1e-05 9_[+4]_3 chr16:85004282-85004302 3.1e-05 9_[+4]_3 chr2:177005481-177005501 3.1e-05 7_[+4]_5 chr13:100018526-10001854 4.5e-05 12_[+4] chr16:19897713-19897733 4.5e-05 1_[+4]_11 chr1:8703807-8703827 8.4e-05 [+4]_12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGTGTKTG MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AGTGTKTG width=8 seqs=8 chr11:62494793-62494813 ( 9) AGTGTTTG 1 chr7:21985718-21985738 ( 7) AGTGTTAG 1 chr10:115614015-11561403 ( 10) TGTGTTTG 1 chr16:85004282-85004302 ( 10) AGTGTGTG 1 chr2:177005481-177005501 ( 8) AGTGTGTG 1 chr13:100018526-10001854 ( 13) TGTGTTTT 1 chr16:19897713-19897733 ( 2) AGTGTGTT 1 chr1:8703807-8703827 ( 1) AATGTTAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGTGTKTG MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 8.66267 E= 4.9e+002 220 -965 -965 52 -38 -965 139 -965 -965 -965 -965 251 -965 -965 159 -965 -965 -965 -965 251 -965 -965 17 184 62 -965 -965 210 -965 -965 117 52 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGTGTKTG MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 8 E= 4.9e+002 0.750000 0.000000 0.000000 0.250000 0.125000 0.000000 0.875000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.375000 0.625000 0.250000 0.000000 0.000000 0.750000 0.000000 0.000000 0.750000 0.250000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGTGTKTG MEME-4 regular expression -------------------------------------------------------------------------------- [AT]GTGT[TG][TA][GT] -------------------------------------------------------------------------------- Time 6.34 secs. ******************************************************************************** ******************************************************************************** MOTIF AAAAAGMR MEME-5 width = 8 sites = 2 llr = 23 E-value = 2.2e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAAAAGMR MEME-5 Description -------------------------------------------------------------------------------- Simplified A aaaaa:55 pos.-specific C ::::::5: probability G :::::a:5 matrix T :::::::: bits 2.6 ***** 2.4 ***** 2.1 ***** 1.8 ***** Relative 1.6 ****** Entropy 1.3 ****** (16.9 bits) 1.0 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel AAAAAGAA consensus CG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAGMR MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr8:128748416-128748436 2 1.02e-06 G AAAAAGAA CGGAGGGAGG chr13:41885434-41885454 4 9.35e-06 GCC AAAAAGCG GAGCCCAGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAGMR MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr8:128748416-128748436 1e-06 1_[+5]_11 chr13:41885434-41885454 9.4e-06 3_[+5]_9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAGMR MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AAAAAGMR width=8 seqs=2 chr8:128748416-128748436 ( 2) AAAAAGAA 1 chr13:41885434-41885454 ( 4) AAAAAGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAGMR MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.6653 E= 2.2e+003 261 -765 -765 -765 261 -765 -765 -765 261 -765 -765 -765 261 -765 -765 -765 261 -765 -765 -765 -765 -765 158 -765 161 60 -765 -765 161 -765 59 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAGMR MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.2e+003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAGMR MEME-5 regular expression -------------------------------------------------------------------------------- AAAAAG[AC][AG] -------------------------------------------------------------------------------- Time 7.11 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:9555486-9555506 1.07e-01 20 chr19:46282717-46282737 1.88e-01 20 chr6:37137575-37137595 8.26e-02 20 chr15:44119229-44119249 9.67e-01 20 chr22:38966072-38966092 6.15e-03 20 chr16:3019249-3019269 3.37e-01 20 chr11:9595098-9595118 4.95e-01 20 chr6:35420211-35420231 1.00e+00 20 chr19:16222125-16222145 2.92e-01 20 chr17:60501152-60501172 3.36e-01 20 chr3:13461903-13461923 1.00e+00 20 chr16:30710236-30710256 9.74e-01 20 chr8:26435207-26435227 9.31e-02 20 chr10:70231632-70231652 2.43e-01 20 chr2:71503663-71503683 9.99e-01 20 chr12:7126208-7126228 9.44e-01 20 chr16:29984763-29984783 4.30e-01 20 chr11:58912291-58912311 4.35e-01 20 chr13:114238877-11423889 5.17e-01 20 chrX:153238342-153238362 1.00e+00 20 chr17:40897221-40897241 2.55e-01 20 chr14:50154903-50154923 8.69e-01 20 chr6:89855657-89855677 8.53e-01 20 chr21:37757765-37757785 8.67e-01 20 chr3:171515345-171515365 7.45e-02 20 chr10:43892071-43892091 7.72e-01 20 chr2:96822935-96822955 7.51e-01 20 chr1:16173936-16173956 9.93e-01 20 chr16:90074423-90074443 9.10e-01 20 chr14:105994777-10599479 1.96e-01 20 chr3:52058014-52058034 9.97e-01 20 chr16:19897713-19897733 5.71e-02 1_[+4(4.50e-05)]_11 chr2:242823405-242823425 3.40e-02 10_[+1(7.76e-05)]_2 chr2:153575194-153575214 9.58e-01 20 chr8:145669663-145669683 2.63e-01 20 chrX:153707449-153707469 5.97e-02 20 chr21:33104672-33104692 5.53e-01 20 chr14:23426333-23426353 9.39e-02 20 chr7:134671647-134671667 1.00e+00 20 chr1:91966514-91966534 1.14e-01 20 chr2:177005481-177005501 2.14e-02 7_[+4(3.07e-05)]_5 chr3:197237108-197237128 1.19e-01 20 chr11:111472765-11147278 6.96e-01 20 chr7:2710774-2710794 9.38e-01 20 chr17:34838951-34838971 9.45e-01 20 chrX:19881777-19881797 9.72e-01 20 chr7:50517949-50517969 4.68e-01 20 chr1:211870875-211870895 1.00e+00 20 chr7:128116706-128116726 1.00e+00 20 chr5:150036131-150036151 8.75e-01 20 chr4:40058591-40058611 3.90e-01 20 chr2:48010307-48010327 6.32e-02 20 chr11:85565946-85565966 8.52e-01 20 chr22:18507323-18507343 9.99e-01 20 chr16:29937826-29937846 9.22e-01 20 chr1:24307179-24307199 4.72e-04 1_[+1(1.34e-06)]_11 chr6:90539492-90539512 6.13e-03 [+1(8.08e-05)]_12 chr6:36391145-36391165 9.98e-01 20 chr2:219432984-219433004 4.98e-01 20 chr22:42095523-42095543 6.72e-01 20 chr16:85722560-85722580 5.94e-01 20 chr1:8703807-8703827 5.76e-02 [+4(8.45e-05)]_12 chr15:43663623-43663643 6.63e-01 20 chr16:57015452-57015472 5.59e-04 9_[+3(2.69e-05)]_3 chr17:43117184-43117204 3.39e-05 [+2(1.17e-06)]_12 chr19:15375085-15375105 2.40e-02 20 chr17:40333468-40333488 7.25e-01 20 chr7:155137661-155137681 2.20e-01 20 chr10:22292331-22292351 9.80e-01 20 chr15:41234168-41234188 6.75e-01 20 chr6:41473089-41473109 6.60e-03 20 chr13:98628451-98628471 1.00e+00 20 chr13:34117076-34117096 6.87e-01 20 chr17:48278112-48278132 9.03e-01 20 chr2:136743549-136743569 7.46e-01 20 chr2:174219421-174219441 3.02e-01 20 chr11:67723250-67723270 9.94e-01 20 chrX:15693364-15693384 7.96e-01 20 chrX:48659876-48659896 8.67e-01 20 chr1:59248110-59248130 9.92e-01 20 chr1:31867691-31867711 9.84e-01 20 chr3:47563764-47563784 5.63e-01 20 chr17:58677194-58677214 5.07e-01 20 chr16:15850166-15850186 8.66e-01 20 chr16:30103942-30103962 8.11e-01 20 chr7:102920437-102920457 8.10e-01 20 chr1:6844937-6844957 9.20e-01 20 chr11:74303674-74303694 5.23e-01 20 chr2:203103407-203103427 5.62e-01 20 chr19:50184120-50184140 9.58e-01 20 chr16:11837007-11837027 3.86e-01 20 chr17:71278279-71278299 9.93e-01 20 chr11:69458205-69458225 8.95e-01 20 chr4:156588729-156588749 2.94e-01 20 chr1:46050238-46050258 5.73e-01 20 chr15:75494378-75494398 9.37e-01 20 chr7:23513854-23513874 4.57e-01 20 chr21:37885896-37885916 5.88e-02 20 chr6:37467585-37467605 9.82e-01 20 chr6:31632917-31632937 6.81e-05 3_[+1(7.41e-06)]_9 chr12:31226907-31226927 6.57e-01 20 chr13:41885434-41885454 7.28e-04 3_[+5(9.35e-06)]_9 chr2:73404560-73404580 1.00e+00 20 chr9:123837085-123837105 9.83e-01 20 chr11:72525509-72525529 9.59e-01 20 chr19:56015141-56015161 8.17e-01 20 chr9:94860408-94860428 9.33e-01 20 chr11:75863380-75863400 9.94e-01 20 chr2:58468525-58468545 8.77e-01 20 chr12:49524573-49524593 3.31e-01 20 chr1:180502890-180502910 8.56e-01 20 chr8:128748416-128748436 3.43e-05 1_[+5(1.02e-06)]_11 chr17:29159026-29159046 2.75e-02 [+3(7.18e-05)]_12 chr12:57146074-57146094 9.06e-02 20 chr12:54673859-54673879 9.99e-01 20 chr19:797925-797945 9.93e-01 20 chr3:178764528-178764548 8.49e-01 20 chr11:68228394-68228414 7.85e-01 20 chr2:152882379-152882399 2.65e-05 1_[+2(7.25e-06)]_11 chr16:58137092-58137112 9.91e-01 20 chr1:51434227-51434247 3.64e-01 20 chr6:27725255-27725275 8.57e-01 20 chr17:43463017-43463037 8.71e-01 20 chr2:128459422-128459442 9.51e-01 20 chr20:32274199-32274219 9.93e-03 12_[+1(6.89e-05)] chr2:132250620-132250640 5.13e-01 20 chr19:10305267-10305287 5.26e-01 20 chr12:56843078-56843098 8.30e-01 20 chr16:30006883-30006903 5.00e-03 [+3(1.36e-05)]_12 chr18:61616674-61616694 4.88e-01 20 chr6:44355618-44355638 1.00e+00 20 chr16:11043477-11043497 9.90e-01 20 chr19:267484-267504 8.98e-01 20 chr12:15942407-15942427 8.88e-01 20 chr12:98910312-98910332 2.40e-03 20 chr1:937360-937380 7.93e-01 20 chr19:18281852-18281872 9.99e-01 20 chr7:35077576-35077596 6.59e-01 20 chr6:24775542-24775562 6.27e-01 20 chr5:174905593-174905613 5.65e-01 20 chr17:7819171-7819191 9.93e-01 20 chr4:39367958-39367978 3.72e-02 20 chr1:36235558-36235578 1.47e-01 20 chr2:166810663-166810683 9.67e-01 20 chr2:62081201-62081221 9.99e-01 20 chr15:48624420-48624440 9.70e-01 20 chr9:129933181-129933201 9.59e-01 20 chr11:46504839-46504859 4.43e-01 20 chr9:133569266-133569286 1.34e-02 20 chr5:134734868-134734888 1.00e+00 20 chr9:128508575-128508595 1.81e-01 20 chr19:59055933-59055953 2.95e-01 20 chr19:5978330-5978350 5.78e-01 20 chr1:59762235-59762255 7.66e-01 20 chr4:1872425-1872445 1.00e+00 20 chr16:67189339-67189359 1.00e+00 20 chr13:40634642-40634662 1.44e-01 20 chr19:48673554-48673574 2.95e-01 20 chr17:45266425-45266445 9.66e-01 20 chr19:14247524-14247544 1.08e-01 20 chr7:100797558-100797578 4.65e-03 [+3(3.61e-05)]_12 chr19:17666634-17666654 4.02e-01 20 chr10:121632322-12163234 9.99e-01 20 chr6:33679409-33679429 1.00e+00 20 chr9:129622663-129622683 9.79e-01 20 chr12:123011803-12301182 2.09e-01 20 chr20:25388351-25388371 3.13e-01 20 chr7:148581683-148581703 9.99e-01 20 chr5:176560567-176560587 6.68e-01 20 chr16:85004282-85004302 1.81e-02 9_[+4(3.07e-05)]_3 chr6:159125441-159125461 8.62e-01 20 chr17:46570064-46570084 9.96e-01 20 chr16:30064350-30064370 2.77e-01 20 chr19:49164379-49164399 9.90e-02 20 chr22:46546091-46546111 9.79e-01 20 chr1:155197584-155197604 3.96e-02 20 chr2:130939154-130939174 5.31e-01 20 chr12:69753768-69753788 2.27e-01 20 chr8:95907771-95907791 6.94e-01 20 chr8:22740564-22740584 1.76e-02 20 chr1:172413144-172413164 6.53e-01 20 chr3:196729965-196729985 5.77e-01 20 chr1:208042509-208042529 9.93e-01 20 chr10:115614015-11561403 4.99e-05 9_[+4(3.07e-05)]_3 chr3:48129180-48129200 8.21e-01 20 chr22:50946683-50946703 1.99e-02 20 chr2:215674202-215674222 7.41e-01 20 chr10:62538105-62538125 9.98e-01 20 chr19:47777106-47777126 9.79e-01 20 chr17:38024400-38024420 1.00e+00 20 chr12:31479261-31479281 2.77e-04 9_[+3(9.10e-06)]_3 chr19:36103720-36103740 5.19e-01 20 chr9:137000967-137000987 7.44e-04 2_[+1(4.10e-05)]_10 chr8:143808537-143808557 9.98e-01 20 chr6:11094252-11094272 1.00e+00 20 chr12:53718734-53718754 9.99e-01 20 chr11:58874073-58874093 1.00e+00 20 chr12:76478404-76478424 2.63e-01 20 chr5:75699006-75699026 9.91e-01 20 chr17:40172034-40172054 9.91e-01 20 chr16:88870143-88870163 1.00e+00 20 chr16:75466996-75467016 6.56e-01 20 chr7:21985718-21985738 6.66e-03 6_[+4(3.07e-05)]_6 chr12:122124971-12212499 1.95e-01 20 chr1:36348722-36348742 7.97e-01 20 chr3:156806746-156806766 9.96e-01 20 chr17:42287926-42287946 5.61e-03 5_[+3(4.48e-05)]_7 chr1:151253865-151253885 4.66e-03 2_[+2(7.58e-05)]_10 chr17:46048743-46048763 9.07e-01 20 chr19:45909491-45909511 4.27e-02 20 chr3:56717473-56717493 9.73e-01 20 chr17:58114575-58114595 2.70e-04 1_[+1(6.58e-05)]_11 chr20:60982551-60982571 8.47e-01 20 chr8:120868102-120868122 2.48e-01 20 chr3:186524191-186524211 7.70e-01 20 chr11:65029443-65029463 3.58e-03 8_[+3(9.10e-06)]_4 chr9:112891480-112891500 4.61e-03 7_[+1(8.84e-06)]_5 chr12:94541996-94542016 9.72e-01 20 chr5:175843530-175843550 8.08e-01 20 chr19:54693211-54693231 8.92e-01 20 chr10:16859885-16859905 4.14e-01 20 chr3:38388463-38388483 9.98e-01 20 chr14:91526879-91526899 9.20e-01 20 chr12:96793227-96793247 9.77e-01 20 chr1:161410342-161410362 7.66e-01 20 chr13:33160503-33160523 9.71e-01 20 chr15:40397271-40397291 6.13e-01 20 chr13:25875819-25875839 1.47e-01 20 chr15:91473509-91473529 4.76e-02 20 chr5:137799928-137799948 7.83e-01 20 chr11:62494793-62494813 1.12e-02 8_[+4(5.65e-06)]_4 chr1:46050481-46050501 4.27e-02 20 chr22:35795962-35795982 7.12e-01 20 chr2:220406517-220406537 3.60e-01 20 chr6:20534683-20534703 9.12e-04 5_[+2(5.90e-06)]_7 chr22:42327977-42327997 3.44e-01 20 chr13:100018526-10001854 2.24e-02 12_[+4(4.50e-05)] chr15:42840983-42841003 9.67e-01 20 chr9:130830642-130830662 1.00e+00 20 chr12:54611026-54611046 2.00e-04 11_[+5(9.35e-06)]_1 chr6:17706216-17706236 5.63e-03 10_[+1(1.50e-05)]_2 chr5:139145336-139145356 9.95e-01 20 chr11:125495871-12549589 7.83e-01 20 chr13:61821980-61822000 8.17e-01 20 chr2:128145367-128145387 1.62e-01 20 chr20:42378619-42378639 9.97e-01 20 chr6:97731030-97731050 1.02e-01 20 chr2:75185742-75185762 6.30e-01 20 chr1:249200527-249200547 8.42e-01 20 chr3:196696848-196696868 8.20e-01 20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c22n04.farnam.hpc.yale.internal ********************************************************************************