******************************************************************************** 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/NKRF.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr15:32907750-32907770 1.0000 20 chr4:1723275-1723295 1.0000 20 chr15:30918349-30918369 1.0000 20 chr10:70231457-70231477 1.0000 20 chr1:28052729-28052749 1.0000 20 chr16:4784681-4784701 1.0000 20 chr4:83933945-83933965 1.0000 20 chr20:42295804-42295824 1.0000 20 chr4:159592885-159592905 1.0000 20 chr4:178231087-178231107 1.0000 20 chr3:20083060-20083080 1.0000 20 chr6:167412450-167412470 1.0000 20 chr12:9600702-9600722 1.0000 20 chr10:124639347-12463936 1.0000 20 chr3:194392801-194392821 1.0000 20 chr16:3030389-3030409 1.0000 20 chr1:45476882-45476902 1.0000 20 chr17:4901048-4901068 1.0000 20 chr19:54024403-54024423 1.0000 20 chr4:154265889-154265909 1.0000 20 chr14:105957743-10595776 1.0000 20 chr8:145669688-145669708 1.0000 20 chr8:27695259-27695279 1.0000 20 chr8:101157958-101157978 1.0000 20 chrX:14891089-14891109 1.0000 20 chr17:7477324-7477344 1.0000 20 chr16:46723620-46723640 1.0000 20 chr1:28845192-28845212 1.0000 20 chr11:58912316-58912336 1.0000 20 chr3:52188379-52188399 1.0000 20 chr15:68346379-68346399 1.0000 20 chr17:1419791-1419811 1.0000 20 chr18:47901524-47901544 1.0000 20 chr2:114384884-114384904 1.0000 20 chr12:122150770-12215079 1.0000 20 chr16:81040244-81040264 1.0000 20 chr21:33651244-33651264 1.0000 20 chr19:36391396-36391416 1.0000 20 chr15:66797691-66797711 1.0000 20 chr1:93646373-93646393 1.0000 20 chrX:69509980-69510000 1.0000 20 chr8:21999316-21999336 1.0000 20 chr2:200775816-200775836 1.0000 20 chr2:97001602-97001622 1.0000 20 chr6:31831058-31831078 1.0000 20 chr8:95487217-95487237 1.0000 20 chr16:838757-838777 1.0000 20 chr12:99038653-99038673 1.0000 20 chr15:40401012-40401032 1.0000 20 chr5:162887745-162887765 1.0000 20 chr6:86388839-86388859 1.0000 20 chr1:53792206-53792226 1.0000 20 chr16:30773272-30773292 1.0000 20 chr16:87902234-87902254 1.0000 20 chr4:174255953-174255973 1.0000 20 chr16:1429566-1429586 1.0000 20 chr22:41682045-41682065 1.0000 20 chr15:40615715-40615735 1.0000 20 chr19:11492194-11492214 1.0000 20 chr15:40886503-40886523 1.0000 20 chr20:33292174-33292194 1.0000 20 chr10:60027998-60028018 1.0000 20 chr14:77786892-77786912 1.0000 20 chr4:2243650-2243670 1.0000 20 chr1:176176512-176176532 1.0000 20 chr17:57233148-57233168 1.0000 20 chr10:5454557-5454577 1.0000 20 chr17:79651221-79651241 1.0000 20 chr8:120868027-120868047 1.0000 20 chr10:127585196-12758521 1.0000 20 chr8:145703494-145703514 1.0000 20 chr22:51222018-51222038 1.0000 20 chr9:79009584-79009604 1.0000 20 chr17:260209-260229 1.0000 20 chr19:5905030-5905050 1.0000 20 chr2:230787319-230787339 1.0000 20 chr12:4648066-4648086 1.0000 20 chr15:41624626-41624646 1.0000 20 chr1:2322852-2322872 1.0000 20 chr14:102771371-10277139 1.0000 20 chr5:137667967-137667987 1.0000 20 chr1:27024621-27024641 1.0000 20 chr1:227128108-227128128 1.0000 20 chr9:36572963-36572983 1.0000 20 chr3:88198685-88198705 1.0000 20 chr19:50321097-50321117 1.0000 20 chr15:41625256-41625276 1.0000 20 chr5:68485487-68485507 1.0000 20 chr4:83931835-83931855 1.0000 20 chr16:23690203-23690223 1.0000 20 chr1:167189500-167189520 1.0000 20 chr5:10442088-10442108 1.0000 20 chr17:1531863-1531883 1.0000 20 chr21:47744270-47744290 1.0000 20 chr19:53073911-53073931 1.0000 20 chr2:234763131-234763151 1.0000 20 chr7:36429504-36429524 1.0000 20 chr2:62081336-62081356 1.0000 20 chr5:138728958-138728978 1.0000 20 chr1:114301725-114301745 1.0000 20 chr8:357021-357041 1.0000 20 chr19:48673487-48673507 1.0000 20 chr19:59085109-59085129 1.0000 20 chr1:68962716-68962736 1.0000 20 chr4:7044624-7044644 1.0000 20 chr1:52869960-52869980 1.0000 20 chr17:21002851-21002871 1.0000 20 chr17:79679411-79679431 1.0000 20 chr18:56338403-56338423 1.0000 20 chr5:1295080-1295100 1.0000 20 chr3:33759556-33759576 1.0000 20 chrX:70273144-70273164 1.0000 20 chr19:14247343-14247363 1.0000 20 chr21:34100699-34100719 1.0000 20 chr17:29159099-29159119 1.0000 20 chr21:33765214-33765234 1.0000 20 chr12:9436380-9436400 1.0000 20 chr9:131842946-131842966 1.0000 20 chr19:6199402-6199422 1.0000 20 chr6:153304115-153304135 1.0000 20 chr15:48624482-48624502 1.0000 20 chr1:156542277-156542297 1.0000 20 chr1:43148873-43148893 1.0000 20 chr5:79950262-79950282 1.0000 20 chr8:27632121-27632141 1.0000 20 chr15:40987458-40987478 1.0000 20 chr7:50517962-50517982 1.0000 20 chr19:58874239-58874259 1.0000 20 chr1:45205563-45205583 1.0000 20 chr2:243030881-243030901 1.0000 20 chr10:104474551-10447457 1.0000 20 chr1:212209208-212209228 1.0000 20 chr4:184427592-184427612 1.0000 20 chr16:20817726-20817746 1.0000 20 chr9:82186254-82186274 1.0000 20 chr4:13486412-13486432 1.0000 20 chr19:47734064-47734084 1.0000 20 chr13:111365036-11136505 1.0000 20 chr6:157101540-157101560 1.0000 20 chr7:100136353-100136373 1.0000 20 chr1:1051864-1051884 1.0000 20 chr19:53426249-53426269 1.0000 20 chr16:1832421-1832441 1.0000 20 chr20:54967177-54967197 1.0000 20 chr4:3956951-3956971 1.0000 20 chr16:2510191-2510211 1.0000 20 chr20:47663016-47663036 1.0000 20 chr1:24286026-24286046 1.0000 20 chr7:158497363-158497383 1.0000 20 chr4:104119432-104119452 1.0000 20 chr14:73393452-73393472 1.0000 20 chr10:95256402-95256422 1.0000 20 chr6:26251044-26251064 1.0000 20 chr4:90032321-90032341 1.0000 20 chr2:242641133-242641153 1.0000 20 chr5:137667380-137667400 1.0000 20 chr3:160117520-160117540 1.0000 20 chr12:110905893-11090591 1.0000 20 chr19:3185383-3185403 1.0000 20 chr5:149737552-149737572 1.0000 20 chr19:10828966-10828986 1.0000 20 chr16:75590021-75590041 1.0000 20 chr13:50655981-50656001 1.0000 20 chr2:68385123-68385143 1.0000 20 chr1:46052141-46052161 1.0000 20 chr1:36235438-36235458 1.0000 20 chr18:14132346-14132366 1.0000 20 chr6:27862230-27862250 1.0000 20 chr12:105380208-10538022 1.0000 20 chr3:49055885-49055905 1.0000 20 chr20:32274139-32274159 1.0000 20 chr17:42219376-42219396 1.0000 20 chr11:9595349-9595369 1.0000 20 chr9:130830638-130830658 1.0000 20 chr2:88926783-88926803 1.0000 20 chr17:38574054-38574074 1.0000 20 chr19:36545855-36545875 1.0000 20 chr17:79875898-79875918 1.0000 20 chr3:50374642-50374662 1.0000 20 chr20:36156134-36156154 1.0000 20 chr10:14920974-14920994 1.0000 20 chr1:24104986-24105006 1.0000 20 chr15:91260705-91260725 1.0000 20 chr1:226496791-226496811 1.0000 20 chr11:66057126-66057146 1.0000 20 chr8:41908638-41908658 1.0000 20 chr21:15399808-15399828 1.0000 20 chr15:85524074-85524094 1.0000 20 chr12:118810538-11881055 1.0000 20 chr8:95908115-95908135 1.0000 20 chr17:41322166-41322186 1.0000 20 chr2:242626106-242626126 1.0000 20 chr7:100450137-100450157 1.0000 20 chr19:30335511-30335531 1.0000 20 chr7:23514254-23514274 1.0000 20 chr6:126661334-126661354 1.0000 20 chr14:77843591-77843611 1.0000 20 chr3:49967119-49967139 1.0000 20 chr10:102820373-10282039 1.0000 20 chr8:145743130-145743150 1.0000 20 chr8:124408574-124408594 1.0000 20 chr17:4046105-4046125 1.0000 20 chr22:19467480-19467500 1.0000 20 chr1:29241174-29241194 1.0000 20 chr14:103995620-10399564 1.0000 20 chr6:33359695-33359715 1.0000 20 chr22:38240129-38240149 1.0000 20 chr6:80714404-80714424 1.0000 20 chr5:175815501-175815521 1.0000 20 chr17:78388805-78388825 1.0000 20 chr16:2479717-2479737 1.0000 20 chr4:120987875-120987895 1.0000 20 chr17:37558971-37558991 1.0000 20 chr12:69754072-69754092 1.0000 20 chr2:10262885-10262905 1.0000 20 chr19:18304138-18304158 1.0000 20 chr8:63951284-63951304 1.0000 20 chr10:129924575-12992459 1.0000 20 chr20:37555116-37555136 1.0000 20 chr1:211848908-211848928 1.0000 20 chr4:1857739-1857759 1.0000 20 chr3:197687200-197687220 1.0000 20 chr2:223520659-223520679 1.0000 20 chr2:136874478-136874498 1.0000 20 chr15:59397376-59397396 1.0000 20 chr3:52804832-52804852 1.0000 20 chr6:42016627-42016647 1.0000 20 chr4:186125397-186125417 1.0000 20 chr4:17812657-17812677 1.0000 20 chr1:160255081-160255101 1.0000 20 chr17:79818304-79818324 1.0000 20 chr2:73441502-73441522 1.0000 20 chr19:11639564-11639584 1.0000 20 chr10:99160982-99161002 1.0000 20 chr8:22526453-22526473 1.0000 20 chr3:129830121-129830141 1.0000 20 chr16:5147614-5147634 1.0000 20 chr22:30821850-30821870 1.0000 20 chr17:8113852-8113872 1.0000 20 chr18:2571592-2571612 1.0000 20 chr8:101170556-101170576 1.0000 20 chr16:3018975-3018995 1.0000 20 chr4:128802158-128802178 1.0000 20 chr9:88556331-88556351 1.0000 20 chr12:110841369-11084138 1.0000 20 chr1:1821622-1821642 1.0000 20 chr19:13048968-13048988 1.0000 20 chr6:5261337-5261357 1.0000 20 chr15:36871423-36871443 1.0000 20 chr13:21141415-21141435 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_NKRF/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/GM12878/fasta/RankLinear0.6_10/NKRF.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 0.16 C 0.323 G 0.348 T 0.169 Background letter frequencies (from file dataset with add-one prior applied): A 0.16 C 0.323 G 0.348 T 0.169 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CTTARTTT MEME-1 width = 8 sites = 5 llr = 53 E-value = 2.6e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTTARTTT MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::284::: pos.-specific C 8::::2:: probability G ::::6::: matrix T 2a82:8aa bits 2.6 * ** 2.4 * ** 2.1 * ** 1.8 *** ** Relative 1.6 *** *** Entropy 1.3 *** *** (15.2 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel CTTAGTTT consensus T ATAC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTARTTT MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3:88198685-88198705 2 1.14e-06 A CTTAATTT AAGGAACCAA chrX:69509980-69510000 12 5.51e-06 GGAAGGGACA TTTAGTTT G chr9:82186254-82186274 13 7.80e-06 CCTCCACCCT CTTTATTT chr5:137667967-137667987 1 1.01e-05 . CTAAGTTT TGCTGGCCTT chr17:41322166-41322186 9 2.21e-05 AACGCGGC CTTAGCTT CCTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTARTTT MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3:88198685-88198705 1.1e-06 1_[+1]_11 chrX:69509980-69510000 5.5e-06 11_[+1]_1 chr9:82186254-82186274 7.8e-06 12_[+1] chr5:137667967-137667987 1e-05 [+1]_12 chr17:41322166-41322186 2.2e-05 8_[+1]_4 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTARTTT MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTTARTTT width=8 seqs=5 chr3:88198685-88198705 ( 2) CTTAATTT 1 chrX:69509980-69510000 ( 12) TTTAGTTT 1 chr9:82186254-82186274 ( 13) CTTTATTT 1 chr5:137667967-137667987 ( 1) CTAAGTTT 1 chr17:41322166-41322186 ( 9) CTTAGCTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTARTTT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.2866 E= 2.6e+002 -897 131 -897 24 -897 -897 -897 256 32 -897 -897 224 232 -897 -897 24 132 -897 79 -897 -897 -69 -897 224 -897 -897 -897 256 -897 -897 -897 256 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTARTTT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 2.6e+002 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.000000 1.000000 0.200000 0.000000 0.000000 0.800000 0.800000 0.000000 0.000000 0.200000 0.400000 0.000000 0.600000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTARTTT MEME-1 regular expression -------------------------------------------------------------------------------- [CT]T[TA][AT][GA][TC]TT -------------------------------------------------------------------------------- Time 2.39 secs. ******************************************************************************** ******************************************************************************** MOTIF ARGGAAGV MEME-2 width = 8 sites = 10 llr = 84 E-value = 3.9e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif ARGGAAGV MEME-2 Description -------------------------------------------------------------------------------- Simplified A 95:3a9:4 pos.-specific C :::1:::3 probability G :5a6::a3 matrix T 1::::1:: bits 2.6 * 2.4 * 2.1 * ** 1.8 * ** Relative 1.6 * * *** Entropy 1.3 * * *** (12.1 bits) 1.1 *** *** 0.8 *** *** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel AAGGAAGA consensus G A C sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARGGAAGV MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr7:23514254-23514274 12 6.45e-06 CCCAACCCCC AAGGAAGA A chr4:13486412-13486432 10 2.05e-05 AACCGGACC AGGGAAGA GGG chr19:13048968-13048988 5 2.46e-05 GGCT AAGAAAGC CTTGCCCA chr16:30773272-30773292 2 4.75e-05 G AAGGAAGG CGGAAAGCGC chrX:70273144-70273164 8 6.06e-05 AGGTTGC AGGAAAGC GCAGT chr19:11492194-11492214 6 8.96e-05 ACATT AGGAAAGG GGGTGTG chr8:95908115-95908135 11 1.10e-04 CGGCGCGCCC AGGGAAGG CA chr1:24286026-24286046 5 1.24e-04 GCGG TAGGAAGA GCCGAGAG chr11:66057126-66057146 2 1.41e-04 C AAGCAAGC CCCAGGATGC chr20:47663016-47663036 1 1.80e-04 . AGGGATGA GGCGCTCCCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARGGAAGV MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:23514254-23514274 6.5e-06 11_[+2]_1 chr4:13486412-13486432 2e-05 9_[+2]_3 chr19:13048968-13048988 2.5e-05 4_[+2]_8 chr16:30773272-30773292 4.8e-05 1_[+2]_11 chrX:70273144-70273164 6.1e-05 7_[+2]_5 chr19:11492194-11492214 9e-05 5_[+2]_7 chr8:95908115-95908135 0.00011 10_[+2]_2 chr1:24286026-24286046 0.00012 4_[+2]_8 chr11:66057126-66057146 0.00014 1_[+2]_11 chr20:47663016-47663036 0.00018 [+2]_12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARGGAAGV MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ARGGAAGV width=8 seqs=10 chr7:23514254-23514274 ( 12) AAGGAAGA 1 chr4:13486412-13486432 ( 10) AGGGAAGA 1 chr19:13048968-13048988 ( 5) AAGAAAGC 1 chr16:30773272-30773292 ( 2) AAGGAAGG 1 chrX:70273144-70273164 ( 8) AGGAAAGC 1 chr19:11492194-11492214 ( 6) AGGAAAGG 1 chr8:95908115-95908135 ( 11) AGGGAAGG 1 chr1:24286026-24286046 ( 5) TAGGAAGA 1 chr11:66057126-66057146 ( 2) AAGCAAGC 1 chr20:47663016-47663036 ( 1) AGGGATGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARGGAAGV MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 9.81663 E= 3.9e+003 249 -997 -997 -76 164 -997 52 -997 -997 -997 152 -997 90 -169 79 -997 264 -997 -997 -997 249 -997 -997 -76 -997 -997 152 -997 132 -10 -21 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARGGAAGV MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 10 E= 3.9e+003 0.900000 0.000000 0.000000 0.100000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.300000 0.100000 0.600000 0.000000 1.000000 0.000000 0.000000 0.000000 0.900000 0.000000 0.000000 0.100000 0.000000 0.000000 1.000000 0.000000 0.400000 0.300000 0.300000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARGGAAGV MEME-2 regular expression -------------------------------------------------------------------------------- A[AG]G[GA]AAG[ACG] -------------------------------------------------------------------------------- Time 3.18 secs. ******************************************************************************** ******************************************************************************** MOTIF AAAMCAKA MEME-3 width = 8 sites = 2 llr = 24 E-value = 1.8e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAAMCAKA MEME-3 Description -------------------------------------------------------------------------------- Simplified A aaa5:a:a pos.-specific C :::5a::: probability G ::::::5: matrix T ::::::5: bits 2.6 *** * * 2.4 *** * * 2.1 *** * * 1.8 *** * * Relative 1.6 *** ** * Entropy 1.3 *** ** * (17.0 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel AAAACAGA consensus C T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAMCAKA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr17:21002851-21002871 12 2.76e-06 GCCTGTACCC AAACCATA A chr19:3185383-3185403 6 4.65e-06 tgcac aaaacaga caaaagt -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAMCAKA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr17:21002851-21002871 2.8e-06 11_[+3]_1 chr19:3185383-3185403 4.7e-06 5_[+3]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAMCAKA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AAAMCAKA width=8 seqs=2 chr17:21002851-21002871 ( 12) AAACCATA 1 chr19:3185383-3185403 ( 6) AAAACAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAMCAKA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.6653 E= 1.8e+003 263 -765 -765 -765 263 -765 -765 -765 263 -765 -765 -765 163 63 -765 -765 -765 163 -765 -765 263 -765 -765 -765 -765 -765 52 156 263 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAMCAKA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.8e+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 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAMCAKA MEME-3 regular expression -------------------------------------------------------------------------------- AAA[AC]CA[GT]A -------------------------------------------------------------------------------- Time 3.96 secs. ******************************************************************************** ******************************************************************************** MOTIF GSAGARKH MEME-4 width = 8 sites = 14 llr = 112 E-value = 3.0e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GSAGARKH MEME-4 Description -------------------------------------------------------------------------------- Simplified A ::a:a4:4 pos.-specific C :5:::::4 probability G a5:a:66: matrix T ::::::42 bits 2.6 * * 2.4 * * 2.1 * * 1.8 * * Relative 1.6 * *** Entropy 1.3 * *** (11.5 bits) 1.1 * ***** 0.8 * ****** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel GCAGAGGC consensus G ATA sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSAGARKH MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr22:38240129-38240149 3 2.75e-05 AA GGAGAAGA GGCCCTCAGC chr4:159592885-159592905 10 2.75e-05 GAAGAGGAG GGAGAAGA GGG chr18:14132346-14132366 10 4.57e-05 GAGTGAGTG GCAGAATC ACC chr10:104474551-10447457 11 1.07e-04 ACTTCCACCT GCAGAAGC CA chr15:66797691-66797711 10 1.07e-04 AACTGCGCA GCAGAGGA CTT chr12:9600702-9600722 9 1.07e-04 CTTCGCCG GCAGAATT GCTA chr1:211848908-211848928 4 1.62e-04 GAT GGAGAAGC CCCCGAGCA chr21:34100699-34100719 1 1.62e-04 . GGAGAGGA GGAAGGGCTC chr21:47744270-47744290 9 1.62e-04 CCCTGCCA GGAGAGGA CGCG chr2:114384884-114384904 13 1.91e-04 TCGAGAGCGC GCAGAGTC chr22:30821850-30821870 10 2.61e-04 GCCGTGGCG GGAGAGTC ATG chr16:4784681-4784701 6 2.61e-04 TGGAG GCAGAGGC CTGAGGT chr12:9436380-9436400 13 3.34e-04 CTGTGTGGCA GCAGAGGT chr7:36429504-36429524 10 3.34e-04 CTGGTTGTG GGAGAGTT CCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSAGARKH MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr22:38240129-38240149 2.8e-05 2_[+4]_10 chr4:159592885-159592905 2.8e-05 9_[+4]_3 chr18:14132346-14132366 4.6e-05 9_[+4]_3 chr10:104474551-10447457 0.00011 10_[+4]_2 chr15:66797691-66797711 0.00011 9_[+4]_3 chr12:9600702-9600722 0.00011 8_[+4]_4 chr1:211848908-211848928 0.00016 3_[+4]_9 chr21:34100699-34100719 0.00016 [+4]_12 chr21:47744270-47744290 0.00016 8_[+4]_4 chr2:114384884-114384904 0.00019 12_[+4] chr22:30821850-30821870 0.00026 9_[+4]_3 chr16:4784681-4784701 0.00026 5_[+4]_7 chr12:9436380-9436400 0.00033 12_[+4] chr7:36429504-36429524 0.00033 9_[+4]_3 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSAGARKH MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GSAGARKH width=8 seqs=14 chr22:38240129-38240149 ( 3) GGAGAAGA 1 chr4:159592885-159592905 ( 10) GGAGAAGA 1 chr18:14132346-14132366 ( 10) GCAGAATC 1 chr10:104474551-10447457 ( 11) GCAGAAGC 1 chr15:66797691-66797711 ( 10) GCAGAGGA 1 chr12:9600702-9600722 ( 9) GCAGAATT 1 chr1:211848908-211848928 ( 4) GGAGAAGC 1 chr21:34100699-34100719 ( 1) GGAGAGGA 1 chr21:47744270-47744290 ( 9) GGAGAGGA 1 chr2:114384884-114384904 ( 13) GCAGAGTC 1 chr22:30821850-30821870 ( 10) GGAGAGTC 1 chr16:4784681-4784701 ( 6) GCAGAGGC 1 chr12:9436380-9436400 ( 13) GCAGAGGT 1 chr7:36429504-36429524 ( 10) GGAGAGTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSAGARKH MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 8.4605 E= 3.0e+003 -1045 -1045 152 -1045 -1045 63 52 -1045 264 -1045 -1045 -1045 -1045 -1045 152 -1045 264 -1045 -1045 -1045 142 -1045 72 -1045 -1045 -1045 89 108 115 41 -1045 34 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSAGARKH MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 14 E= 3.0e+003 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.428571 0.000000 0.571429 0.000000 0.000000 0.000000 0.642857 0.357143 0.357143 0.428571 0.000000 0.214286 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GSAGARKH MEME-4 regular expression -------------------------------------------------------------------------------- G[CG]AGA[GA][GT][CAT] -------------------------------------------------------------------------------- Time 4.75 secs. ******************************************************************************** ******************************************************************************** MOTIF AACTGYAA MEME-5 width = 8 sites = 2 llr = 24 E-value = 2.0e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif AACTGYAA MEME-5 Description -------------------------------------------------------------------------------- Simplified A aa::::aa pos.-specific C ::a::5:: probability G ::::a::: matrix T :::a:5:: bits 2.6 ** * ** 2.4 ** * ** 2.1 ** * ** 1.8 ** * ** Relative 1.6 ***** ** Entropy 1.3 ***** ** (17.4 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel AACTGCAA consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACTGYAA MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr12:4648066-4648086 10 2.10e-06 GAATTTGAG AACTGTAA ATA chr15:40987458-40987478 2 6.13e-06 G AACTGCAA CTCATCTGGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACTGYAA MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr12:4648066-4648086 2.1e-06 9_[+5]_3 chr15:40987458-40987478 6.1e-06 1_[+5]_11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACTGYAA MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AACTGYAA width=8 seqs=2 chr12:4648066-4648086 ( 10) AACTGTAA 1 chr15:40987458-40987478 ( 2) AACTGCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACTGYAA MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.6653 E= 2.0e+003 263 -765 -765 -765 263 -765 -765 -765 -765 163 -765 -765 -765 -765 -765 256 -765 -765 152 -765 -765 63 -765 156 263 -765 -765 -765 263 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACTGYAA MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.0e+003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.500000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACTGYAA MEME-5 regular expression -------------------------------------------------------------------------------- AACTG[CT]AA -------------------------------------------------------------------------------- Time 5.65 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr15:32907750-32907770 1.95e-02 20 chr4:1723275-1723295 1.91e-01 20 chr15:30918349-30918369 7.34e-01 20 chr10:70231457-70231477 5.48e-01 20 chr1:28052729-28052749 4.46e-01 20 chr16:4784681-4784701 2.40e-02 20 chr4:83933945-83933965 8.27e-01 20 chr20:42295804-42295824 1.00e+00 20 chr4:159592885-159592905 4.62e-03 9_[+4(2.75e-05)]_3 chr4:178231087-178231107 8.40e-01 20 chr3:20083060-20083080 4.77e-01 20 chr6:167412450-167412470 9.53e-01 20 chr12:9600702-9600722 1.53e-03 20 chr10:124639347-12463936 5.59e-01 20 chr3:194392801-194392821 8.08e-01 20 chr16:3030389-3030409 9.98e-01 20 chr1:45476882-45476902 6.99e-01 20 chr17:4901048-4901068 5.62e-01 20 chr19:54024403-54024423 8.02e-01 20 chr4:154265889-154265909 1.24e-01 20 chr14:105957743-10595776 9.97e-01 20 chr8:145669688-145669708 9.97e-01 20 chr8:27695259-27695279 4.39e-01 20 chr8:101157958-101157978 9.97e-01 20 chrX:14891089-14891109 8.80e-01 20 chr17:7477324-7477344 9.21e-01 20 chr16:46723620-46723640 7.15e-01 20 chr1:28845192-28845212 7.06e-01 20 chr11:58912316-58912336 2.85e-01 20 chr3:52188379-52188399 4.41e-01 20 chr15:68346379-68346399 5.01e-01 20 chr17:1419791-1419811 1.00e+00 20 chr18:47901524-47901544 2.61e-01 20 chr2:114384884-114384904 1.12e-01 20 chr12:122150770-12215079 9.99e-01 20 chr16:81040244-81040264 3.11e-01 20 chr21:33651244-33651264 2.63e-01 20 chr19:36391396-36391416 6.81e-01 20 chr15:66797691-66797711 3.14e-03 20 chr1:93646373-93646393 5.66e-03 20 chrX:69509980-69510000 4.82e-04 11_[+1(5.51e-06)]_1 chr8:21999316-21999336 8.48e-01 20 chr2:200775816-200775836 3.18e-02 20 chr2:97001602-97001622 4.02e-01 20 chr6:31831058-31831078 9.73e-01 20 chr8:95487217-95487237 3.16e-01 20 chr16:838757-838777 1.38e-02 20 chr12:99038653-99038673 2.68e-01 20 chr15:40401012-40401032 6.27e-01 20 chr5:162887745-162887765 5.11e-02 20 chr6:86388839-86388859 4.07e-02 20 chr1:53792206-53792226 2.62e-02 20 chr16:30773272-30773292 6.42e-03 1_[+2(4.75e-05)]_11 chr16:87902234-87902254 1.69e-01 20 chr4:174255953-174255973 7.11e-01 20 chr16:1429566-1429586 2.38e-01 20 chr22:41682045-41682065 8.49e-01 20 chr15:40615715-40615735 9.98e-01 20 chr19:11492194-11492214 1.43e-02 5_[+2(8.96e-05)]_7 chr15:40886503-40886523 3.17e-01 20 chr20:33292174-33292194 6.67e-01 20 chr10:60027998-60028018 7.42e-03 20 chr14:77786892-77786912 9.98e-01 20 chr4:2243650-2243670 2.58e-02 20 chr1:176176512-176176532 4.42e-01 20 chr17:57233148-57233168 1.67e-01 20 chr10:5454557-5454577 8.89e-01 20 chr17:79651221-79651241 9.78e-01 20 chr8:120868027-120868047 6.57e-01 20 chr10:127585196-12758521 3.44e-01 20 chr8:145703494-145703514 9.92e-01 20 chr22:51222018-51222038 9.47e-01 20 chr9:79009584-79009604 4.75e-02 20 chr17:260209-260229 4.59e-01 20 chr19:5905030-5905050 9.21e-01 20 chr2:230787319-230787339 5.27e-02 20 chr12:4648066-4648086 1.44e-04 9_[+5(2.10e-06)]_3 chr15:41624626-41624646 7.00e-01 20 chr1:2322852-2322872 3.70e-01 20 chr14:102771371-10277139 8.73e-01 20 chr5:137667967-137667987 1.83e-02 [+1(1.01e-05)]_12 chr1:27024621-27024641 6.07e-01 20 chr1:227128108-227128128 1.00e+00 20 chr9:36572963-36572983 9.91e-01 20 chr3:88198685-88198705 9.19e-07 1_[+1(1.14e-06)]_11 chr19:50321097-50321117 6.24e-02 20 chr15:41625256-41625276 1.00e+00 20 chr5:68485487-68485507 9.36e-01 20 chr4:83931835-83931855 9.67e-01 20 chr16:23690203-23690223 3.31e-01 20 chr1:167189500-167189520 6.28e-02 20 chr5:10442088-10442108 6.10e-01 20 chr17:1531863-1531883 9.80e-01 20 chr21:47744270-47744290 9.72e-03 20 chr19:53073911-53073931 9.50e-02 20 chr2:234763131-234763151 4.86e-01 20 chr7:36429504-36429524 1.96e-01 20 chr2:62081336-62081356 1.99e-01 20 chr5:138728958-138728978 9.36e-01 20 chr1:114301725-114301745 6.24e-01 20 chr8:357021-357041 9.88e-01 20 chr19:48673487-48673507 6.35e-01 20 chr19:59085109-59085129 1.53e-01 20 chr1:68962716-68962736 5.69e-01 20 chr4:7044624-7044644 9.88e-01 20 chr1:52869960-52869980 4.83e-01 20 chr17:21002851-21002871 1.14e-04 11_[+3(2.76e-06)]_1 chr17:79679411-79679431 9.96e-01 20 chr18:56338403-56338423 2.93e-01 20 chr5:1295080-1295100 7.37e-01 20 chr3:33759556-33759576 9.91e-01 20 chrX:70273144-70273164 1.50e-03 7_[+2(6.06e-05)]_5 chr19:14247343-14247363 5.79e-01 20 chr21:34100699-34100719 8.76e-03 20 chr17:29159099-29159119 6.27e-01 20 chr21:33765214-33765234 5.95e-01 20 chr12:9436380-9436400 3.21e-02 20 chr9:131842946-131842966 9.06e-01 20 chr19:6199402-6199422 3.70e-01 20 chr6:153304115-153304135 1.73e-01 20 chr15:48624482-48624502 8.01e-01 20 chr1:156542277-156542297 4.71e-01 20 chr1:43148873-43148893 8.84e-01 20 chr5:79950262-79950282 4.38e-01 20 chr8:27632121-27632141 2.85e-01 20 chr15:40987458-40987478 3.30e-03 1_[+5(6.13e-06)]_11 chr7:50517962-50517982 1.00e+00 20 chr19:58874239-58874259 9.07e-01 20 chr1:45205563-45205583 5.42e-01 20 chr2:243030881-243030901 9.39e-01 20 chr10:104474551-10447457 7.34e-03 20 chr1:212209208-212209228 3.59e-01 20 chr4:184427592-184427612 7.43e-01 20 chr16:20817726-20817746 9.99e-01 20 chr9:82186254-82186274 2.39e-02 12_[+1(7.80e-06)] chr4:13486412-13486432 1.32e-03 9_[+2(2.05e-05)]_3 chr19:47734064-47734084 3.12e-01 20 chr13:111365036-11136505 4.54e-01 20 chr6:157101540-157101560 7.27e-01 20 chr7:100136353-100136373 9.47e-01 20 chr1:1051864-1051884 9.97e-01 20 chr19:53426249-53426269 9.10e-01 20 chr16:1832421-1832441 9.37e-01 20 chr20:54967177-54967197 3.55e-01 20 chr4:3956951-3956971 9.65e-01 20 chr16:2510191-2510211 4.31e-01 20 chr20:47663016-47663036 1.24e-01 20 chr1:24286026-24286046 1.29e-02 20 chr7:158497363-158497383 9.72e-01 20 chr4:104119432-104119452 6.36e-01 20 chr14:73393452-73393472 1.00e+00 20 chr10:95256402-95256422 8.33e-01 20 chr6:26251044-26251064 2.50e-01 20 chr4:90032321-90032341 9.97e-01 20 chr2:242641133-242641153 6.65e-01 20 chr5:137667380-137667400 1.15e-02 20 chr3:160117520-160117540 6.24e-01 20 chr12:110905893-11090591 7.21e-01 20 chr19:3185383-3185403 1.55e-04 5_[+3(4.65e-06)]_7 chr5:149737552-149737572 9.03e-02 20 chr19:10828966-10828986 2.78e-01 20 chr16:75590021-75590041 1.09e-01 20 chr13:50655981-50656001 7.69e-01 20 chr2:68385123-68385143 1.32e-01 20 chr1:46052141-46052161 7.03e-02 20 chr1:36235438-36235458 1.45e-01 20 chr18:14132346-14132366 1.30e-02 9_[+4(4.57e-05)]_3 chr6:27862230-27862250 1.65e-01 20 chr12:105380208-10538022 7.73e-01 20 chr3:49055885-49055905 4.90e-01 20 chr20:32274139-32274159 8.50e-01 20 chr17:42219376-42219396 9.20e-01 20 chr11:9595349-9595369 3.56e-01 20 chr9:130830638-130830658 9.98e-01 20 chr2:88926783-88926803 8.22e-01 20 chr17:38574054-38574074 4.82e-01 20 chr19:36545855-36545875 9.94e-01 20 chr17:79875898-79875918 8.77e-01 20 chr3:50374642-50374662 2.87e-01 20 chr20:36156134-36156154 9.68e-01 20 chr10:14920974-14920994 9.98e-01 20 chr1:24104986-24105006 9.57e-01 20 chr15:91260705-91260725 8.33e-01 20 chr1:226496791-226496811 6.40e-01 20 chr11:66057126-66057146 2.27e-02 20 chr8:41908638-41908658 5.44e-01 20 chr21:15399808-15399828 3.04e-01 20 chr15:85524074-85524094 7.48e-01 20 chr12:118810538-11881055 9.86e-01 20 chr8:95908115-95908135 1.10e-01 20 chr17:41322166-41322186 3.68e-02 8_[+1(2.21e-05)]_4 chr2:242626106-242626126 8.10e-01 20 chr7:100450137-100450157 5.35e-02 20 chr19:30335511-30335531 9.96e-01 20 chr7:23514254-23514274 9.75e-04 11_[+2(6.45e-06)]_1 chr6:126661334-126661354 6.10e-01 20 chr14:77843591-77843611 3.65e-01 20 chr3:49967119-49967139 9.77e-01 20 chr10:102820373-10282039 7.44e-01 20 chr8:145743130-145743150 8.49e-01 20 chr8:124408574-124408594 1.15e-01 20 chr17:4046105-4046125 7.82e-01 20 chr22:19467480-19467500 2.95e-01 20 chr1:29241174-29241194 1.99e-01 20 chr14:103995620-10399564 8.74e-01 20 chr6:33359695-33359715 7.83e-01 20 chr22:38240129-38240149 3.41e-03 2_[+4(2.75e-05)]_10 chr6:80714404-80714424 2.92e-01 20 chr5:175815501-175815521 4.50e-01 20 chr17:78388805-78388825 7.17e-02 20 chr16:2479717-2479737 5.71e-01 20 chr4:120987875-120987895 3.65e-01 20 chr17:37558971-37558991 4.16e-01 20 chr12:69754072-69754092 3.94e-01 20 chr2:10262885-10262905 9.83e-01 20 chr19:18304138-18304158 1.41e-01 20 chr8:63951284-63951304 6.10e-01 20 chr10:129924575-12992459 9.75e-01 20 chr20:37555116-37555136 9.98e-01 20 chr1:211848908-211848928 7.04e-02 20 chr4:1857739-1857759 9.98e-01 20 chr3:197687200-197687220 9.75e-02 20 chr2:223520659-223520679 9.77e-01 20 chr2:136874478-136874498 4.63e-01 20 chr15:59397376-59397396 8.16e-01 20 chr3:52804832-52804852 7.79e-01 20 chr6:42016627-42016647 9.85e-01 20 chr4:186125397-186125417 9.41e-01 20 chr4:17812657-17812677 8.05e-01 20 chr1:160255081-160255101 8.45e-01 20 chr17:79818304-79818324 8.22e-01 20 chr2:73441502-73441522 9.47e-01 20 chr19:11639564-11639584 2.13e-01 20 chr10:99160982-99161002 6.49e-01 20 chr8:22526453-22526473 7.26e-01 20 chr3:129830121-129830141 3.72e-01 20 chr16:5147614-5147634 9.98e-01 20 chr22:30821850-30821870 1.10e-01 20 chr17:8113852-8113872 2.87e-01 20 chr18:2571592-2571612 6.65e-01 20 chr8:101170556-101170576 2.64e-01 20 chr16:3018975-3018995 4.24e-01 20 chr4:128802158-128802178 5.22e-01 20 chr9:88556331-88556351 9.96e-01 20 chr12:110841369-11084138 2.64e-01 20 chr1:1821622-1821642 9.25e-01 20 chr19:13048968-13048988 2.83e-03 4_[+2(2.46e-05)]_8 chr6:5261337-5261357 5.22e-01 20 chr15:36871423-36871443 3.35e-02 20 chr13:21141415-21141435 9.36e-01 20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c22n05.farnam.hpc.yale.internal ********************************************************************************