******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.3.3 (Release date: Sun Feb 7 15:39:52 2021 -0800) For further information on how to interpret these results please access https://meme-suite.org/meme. To get a copy of the MEME Suite software please access https://meme-suite.org. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** PRIMARY SEQUENCES= ../result/final_prediction/worm/fasta/RankLinear2.0_40/unc-86.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chrV:8912319-8912399 1.0000 80 chrIV:10189299-10189379 1.0000 80 chrIII:6139487-6139567 1.0000 80 chrX:12532572-12532652 1.0000 80 chrIII:3216031-3216111 1.0000 80 chrII:14196108-14196188 1.0000 80 chrIII:8217412-8217492 1.0000 80 chrX:3517311-3517391 1.0000 80 chrIV:636540-636620 1.0000 80 chrI:2676812-2676892 1.0000 80 chrX:17322618-17322698 1.0000 80 chrI:13007714-13007794 1.0000 80 chrI:4404692-4404772 1.0000 80 chrIII:8219308-8219388 1.0000 80 chrIII:8211703-8211783 1.0000 80 chrX:3883371-3883451 1.0000 80 chrX:12534635-12534715 1.0000 80 chrX:6954809-6954889 1.0000 80 chrII:2198739-2198819 1.0000 80 chrI:296308-296388 1.0000 80 chrX:3038303-3038383 1.0000 80 chrIII:8216378-8216458 1.0000 80 chrX:8591987-8592067 1.0000 80 chrX:2268951-2269031 1.0000 80 chrIII:42279-42359 1.0000 80 chrX:2955782-2955862 1.0000 80 chrX:16778576-16778656 1.0000 80 chrX:2266493-2266573 1.0000 80 chrX:4633168-4633248 1.0000 80 chrIII:10282659-10282739 1.0000 80 chrX:10763285-10763365 1.0000 80 chrV:4229867-4229947 1.0000 80 chrIII:8218311-8218391 1.0000 80 chrX:12198428-12198508 1.0000 80 chrIII:9311800-9311880 1.0000 80 chrIII:8220205-8220285 1.0000 80 chrIII:8215104-8215184 1.0000 80 chrX:12100152-12100232 1.0000 80 chrX:15215461-15215541 1.0000 80 chrIII:5626063-5626143 1.0000 80 chrI:8387099-8387179 1.0000 80 chrIII:6697196-6697276 1.0000 80 chrIII:4483148-4483228 1.0000 80 chrI:7363660-7363740 1.0000 80 chrIV:7784947-7785027 1.0000 80 chrIII:5998827-5998907 1.0000 80 chrV:5089891-5089971 1.0000 80 chrI:7409772-7409852 1.0000 80 chrX:3669990-3670070 1.0000 80 chrIV:3821643-3821723 1.0000 80 chrII:7955686-7955766 1.0000 80 chrII:4505104-4505184 1.0000 80 chrIV:925931-926011 1.0000 80 chrIII:8229663-8229743 1.0000 80 chrV:11850959-11851039 1.0000 80 chrX:9956623-9956703 1.0000 80 chrX:7776767-7776847 1.0000 80 chrII:10997445-10997525 1.0000 80 chrII:5305266-5305346 1.0000 80 chrX:737136-737216 1.0000 80 chrX:15555061-15555141 1.0000 80 chrX:4091686-4091766 1.0000 80 chrIV:647691-647771 1.0000 80 chrIII:5757794-5757874 1.0000 80 chrII:10746220-10746300 1.0000 80 chrIV:5337754-5337834 1.0000 80 chrI:14276671-14276751 1.0000 80 chrIV:4052863-4052943 1.0000 80 chrX:12513607-12513687 1.0000 80 chrV:8767280-8767360 1.0000 80 chrX:14838472-14838552 1.0000 80 chrI:8045379-8045459 1.0000 80 chrIV:10507711-10507791 1.0000 80 chrIII:6352609-6352689 1.0000 80 chrX:5027643-5027723 1.0000 80 chrX:13364958-13365038 1.0000 80 chrIII:5824715-5824795 1.0000 80 chrII:8618999-8619079 1.0000 80 chrV:13070333-13070413 1.0000 80 chrI:2414204-2414284 1.0000 80 chrIII:12613387-12613467 1.0000 80 chrX:9141400-9141480 1.0000 80 chrV:13401497-13401577 1.0000 80 chrII:8951311-8951391 1.0000 80 chrX:12569923-12570003 1.0000 80 chrI:878285-878365 1.0000 80 chrI:11939036-11939116 1.0000 80 chrX:12960161-12960241 1.0000 80 chrX:2729349-2729429 1.0000 80 chrX:15668842-15668922 1.0000 80 chrIII:5643538-5643618 1.0000 80 chrIII:4127471-4127551 1.0000 80 chrIV:14773576-14773656 1.0000 80 chrIII:29778-29858 1.0000 80 chrIV:5292170-5292250 1.0000 80 chrX:2645476-2645556 1.0000 80 chrIII:6649797-6649877 1.0000 80 chrX:15008860-15008940 1.0000 80 chrX:10838786-10838866 1.0000 80 chrIV:6836093-6836173 1.0000 80 chrX:2441301-2441381 1.0000 80 chrIII:6658148-6658228 1.0000 80 chrX:8354544-8354624 1.0000 80 chrII:1808368-1808448 1.0000 80 chrX:6887927-6888007 1.0000 80 chrII:10829173-10829253 1.0000 80 chrIII:12780699-12780779 1.0000 80 chrI:6437560-6437640 1.0000 80 chrI:6394395-6394475 1.0000 80 chrII:9755627-9755707 1.0000 80 chrX:12512625-12512705 1.0000 80 chrIV:2859756-2859836 1.0000 80 chrV:8169304-8169384 1.0000 80 chrI:9494660-9494740 1.0000 80 chrII:13503829-13503909 1.0000 80 chrIII:10574787-10574867 1.0000 80 chrX:4229596-4229676 1.0000 80 chrV:1303532-1303612 1.0000 80 chrX:12204497-12204577 1.0000 80 chrX:7233147-7233227 1.0000 80 chrX:2084201-2084281 1.0000 80 chrIV:15814226-15814306 1.0000 80 chrIII:3220468-3220548 1.0000 80 chrX:11646179-11646259 1.0000 80 chrII:601458-601538 1.0000 80 chrIV:6541572-6541652 1.0000 80 chrI:10756554-10756634 1.0000 80 chrIV:7623992-7624072 1.0000 80 chrIII:13042981-13043061 1.0000 80 chrV:8663103-8663183 1.0000 80 chrI:3650747-3650827 1.0000 80 chrI:7398956-7399036 1.0000 80 chrX:3152428-3152508 1.0000 80 chrIII:9971501-9971581 1.0000 80 chrII:7968266-7968346 1.0000 80 chrV:3837558-3837638 1.0000 80 chrI:4406176-4406256 1.0000 80 chrIV:6393559-6393639 1.0000 80 chrIII:7357528-7357608 1.0000 80 chrI:7342571-7342651 1.0000 80 chrII:11382346-11382426 1.0000 80 chrIV:8583131-8583211 1.0000 80 chrX:7012004-7012084 1.0000 80 chrX:11607571-11607651 1.0000 80 chrIV:7224750-7224830 1.0000 80 chrX:16737593-16737673 1.0000 80 chrII:11306258-11306338 1.0000 80 chrX:15355771-15355851 1.0000 80 chrIV:11450923-11451003 1.0000 80 chrV:12530351-12530431 1.0000 80 chrIII:7264013-7264093 1.0000 80 chrX:5031926-5032006 1.0000 80 chrX:3520107-3520187 1.0000 80 chrI:14802468-14802548 1.0000 80 chrI:5719085-5719165 1.0000 80 chrII:12691024-12691104 1.0000 80 chrIV:2858885-2858965 1.0000 80 chrII:14036902-14036982 1.0000 80 chrII:9121114-9121194 1.0000 80 chrX:17317143-17317223 1.0000 80 chrX:2830410-2830490 1.0000 80 chrX:4859789-4859869 1.0000 80 chrI:8581625-8581705 1.0000 80 chrX:11668219-11668299 1.0000 80 chrIV:659693-659773 1.0000 80 chrV:9107065-9107145 1.0000 80 chrIV:4584862-4584942 1.0000 80 chrII:10284890-10284970 1.0000 80 chrX:16485995-16486075 1.0000 80 chrIV:6834799-6834879 1.0000 80 chrIII:764577-764657 1.0000 80 chrIV:10461955-10462035 1.0000 80 chrV:17784948-17785028 1.0000 80 chrV:7727072-7727152 1.0000 80 chrIV:11790736-11790816 1.0000 80 chrV:12030761-12030841 1.0000 80 chrV:10516623-10516703 1.0000 80 chrV:7762594-7762674 1.0000 80 chrIV:1978201-1978281 1.0000 80 chrII:6766669-6766749 1.0000 80 chrI:2960667-2960747 1.0000 80 chrI:9385527-9385607 1.0000 80 chrIII:1797060-1797140 1.0000 80 chrIV:6954683-6954763 1.0000 80 chrX:12175252-12175332 1.0000 80 chrV:18069404-18069484 1.0000 80 chrI:7369070-7369150 1.0000 80 chrX:5122850-5122930 1.0000 80 chrIII:10579021-10579101 1.0000 80 chrV:6867426-6867506 1.0000 80 chrV:9128749-9128829 1.0000 80 chrIV:7660897-7660977 1.0000 80 chrIII:8395095-8395175 1.0000 80 chrV:14487506-14487586 1.0000 80 chrII:4134822-4134902 1.0000 80 chrIII:3140759-3140839 1.0000 80 chrII:14052106-14052186 1.0000 80 chrV:13029031-13029111 1.0000 80 chrV:16754044-16754124 1.0000 80 chrX:17158396-17158476 1.0000 80 chrX:6249117-6249197 1.0000 80 chrX:3901829-3901909 1.0000 80 chrIV:4482986-4483066 1.0000 80 chrIII:3559131-3559211 1.0000 80 chrI:3101010-3101090 1.0000 80 chrI:4484992-4485072 1.0000 80 chrIII:30559-30639 1.0000 80 chrIII:7193379-7193459 1.0000 80 chrII:2962650-2962730 1.0000 80 chrII:5042591-5042671 1.0000 80 chrX:4319150-4319230 1.0000 80 chrIII:1743670-1743750 1.0000 80 chrX:9691950-9692030 1.0000 80 chrI:7848975-7849055 1.0000 80 chrIV:7223266-7223346 1.0000 80 chrII:12382783-12382863 1.0000 80 chrII:8834708-8834788 1.0000 80 chrII:4453629-4453709 1.0000 80 chrII:14460546-14460626 1.0000 80 chrIV:6956865-6956945 1.0000 80 chrIII:761350-761430 1.0000 80 chrIII:3560356-3560436 1.0000 80 chrIV:10340771-10340851 1.0000 80 chrIII:3622689-3622769 1.0000 80 chrV:1494297-1494377 1.0000 80 chrI:2415609-2415689 1.0000 80 chrI:9454314-9454394 1.0000 80 chrX:8157255-8157335 1.0000 80 chrX:9673089-9673169 1.0000 80 chrIII:3943871-3943951 1.0000 80 chrIII:11673164-11673244 1.0000 80 chrII:7625352-7625432 1.0000 80 chrIII:5689922-5690002 1.0000 80 chrIV:13272608-13272688 1.0000 80 chrIV:9774546-9774626 1.0000 80 chrV:8418161-8418241 1.0000 80 chrX:11403982-11404062 1.0000 80 chrIII:5639992-5640072 1.0000 80 chrI:9090545-9090625 1.0000 80 chrIV:6514876-6514956 1.0000 80 chrIII:10608314-10608394 1.0000 80 chrII:6465835-6465915 1.0000 80 chrV:6661796-6661876 1.0000 80 chrII:11032192-11032272 1.0000 80 chrII:7188556-7188636 1.0000 80 chrX:6740689-6740769 1.0000 80 chrIV:16658880-16658960 1.0000 80 chrX:3703774-3703854 1.0000 80 chrIV:11867963-11868043 1.0000 80 chrIV:14837059-14837139 1.0000 80 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme -oc ../result/final_prediction/worm/inference_raw/MEME/RankLinear2.0_40_unc-86/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/worm/fasta/RankLinear2.0_40/unc-86.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= 20000 N= 250 sample: seed= 0 hsfrac= 0 searchsize= 20000 norand= no csites= 1000 Letter frequencies in dataset: A 0.301 C 0.196 G 0.205 T 0.299 Background letter frequencies (from file dataset with add-one prior applied): A 0.301 C 0.196 G 0.205 T 0.299 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GAATWATT MEME-1 width = 8 sites = 54 llr = 432 E-value = 2.3e-013 ******************************************************************************** -------------------------------------------------------------------------------- Motif GAATWATT MEME-1 Description -------------------------------------------------------------------------------- Simplified A :aa247:: pos.-specific C :::::1:: probability G a::1:::: matrix T :::862aa bits 2.4 * 2.1 * 1.9 * 1.6 *** ** Relative 1.4 *** ** Entropy 1.2 *** ** (11.5 bits) 0.9 **** ** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GAATTATT consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAATWATT MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIV:9774546-9774626 68 4.47e-05 CCAAATGACA GAATTATT CATTT chrII:14460546-14460626 51 4.47e-05 TTTTTCGCTG GAATTATT CAGCCACCAG chrX:9691950-9692030 5 4.47e-05 TCCT GAATTATT CAAACGGTTT chrI:5719085-5719165 68 4.47e-05 TGCTCCTTTT GAATTATT CACCA chrX:3520107-3520187 66 4.47e-05 CGTTTTGTGT GAATTATT CAAAAGT chrI:7398956-7399036 62 4.47e-05 AAACCGCATA GAATTATT GTAACTGAAA chrIV:7623992-7624072 26 4.47e-05 GAAGACGCGT GAATTATT CGAGAAGGAC chrX:11646179-11646259 64 4.47e-05 GGTAGGGGAT GAATTATT CAACTGCAT chrX:7233147-7233227 21 4.47e-05 CCGAGAAATT GAATTATT CATGAGCAAG chrI:6437560-6437640 15 4.47e-05 CGAGCTTTTC GAATTATT CCGAGAAGCA chrIII:6658148-6658228 68 4.47e-05 CACATCGTTT GAATTATT GACGA chrIV:5292170-5292250 63 4.47e-05 CTACTCTAGT GAATTATT CATTCTTATT chrII:4505104-4505184 33 4.47e-05 ACGAGTGACT GAATTATT CATTAGTTCA chrX:4633168-4633248 15 4.47e-05 TGCGTTTTTG GAATTATT TATGGTGAGA chrX:2268951-2269031 19 4.47e-05 TGAGAATGTT GAATTATT CATTACTGTG chrIII:6139487-6139567 28 4.47e-05 AACTCTGCAT GAATTATT CATGTTCGGG chrII:7625352-7625432 33 8.97e-05 ACTGGCCGAT GAATAATT CATGTTTCAC chrX:6249117-6249197 47 8.97e-05 TCCCACTTAT GAATAATT CGTTTTGAGC chrX:5122850-5122930 17 8.97e-05 ATTCCGCGAT GAATAATT TAAGAGTACG chrX:11668219-11668299 15 8.97e-05 AGAATAAGAT GAATAATT AATCAATTTC chrI:14802468-14802548 45 8.97e-05 TTCCAGTTTT GAATAATT CAAATGGTTC chrV:3837558-3837638 21 8.97e-05 CTTACTCGAT GAATAATT TATACGTATC chrIII:5643538-5643618 52 8.97e-05 GGGGGTCTGT GAATAATT TATGAGTACT chrV:13401497-13401577 20 8.97e-05 AGCATCATTT GAATAATT CATACCCACC chrX:14838472-14838552 43 8.97e-05 GGCAACAAAT GAATAATT CCAAGAGTCT chrII:10746220-10746300 12 8.97e-05 AAATTTGAAT GAATAATT CACAAAAGTG chrV:11850959-11851039 43 8.97e-05 GTCGGTCCCT GAATAATT CATAAAAAAT chrX:15215461-15215541 66 8.97e-05 AAAAGTTCTT GAATAATT CATAAGA chrIII:3216031-3216111 3 8.97e-05 TT GAATAATT CAGGAGATGT chrX:17158396-17158476 6 1.34e-04 CAAGT GAATTTTT AAAAAAGCTC chrIII:3140759-3140839 5 1.34e-04 GTAT GAATTTTT AAGCTGATGA chrII:11306258-11306338 16 1.34e-04 AAACTCTTAT GAATTTTT CATGCCATAT chrX:12512625-12512705 37 1.34e-04 AATATTCATC GAATTTTT GGTTTTGGGA chrV:14487506-14487586 47 1.79e-04 TTCAAAACAT GAAATATT CATATAGGAC chrI:878285-878365 70 1.79e-04 CAGTGTGAAT GAAATATT AAT chrX:12100152-12100232 40 1.79e-04 GAAAGAGAAT GAAATATT GAATTCGTTC chrIII:8211703-8211783 12 1.79e-04 CCGAAGCACT GAAATATT CATCAACCTG chrIV:636540-636620 10 1.79e-04 AAAGAAAAT GAAATATT TACACACCTC chrIII:10608314-10608394 20 2.08e-04 ACAATTCTGA GAATTCTT TTTCCTTTTT chrI:3101010-3101090 73 2.08e-04 GGTTAATTAG GAATTCTT chrI:13007714-13007794 53 2.08e-04 AGAATTATCT GAATTCTT AAGGATTCCC chrIII:10579021-10579101 21 2.53e-04 AATAGGGGCT GAATATTT Gagatgaagc chrIII:1797060-1797140 26 2.53e-04 GGCTGCTCAT GAATATTT CATCATTTGC chrV:13070333-13070413 23 2.53e-04 TATCATAATG GAATATTT GAAAGAAGAA chrIV:4052863-4052943 62 2.53e-04 AAGAAGTCAT GAATATTT GGTGTGAAAA chrIV:11867963-11868043 16 2.98e-04 AAGCGAAACT GAAAAATT AATGAGCACC chrIV:925931-926011 13 2.98e-04 CATTTTCGCT GAAAAATT TTCAATAATT chrIII:8215104-8215184 49 2.98e-04 CCTCCTCTTT GAAAAATT AATGGAGGAC chrIV:7223266-7223346 14 3.27e-04 ACTGACTTCA GAATACTT GATACAAGGG chrI:9385527-9385607 2 3.27e-04 C GAATACTT TATTGGCAGT chrX:9956623-9956703 64 3.58e-04 ACATCAGAAT GAAGTATT AATGAGCAG chrIII:5626063-5626143 46 3.58e-04 TTCATCCGCG GAAGTATT TGTATCTTTT chrX:12198428-12198508 3 3.89e-04 CC GAAGAATT CCAAATGAGC chrII:10997445-10997525 21 4.34e-04 AATTCACTCT GAAATTTT AATGAACGTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAATWATT MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIV:9774546-9774626 4.5e-05 67_[+1]_5 chrII:14460546-14460626 4.5e-05 50_[+1]_22 chrX:9691950-9692030 4.5e-05 4_[+1]_68 chrI:5719085-5719165 4.5e-05 67_[+1]_5 chrX:3520107-3520187 4.5e-05 65_[+1]_7 chrI:7398956-7399036 4.5e-05 61_[+1]_11 chrIV:7623992-7624072 4.5e-05 25_[+1]_47 chrX:11646179-11646259 4.5e-05 63_[+1]_9 chrX:7233147-7233227 4.5e-05 20_[+1]_52 chrI:6437560-6437640 4.5e-05 14_[+1]_58 chrIII:6658148-6658228 4.5e-05 67_[+1]_5 chrIV:5292170-5292250 4.5e-05 62_[+1]_10 chrII:4505104-4505184 4.5e-05 32_[+1]_40 chrX:4633168-4633248 4.5e-05 14_[+1]_58 chrX:2268951-2269031 4.5e-05 18_[+1]_54 chrIII:6139487-6139567 4.5e-05 27_[+1]_45 chrII:7625352-7625432 9e-05 32_[+1]_40 chrX:6249117-6249197 9e-05 46_[+1]_26 chrX:5122850-5122930 9e-05 16_[+1]_56 chrX:11668219-11668299 9e-05 14_[+1]_58 chrI:14802468-14802548 9e-05 44_[+1]_28 chrV:3837558-3837638 9e-05 20_[+1]_52 chrIII:5643538-5643618 9e-05 51_[+1]_21 chrV:13401497-13401577 9e-05 19_[+1]_53 chrX:14838472-14838552 9e-05 42_[+1]_30 chrII:10746220-10746300 9e-05 11_[+1]_61 chrV:11850959-11851039 9e-05 42_[+1]_30 chrX:15215461-15215541 9e-05 65_[+1]_7 chrIII:3216031-3216111 9e-05 2_[+1]_70 chrX:17158396-17158476 0.00013 5_[+1]_67 chrIII:3140759-3140839 0.00013 4_[+1]_68 chrII:11306258-11306338 0.00013 15_[+1]_57 chrX:12512625-12512705 0.00013 36_[+1]_36 chrV:14487506-14487586 0.00018 46_[+1]_26 chrI:878285-878365 0.00018 69_[+1]_3 chrX:12100152-12100232 0.00018 39_[+1]_33 chrIII:8211703-8211783 0.00018 11_[+1]_61 chrIV:636540-636620 0.00018 9_[+1]_63 chrIII:10608314-10608394 0.00021 19_[+1]_53 chrI:3101010-3101090 0.00021 72_[+1] chrI:13007714-13007794 0.00021 52_[+1]_20 chrIII:10579021-10579101 0.00025 20_[+1]_52 chrIII:1797060-1797140 0.00025 25_[+1]_47 chrV:13070333-13070413 0.00025 22_[+1]_50 chrIV:4052863-4052943 0.00025 61_[+1]_11 chrIV:11867963-11868043 0.0003 15_[+1]_57 chrIV:925931-926011 0.0003 12_[+1]_60 chrIII:8215104-8215184 0.0003 48_[+1]_24 chrIV:7223266-7223346 0.00033 13_[+1]_59 chrI:9385527-9385607 0.00033 1_[+1]_71 chrX:9956623-9956703 0.00036 63_[+1]_9 chrIII:5626063-5626143 0.00036 45_[+1]_27 chrX:12198428-12198508 0.00039 2_[+1]_70 chrII:10997445-10997525 0.00043 20_[+1]_52 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAATWATT MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GAATWATT width=8 seqs=54 chrIV:9774546-9774626 ( 68) GAATTATT 1 chrII:14460546-14460626 ( 51) GAATTATT 1 chrX:9691950-9692030 ( 5) GAATTATT 1 chrI:5719085-5719165 ( 68) GAATTATT 1 chrX:3520107-3520187 ( 66) GAATTATT 1 chrI:7398956-7399036 ( 62) GAATTATT 1 chrIV:7623992-7624072 ( 26) GAATTATT 1 chrX:11646179-11646259 ( 64) GAATTATT 1 chrX:7233147-7233227 ( 21) GAATTATT 1 chrI:6437560-6437640 ( 15) GAATTATT 1 chrIII:6658148-6658228 ( 68) GAATTATT 1 chrIV:5292170-5292250 ( 63) GAATTATT 1 chrII:4505104-4505184 ( 33) GAATTATT 1 chrX:4633168-4633248 ( 15) GAATTATT 1 chrX:2268951-2269031 ( 19) GAATTATT 1 chrIII:6139487-6139567 ( 28) GAATTATT 1 chrII:7625352-7625432 ( 33) GAATAATT 1 chrX:6249117-6249197 ( 47) GAATAATT 1 chrX:5122850-5122930 ( 17) GAATAATT 1 chrX:11668219-11668299 ( 15) GAATAATT 1 chrI:14802468-14802548 ( 45) GAATAATT 1 chrV:3837558-3837638 ( 21) GAATAATT 1 chrIII:5643538-5643618 ( 52) GAATAATT 1 chrV:13401497-13401577 ( 20) GAATAATT 1 chrX:14838472-14838552 ( 43) GAATAATT 1 chrII:10746220-10746300 ( 12) GAATAATT 1 chrV:11850959-11851039 ( 43) GAATAATT 1 chrX:15215461-15215541 ( 66) GAATAATT 1 chrIII:3216031-3216111 ( 3) GAATAATT 1 chrX:17158396-17158476 ( 6) GAATTTTT 1 chrIII:3140759-3140839 ( 5) GAATTTTT 1 chrII:11306258-11306338 ( 16) GAATTTTT 1 chrX:12512625-12512705 ( 37) GAATTTTT 1 chrV:14487506-14487586 ( 47) GAAATATT 1 chrI:878285-878365 ( 70) GAAATATT 1 chrX:12100152-12100232 ( 40) GAAATATT 1 chrIII:8211703-8211783 ( 12) GAAATATT 1 chrIV:636540-636620 ( 10) GAAATATT 1 chrIII:10608314-10608394 ( 20) GAATTCTT 1 chrI:3101010-3101090 ( 73) GAATTCTT 1 chrI:13007714-13007794 ( 53) GAATTCTT 1 chrIII:10579021-10579101 ( 21) GAATATTT 1 chrIII:1797060-1797140 ( 26) GAATATTT 1 chrV:13070333-13070413 ( 23) GAATATTT 1 chrIV:4052863-4052943 ( 62) GAATATTT 1 chrIV:11867963-11868043 ( 16) GAAAAATT 1 chrIV:925931-926011 ( 13) GAAAAATT 1 chrIII:8215104-8215184 ( 49) GAAAAATT 1 chrIV:7223266-7223346 ( 14) GAATACTT 1 chrI:9385527-9385607 ( 2) GAATACTT 1 chrX:9956623-9956703 ( 64) GAAGTATT 1 chrIII:5626063-5626143 ( 46) GAAGTATT 1 chrX:12198428-12198508 ( 3) GAAGAATT 1 chrII:10997445-10997525 ( 21) GAAATTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAATWATT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 9.59303 E= 2.3e-013 -1240 -1240 229 -1240 173 -1240 -1240 -1240 173 -1240 -1240 -1240 -85 -1240 -188 138 50 -1240 -1240 94 130 -108 -1240 -84 -1240 -1240 -1240 174 -1240 -1240 -1240 174 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAATWATT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 54 E= 2.3e-013 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.055556 0.777778 0.425926 0.000000 0.000000 0.574074 0.740741 0.092593 0.000000 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAATWATT MEME-1 regular expression -------------------------------------------------------------------------------- GAAT[TA]ATT -------------------------------------------------------------------------------- Time 9.98 secs. ******************************************************************************** ******************************************************************************** MOTIF GAARAAGA MEME-2 width = 8 sites = 81 llr = 572 E-value = 2.0e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif GAARAAGA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 3aa67828 pos.-specific C ::::1::: probability G 7::4228: matrix T :::::::2 bits 2.4 2.1 1.9 1.6 ** Relative 1.4 *** * Entropy 1.2 *** *** (10.2 bits) 0.9 **** *** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GAAAAAGA consensus A G A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAARAAGA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIV:16658880-16658960 11 3.13e-05 CTCGCGTGGA GAAAAAGA AAATAACTGG chrIII:30559-30639 27 3.13e-05 AGGAAAAGAA GAAAAAGA TGAAGACTCC chrI:3101010-3101090 17 3.13e-05 TGGAGCCACC GAAAAAGA GAGAGAGAAG chrV:14487506-14487586 16 3.13e-05 TATTTACGCG GAAAAAGA GGGGGGAGCG chrIII:10579021-10579101 57 3.13e-05 atagcatgat gaaaaaga agaagttgaa chrV:17784948-17785028 6 3.13e-05 ATAGA GAAAAAGA TGTGAAAATG chrI:8581625-8581705 64 3.13e-05 GAATGTATTA GAAAAAGA CGAATCGAT chrX:4859789-4859869 66 3.13e-05 GAAGTTCTTG GAAAAAGA GAAAAAA chrX:15355771-15355851 70 3.13e-05 GGAAACCAAA GAAAAAGA TGA chrX:3152428-3152508 52 3.13e-05 AGGAAATGGA GAAAAAGA CGATGAATTA chrI:6394395-6394475 68 3.13e-05 AGAAGGGTGG GAAAAAGA GGAAA chrIII:8211703-8211783 56 3.13e-05 TGTGTAGGAC GAAAAAGA AGAAGAGGCT chrX:3517311-3517391 4 3.13e-05 TCT GAAAAAGA CAATTGGCAA chrIII:3560356-3560436 19 5.25e-05 CGAACCCCCC GAAGAAGA GACGCAGAAG chrIII:1743670-1743750 10 5.25e-05 TTagtagaa gaagaaga agaagttttg chrI:4484992-4485072 8 5.25e-05 agaagaa gaagaaga agCTCGAGAT chrI:2960667-2960747 19 5.25e-05 gagtaggtga gaagaaga gacgcagaga chrI:10756554-10756634 62 5.25e-05 gaatgaggat gaagaaga cgttggagca chrV:1303532-1303612 56 5.25e-05 TGGCGGACAA GAAGAAGA AGCAGCAGGA chrX:10838786-10838866 17 5.25e-05 AAAGAAAAAC GAAGAAGA GAAGAATCCG chrIII:6649797-6649877 37 5.25e-05 TCACTTCAAT GAAGAAGA GCAAGATAAA chrX:2830410-2830490 23 7.38e-05 ACGGAAAATT GAAAGAGA ATAGGAAATT chrIII:4127471-4127551 7 7.38e-05 TCTTGC GAAAGAGA TTCCGTATTC chrX:12100152-12100232 30 7.38e-05 ATGAGTAAGA GAAAGAGA ATGAAATATT chrX:11403982-11404062 51 1.10e-04 TTGAGGGCAT GAAAAGGA ATATGATGAA chrX:13364958-13365038 4 1.10e-04 TCC GAAGGAGA AGAGCGGCGA chrIV:10507711-10507791 32 1.10e-04 ATGGGAGTTA GAAAAGGA GGGAAAAGTG chrIV:3821643-3821723 53 1.10e-04 TGAATGGAGT GAAAAGGA GCTCCGTCAA chrIII:8217412-8217492 23 1.10e-04 AACGAAAAAG GAAAAGGA TGGATGTGAA chrV:12030761-12030841 14 1.70e-04 gtgagaaagg aaaaaaga aagaGCAAGA chrIV:15814226-15814306 9 1.70e-04 GAGAAAAT AAAAAAGA ATTCATAGAA chrI:9494660-9494740 7 1.70e-04 CAAAGA AAAAAAGA AGAAAAGAAG chrV:13401497-13401577 49 1.70e-04 AGAGGACGAT GAAGAGGA CTGGACACTC chrIII:5757794-5757874 42 1.70e-04 GGGATAACAA AAAAAAGA GTTCCGATAG chrV:5089891-5089971 15 1.70e-04 AGTAGAGCAA AAAAAAGA AGAAGTGTCT chrV:13070333-13070413 32 2.01e-04 GGAATATTTG AAAGAAGA ACACATGACC chrII:4505104-4505184 16 2.01e-04 AGTCGTTTGA AAAGAAGA CGAGTGACTG chrIII:9311800-9311880 73 2.01e-04 GTTTCAATTC AAAGAAGA chrIV:6954683-6954763 38 2.53e-04 AAAAAAGTCT GAAAAAGT GAAGCTGTTC chrIII:9971501-9971581 8 2.53e-04 AAACAGA GAAACAGA AACACTTTGC chrIII:5998827-5998907 55 2.53e-04 taagaagaaa gaaaaagt gagagaaaGT chrX:8591987-8592067 1 2.53e-04 . GAAAAAGT TAAGTCTACG chrX:3703774-3703854 45 3.34e-04 AGGAAAAGTA GAAAAAAA AACGTGAGAC chrI:9090545-9090625 38 3.34e-04 AAGTATAAGG GAAAAAAA TAAATGAGAA chrV:16754044-16754124 41 3.34e-04 ATATTTATTC GAAGAAGT TTTCCGCCGA chrX:7012004-7012084 31 3.34e-04 AGCAATTTAC GAAGAAGT CAAAATTCTG chrIV:2859756-2859836 6 3.34e-04 AGTCA GAAAAAAA AAGTTGGAAA chrIII:12780699-12780779 69 3.34e-04 TGCTCGCCCA GAAAAAAA GTCA chrV:11850959-11851039 22 3.34e-04 GAAGCCATGT GAAAAAAA GTAGTCGGTC chrIII:6697196-6697276 29 3.34e-04 TCATCGAAAA GAAGCAGA AAAATAAAGA chrX:15215461-15215541 50 3.34e-04 TTGCGAATCC GAAAAAAA AAGTTCTTGA chrX:15555061-15555141 34 3.65e-04 GCATATTAAT GAAGAAAA AGCGAAAAAG chrII:7955686-7955766 23 3.65e-04 GTGTCTTTCC GAAGAAAA GATGTGAGGA chrIV:9774546-9774626 6 4.20e-04 AGTCA GAAGGGGA TGGAGTGTAA chrIII:5689922-5690002 44 4.20e-04 TAGGAAAACC AAAAGAGA GTAGTACGGG chrIV:4584862-4584942 51 4.20e-04 CTAGTCCACC AAAAGAGA ATCCATTCCA chrX:3883371-3883451 31 4.20e-04 CCAGGAAATG AAAAGAGA GTGAAAGCCA chrX:12532572-12532652 72 4.73e-04 ATAAATTATT AAAAAGGA G chrX:12513607-12513687 53 4.94e-04 CTGGGAATTA AAAGAGGA AAATATTATG chrIII:8220205-8220285 67 4.94e-04 AGTATTCTCT AAAGAGGA ATCTAT chrII:10829173-10829253 26 5.15e-04 AAGAAATAAG GAAAGAGT TGTCGTTTCC chrX:12569923-12570003 36 5.15e-04 ATTGTGAAGC GAAAGAGT GAGAGAGGTG chrII:2198739-2198819 70 5.15e-04 AAATGTCATG GAAAGAGT TGA chrII:12691024-12691104 57 5.96e-04 CACCCCTCCC GAAGGAGT TAATCGGGTT chrIV:10189299-10189379 73 5.96e-04 AGGATTCTGA GAAAAGGT chrV:9128749-9128829 37 7.48e-04 CTCTTCAACA GAAGCGGA GTAGTGAATG chrX:12175252-12175332 54 7.48e-04 ACCAGAATAT AAAACAGA TAAACACAAA chrX:11668219-11668299 36 7.48e-04 CAATTTCAGT GAAGCGGA CCATTCAGCA chrIV:6541572-6541652 60 7.48e-04 TGCTGCTCCA AAAAAAGT GGGCGGAGCA chrX:15008860-15008940 32 7.48e-04 ACAACACGAA GAAGGAAA ATGAATTCTA chrI:878285-878365 36 7.48e-04 GTCACATGCT GAAAAGAA ACGAATGAAT chrIII:5824715-5824795 49 7.48e-04 ATTTTCATCC GAAAAGAA AGAAAAACGA chrII:14052106-14052186 44 8.88e-04 ATGTCATTCA AAAGCAGA CTCCCCTTAC chrX:16778576-16778656 36 8.88e-04 AGTGGGGAGA AAAGCAGA CCAACGAGGT chrIII:42279-42359 67 8.88e-04 GAAAAGACAC AAAAAAAA CTTGAG chrX:3520107-3520187 13 9.34e-04 AAGGTGCGGT AAAGAAAA TCTGAAAGCG chrIV:636540-636620 1 9.34e-04 . AAAGAAAA TGAAATATTT chrX:2729349-2729429 24 1.04e-03 GAAACAGTTA GAAACAAA GAATACATCC chrIII:3220468-3220548 19 1.09e-03 GAGCTATTCA GAAGAAAT CCTCTGCGTC chrIII:4483148-4483228 33 1.09e-03 TCTGGGATGG GAAGAAAT AGTGTTGGAT chrI:14802468-14802548 67 1.15e-03 TGGTTCTTGA GAAAACGA TAGTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAARAAGA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIV:16658880-16658960 3.1e-05 10_[+2]_62 chrIII:30559-30639 3.1e-05 26_[+2]_46 chrI:3101010-3101090 3.1e-05 16_[+2]_56 chrV:14487506-14487586 3.1e-05 15_[+2]_57 chrIII:10579021-10579101 3.1e-05 56_[+2]_16 chrV:17784948-17785028 3.1e-05 5_[+2]_67 chrI:8581625-8581705 3.1e-05 63_[+2]_9 chrX:4859789-4859869 3.1e-05 65_[+2]_7 chrX:15355771-15355851 3.1e-05 69_[+2]_3 chrX:3152428-3152508 3.1e-05 51_[+2]_21 chrI:6394395-6394475 3.1e-05 67_[+2]_5 chrIII:8211703-8211783 3.1e-05 55_[+2]_17 chrX:3517311-3517391 3.1e-05 3_[+2]_69 chrIII:3560356-3560436 5.3e-05 18_[+2]_54 chrIII:1743670-1743750 5.3e-05 9_[+2]_63 chrI:4484992-4485072 5.3e-05 7_[+2]_65 chrI:2960667-2960747 5.3e-05 18_[+2]_54 chrI:10756554-10756634 5.3e-05 61_[+2]_11 chrV:1303532-1303612 5.3e-05 55_[+2]_17 chrX:10838786-10838866 5.3e-05 16_[+2]_56 chrIII:6649797-6649877 5.3e-05 36_[+2]_36 chrX:2830410-2830490 7.4e-05 22_[+2]_50 chrIII:4127471-4127551 7.4e-05 6_[+2]_66 chrX:12100152-12100232 7.4e-05 29_[+2]_43 chrX:11403982-11404062 0.00011 50_[+2]_22 chrX:13364958-13365038 0.00011 3_[+2]_69 chrIV:10507711-10507791 0.00011 31_[+2]_41 chrIV:3821643-3821723 0.00011 52_[+2]_20 chrIII:8217412-8217492 0.00011 22_[+2]_50 chrV:12030761-12030841 0.00017 13_[+2]_59 chrIV:15814226-15814306 0.00017 8_[+2]_64 chrI:9494660-9494740 0.00017 6_[+2]_66 chrV:13401497-13401577 0.00017 48_[+2]_24 chrIII:5757794-5757874 0.00017 41_[+2]_31 chrV:5089891-5089971 0.00017 14_[+2]_58 chrV:13070333-13070413 0.0002 31_[+2]_41 chrII:4505104-4505184 0.0002 15_[+2]_57 chrIII:9311800-9311880 0.0002 72_[+2] chrIV:6954683-6954763 0.00025 37_[+2]_35 chrIII:9971501-9971581 0.00025 7_[+2]_65 chrIII:5998827-5998907 0.00025 54_[+2]_18 chrX:8591987-8592067 0.00025 [+2]_72 chrX:3703774-3703854 0.00033 44_[+2]_28 chrI:9090545-9090625 0.00033 37_[+2]_35 chrV:16754044-16754124 0.00033 40_[+2]_32 chrX:7012004-7012084 0.00033 30_[+2]_42 chrIV:2859756-2859836 0.00033 5_[+2]_67 chrIII:12780699-12780779 0.00033 68_[+2]_4 chrV:11850959-11851039 0.00033 21_[+2]_51 chrIII:6697196-6697276 0.00033 28_[+2]_44 chrX:15215461-15215541 0.00033 49_[+2]_23 chrX:15555061-15555141 0.00036 33_[+2]_39 chrII:7955686-7955766 0.00036 22_[+2]_50 chrIV:9774546-9774626 0.00042 5_[+2]_67 chrIII:5689922-5690002 0.00042 43_[+2]_29 chrIV:4584862-4584942 0.00042 50_[+2]_22 chrX:3883371-3883451 0.00042 30_[+2]_42 chrX:12532572-12532652 0.00047 71_[+2]_1 chrX:12513607-12513687 0.00049 52_[+2]_20 chrIII:8220205-8220285 0.00049 66_[+2]_6 chrII:10829173-10829253 0.00052 25_[+2]_47 chrX:12569923-12570003 0.00052 35_[+2]_37 chrII:2198739-2198819 0.00052 69_[+2]_3 chrII:12691024-12691104 0.0006 56_[+2]_16 chrIV:10189299-10189379 0.0006 72_[+2] chrV:9128749-9128829 0.00075 36_[+2]_36 chrX:12175252-12175332 0.00075 53_[+2]_19 chrX:11668219-11668299 0.00075 35_[+2]_37 chrIV:6541572-6541652 0.00075 59_[+2]_13 chrX:15008860-15008940 0.00075 31_[+2]_41 chrI:878285-878365 0.00075 35_[+2]_37 chrIII:5824715-5824795 0.00075 48_[+2]_24 chrII:14052106-14052186 0.00089 43_[+2]_29 chrX:16778576-16778656 0.00089 35_[+2]_37 chrIII:42279-42359 0.00089 66_[+2]_6 chrX:3520107-3520187 0.00093 12_[+2]_60 chrIV:636540-636620 0.00093 [+2]_72 chrX:2729349-2729429 0.001 23_[+2]_49 chrIII:3220468-3220548 0.0011 18_[+2]_54 chrIII:4483148-4483228 0.0011 32_[+2]_40 chrI:14802468-14802548 0.0012 66_[+2]_6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAARAAGA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GAARAAGA width=8 seqs=81 chrIV:16658880-16658960 ( 11) GAAAAAGA 1 chrIII:30559-30639 ( 27) GAAAAAGA 1 chrI:3101010-3101090 ( 17) GAAAAAGA 1 chrV:14487506-14487586 ( 16) GAAAAAGA 1 chrIII:10579021-10579101 ( 57) GAAAAAGA 1 chrV:17784948-17785028 ( 6) GAAAAAGA 1 chrI:8581625-8581705 ( 64) GAAAAAGA 1 chrX:4859789-4859869 ( 66) GAAAAAGA 1 chrX:15355771-15355851 ( 70) GAAAAAGA 1 chrX:3152428-3152508 ( 52) GAAAAAGA 1 chrI:6394395-6394475 ( 68) GAAAAAGA 1 chrIII:8211703-8211783 ( 56) GAAAAAGA 1 chrX:3517311-3517391 ( 4) GAAAAAGA 1 chrIII:3560356-3560436 ( 19) GAAGAAGA 1 chrIII:1743670-1743750 ( 10) GAAGAAGA 1 chrI:4484992-4485072 ( 8) GAAGAAGA 1 chrI:2960667-2960747 ( 19) GAAGAAGA 1 chrI:10756554-10756634 ( 62) GAAGAAGA 1 chrV:1303532-1303612 ( 56) GAAGAAGA 1 chrX:10838786-10838866 ( 17) GAAGAAGA 1 chrIII:6649797-6649877 ( 37) GAAGAAGA 1 chrX:2830410-2830490 ( 23) GAAAGAGA 1 chrIII:4127471-4127551 ( 7) GAAAGAGA 1 chrX:12100152-12100232 ( 30) GAAAGAGA 1 chrX:11403982-11404062 ( 51) GAAAAGGA 1 chrX:13364958-13365038 ( 4) GAAGGAGA 1 chrIV:10507711-10507791 ( 32) GAAAAGGA 1 chrIV:3821643-3821723 ( 53) GAAAAGGA 1 chrIII:8217412-8217492 ( 23) GAAAAGGA 1 chrV:12030761-12030841 ( 14) AAAAAAGA 1 chrIV:15814226-15814306 ( 9) AAAAAAGA 1 chrI:9494660-9494740 ( 7) AAAAAAGA 1 chrV:13401497-13401577 ( 49) GAAGAGGA 1 chrIII:5757794-5757874 ( 42) AAAAAAGA 1 chrV:5089891-5089971 ( 15) AAAAAAGA 1 chrV:13070333-13070413 ( 32) AAAGAAGA 1 chrII:4505104-4505184 ( 16) AAAGAAGA 1 chrIII:9311800-9311880 ( 73) AAAGAAGA 1 chrIV:6954683-6954763 ( 38) GAAAAAGT 1 chrIII:9971501-9971581 ( 8) GAAACAGA 1 chrIII:5998827-5998907 ( 55) GAAAAAGT 1 chrX:8591987-8592067 ( 1) GAAAAAGT 1 chrX:3703774-3703854 ( 45) GAAAAAAA 1 chrI:9090545-9090625 ( 38) GAAAAAAA 1 chrV:16754044-16754124 ( 41) GAAGAAGT 1 chrX:7012004-7012084 ( 31) GAAGAAGT 1 chrIV:2859756-2859836 ( 6) GAAAAAAA 1 chrIII:12780699-12780779 ( 69) GAAAAAAA 1 chrV:11850959-11851039 ( 22) GAAAAAAA 1 chrIII:6697196-6697276 ( 29) GAAGCAGA 1 chrX:15215461-15215541 ( 50) GAAAAAAA 1 chrX:15555061-15555141 ( 34) GAAGAAAA 1 chrII:7955686-7955766 ( 23) GAAGAAAA 1 chrIV:9774546-9774626 ( 6) GAAGGGGA 1 chrIII:5689922-5690002 ( 44) AAAAGAGA 1 chrIV:4584862-4584942 ( 51) AAAAGAGA 1 chrX:3883371-3883451 ( 31) AAAAGAGA 1 chrX:12532572-12532652 ( 72) AAAAAGGA 1 chrX:12513607-12513687 ( 53) AAAGAGGA 1 chrIII:8220205-8220285 ( 67) AAAGAGGA 1 chrII:10829173-10829253 ( 26) GAAAGAGT 1 chrX:12569923-12570003 ( 36) GAAAGAGT 1 chrII:2198739-2198819 ( 70) GAAAGAGT 1 chrII:12691024-12691104 ( 57) GAAGGAGT 1 chrIV:10189299-10189379 ( 73) GAAAAGGT 1 chrV:9128749-9128829 ( 37) GAAGCGGA 1 chrX:12175252-12175332 ( 54) AAAACAGA 1 chrX:11668219-11668299 ( 36) GAAGCGGA 1 chrIV:6541572-6541652 ( 60) AAAAAAGT 1 chrX:15008860-15008940 ( 32) GAAGGAAA 1 chrI:878285-878365 ( 36) GAAAAGAA 1 chrIII:5824715-5824795 ( 49) GAAAAGAA 1 chrII:14052106-14052186 ( 44) AAAGCAGA 1 chrX:16778576-16778656 ( 36) AAAGCAGA 1 chrIII:42279-42359 ( 67) AAAAAAAA 1 chrX:3520107-3520187 ( 13) AAAGAAAA 1 chrIV:636540-636620 ( 1) AAAGAAAA 1 chrX:2729349-2729429 ( 24) GAAACAAA 1 chrIII:3220468-3220548 ( 19) GAAGAAAT 1 chrIII:4483148-4483228 ( 33) GAAGAAAT 1 chrI:14802468-14802548 ( 67) GAAAACGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAARAAGA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 9.29533 E= 2.0e-009 -21 -1298 186 -1298 173 -1298 -1298 -1298 173 -1298 -1298 -1298 104 -1298 90 -1298 130 -99 -35 -1298 144 -399 -24 -1298 -52 -1298 195 -1298 148 -1298 -1298 -90 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAARAAGA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 81 E= 2.0e-009 0.259259 0.000000 0.740741 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.617284 0.000000 0.382716 0.000000 0.740741 0.098765 0.160494 0.000000 0.814815 0.012346 0.172840 0.000000 0.209877 0.000000 0.790123 0.000000 0.839506 0.000000 0.000000 0.160494 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAARAAGA MEME-2 regular expression -------------------------------------------------------------------------------- [GA]AA[AG]AA[GA]A -------------------------------------------------------------------------------- Time 14.99 secs. ******************************************************************************** ******************************************************************************** MOTIF CTTTTTCT MEME-3 width = 8 sites = 64 llr = 468 E-value = 4.0e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTTTTTCT MEME-3 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C 9:331172 probability G :::::::: matrix T 1a779938 bits 2.4 2.1 1.9 * 1.6 ** Relative 1.4 ** ** Entropy 1.2 ** **** (10.6 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CTTTTTCT consensus CC TC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTTTTCT MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIV:6514876-6514956 47 2.74e-05 TGAGTCTTTC CTTTTTCT CCAAGCATTT chrII:14460546-14460626 12 2.74e-05 AGCATGAAAG CTTTTTCT GGAATAATAA chrIII:30559-30639 64 2.74e-05 ATTTTTTTTT CTTTTTCT TAGAAAAAT chrIV:11790736-11790816 66 2.74e-05 CTCTTACTTT CTTTTTCT CGAGTCG chrIV:6834799-6834879 66 2.74e-05 CGGACATTTC CTTTTTCT TCAACCC chrIV:6541572-6541652 5 2.74e-05 CACT CTTTTTCT TTCCCTTCCT chrIV:925931-926011 32 2.74e-05 TCAATAATTA CTTTTTCT ACCCGCTCGT chrIV:6956865-6956945 9 6.34e-05 TTCTTCTT CTTCTTCT CATCACCAAA chrV:16754044-16754124 6 6.34e-05 TTGCT CTTCTTCT TCGTCTTAAC chrIV:659693-659773 52 6.34e-05 ttttcttctt cttcttct tccatcaatt chrIV:6393559-6393639 8 6.34e-05 CTCTATT CTTCTTCT GTTTTTGCTC chrX:3152428-3152508 4 6.34e-05 TTG CTCTTTCT GCTCAACGAC chrIV:5337754-5337834 10 6.34e-05 GAGCGtctt cttcttct tttcccattc chrIII:8218311-8218391 48 6.34e-05 GACATGACAG CTTCTTCT TCCTCGTTTT chrV:6661796-6661876 62 7.52e-05 TTATTGTACT CTCCTTCT TTTCATCTCA chrX:6954809-6954889 7 7.52e-05 AGGCTT CTCCTTCT TACGCGTGAT chrX:6740689-6740769 72 9.32e-05 TTGGACTTCT CTTTTTCC C chrIII:10608314-10608394 32 9.32e-05 ATTCTTTTTC CTTTTTCC ATTTCTCGTT chrIII:6658148-6658228 45 9.32e-05 AGGATGACAG CTTTTTCC ACAGCCACAT chrI:14802468-14802548 31 1.17e-04 TGTGTATCCC CTCTTTCC AGTTTTGAAT chrV:8663103-8663183 64 1.17e-04 TCTGTTTCTG CTTCTTCC TTCCGTCCG chrII:10829173-10829253 52 1.17e-04 CCTGTCTTCT CTCTTTCC TCTTTTGATT chrIII:5626063-5626143 26 1.17e-04 TGAGTGACAT CTTCTTCC TCTTCATCCG chrI:3650747-3650827 17 1.59e-04 CCCCGTCCCG CTTTTTTT GTCATCCTTC chrX:3669990-3670070 68 1.59e-04 ATTCATATAA CTTTTTTT TTTCA chrX:4633168-4633248 69 1.59e-04 CATGGAATCA CTTTTTTT GCAG chrII:12382783-12382863 46 1.77e-04 TTGTGCTCGG CTTTCTCT GCGTCTCGCC chrIII:7264013-7264093 15 1.77e-04 CCCTTTCCAT CTTTCTCT CTTCTCCATC chrX:16737593-16737673 48 1.77e-04 CTAACCTTTT CTTTCTCT CTCTCGTTTC chrX:16485995-16486075 34 1.84e-04 CATTTTCTCC CTCCTTCC CCTACCCACT chrIV:14837059-14837139 72 2.57e-04 CGTCTCTGTG CTCTTTTT G chrII:8834708-8834788 49 2.57e-04 TTCTATGTTG CTCTTTTT TCGACTCAGC chrX:9691950-9692030 35 2.57e-04 GTTCTCTTTT CTTCTTTT CACTGCACTT chrII:4134822-4134902 31 2.57e-04 CATCCGCTTC CTTTTCCT GTATCTGATT chrV:14487506-14487586 70 2.57e-04 AGGACCTTCC CTTTTCCT GAC chrV:18069404-18069484 51 2.57e-04 GTCTGCATCT CTTCTTTT ACACACTATT chrX:17317143-17317223 45 2.57e-04 TGCATTTCAT CTCTTTTT TCTTTTCTAG chrI:2414204-2414284 37 2.57e-04 CCATTTGTCT CTCTTTTT TCATCGTTCT chrV:13070333-13070413 63 2.57e-04 TTCACTGTAT CTCTTTTT TGCTCGTGCT chrI:8045379-8045459 72 2.57e-04 CTTATTCATG CTCTTTTT T chrIII:8229663-8229743 46 2.57e-04 CACTCTCTTG CTTTTCCT ACTTTTTTCA chrX:10763285-10763365 58 2.57e-04 CGGGCTTTTC CTTTTCCT TTAAATATTA chrI:2676812-2676892 30 2.57e-04 TTACGAATGG CTCTTTTT TGAGTGTTTT chrX:3520107-3520187 46 2.81e-04 GCTTTTCTCC CTCTCTCT CTCGTTTTGT chrIII:6649797-6649877 17 2.81e-04 TCATTCTTCC CTTCCTCT TTTCACTTCA chrX:2268951-2269031 43 2.81e-04 TGTGTACTCT CTCTCTCT CACGCCTAGA chrI:5719085-5719165 60 3.22e-04 CTCTTTTCTG CTCCTTTT GAATTATTCA chrII:7968266-7968346 21 3.30e-04 GTCTTCTTGT CTCCCTCT ATCCATATCT chrI:7369070-7369150 18 3.65e-04 GTATCCTCTG CTTTTTTC TAAAATTTTG chrIV:4584862-4584942 35 3.65e-04 CCAGTATTCA CTCCTCCT AGTCCACCAA chrX:2266493-2266573 32 3.65e-04 TACGTAGTGA CTTTTTTC ATGAATATAT chrI:2415609-2415689 48 4.19e-04 TTGTTGTGCA TTTTTTCT TCTCAGAAGC chrX:8354544-8354624 9 4.19e-04 ATTGTTCA TTTTTTCT TCCCCATTCA chrX:2645476-2645556 62 4.19e-04 CCTCGAAGTT TTTTTTCT CTAGCAATAT chrIII:29778-29858 57 4.19e-04 GTTATTCTAT TTTTTTCT TGTTATATAT chrIII:3216031-3216111 26 4.19e-04 GATGTACCCG TTTTTTCT CAGAATTCCA chrV:8912319-8912399 65 4.19e-04 AAGAATCCGT TTTTTTCT TGCTACAA chrI:4484992-4485072 39 4.67e-04 GAAGCCTTCT CTTCTTTC CTTAATGGAC chrV:9107065-9107145 14 4.67e-04 TCTCGGAATT CTCTTTTC ATTGAGATGA chrX:14838472-14838552 73 5.65e-04 ACGATCAGAT TTCTTTCT chrX:4319150-4319230 50 5.92e-04 CACCGTAGTT CTTCTCCC TTCAAGGACA chrIII:6139487-6139567 2 5.92e-04 T CTCTTCCC TACTGGCAAA chrIII:3140759-3140839 24 6.90e-04 AGCTGATGAT CTTCCTTT TTCATTCATT chrV:12530351-12530431 23 6.90e-04 CCGTGCCTGA CTTCCTTT TGAAGGACGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTTTTCT MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIV:6514876-6514956 2.7e-05 46_[+3]_26 chrII:14460546-14460626 2.7e-05 11_[+3]_61 chrIII:30559-30639 2.7e-05 63_[+3]_9 chrIV:11790736-11790816 2.7e-05 65_[+3]_7 chrIV:6834799-6834879 2.7e-05 65_[+3]_7 chrIV:6541572-6541652 2.7e-05 4_[+3]_68 chrIV:925931-926011 2.7e-05 31_[+3]_41 chrIV:6956865-6956945 6.3e-05 8_[+3]_64 chrV:16754044-16754124 6.3e-05 5_[+3]_67 chrIV:659693-659773 6.3e-05 51_[+3]_21 chrIV:6393559-6393639 6.3e-05 7_[+3]_65 chrX:3152428-3152508 6.3e-05 3_[+3]_69 chrIV:5337754-5337834 6.3e-05 9_[+3]_63 chrIII:8218311-8218391 6.3e-05 47_[+3]_25 chrV:6661796-6661876 7.5e-05 61_[+3]_11 chrX:6954809-6954889 7.5e-05 6_[+3]_66 chrX:6740689-6740769 9.3e-05 71_[+3]_1 chrIII:10608314-10608394 9.3e-05 31_[+3]_41 chrIII:6658148-6658228 9.3e-05 44_[+3]_28 chrI:14802468-14802548 0.00012 30_[+3]_42 chrV:8663103-8663183 0.00012 63_[+3]_9 chrII:10829173-10829253 0.00012 51_[+3]_21 chrIII:5626063-5626143 0.00012 25_[+3]_47 chrI:3650747-3650827 0.00016 16_[+3]_56 chrX:3669990-3670070 0.00016 67_[+3]_5 chrX:4633168-4633248 0.00016 68_[+3]_4 chrII:12382783-12382863 0.00018 45_[+3]_27 chrIII:7264013-7264093 0.00018 14_[+3]_58 chrX:16737593-16737673 0.00018 47_[+3]_25 chrX:16485995-16486075 0.00018 33_[+3]_39 chrIV:14837059-14837139 0.00026 71_[+3]_1 chrII:8834708-8834788 0.00026 48_[+3]_24 chrX:9691950-9692030 0.00026 34_[+3]_38 chrII:4134822-4134902 0.00026 30_[+3]_42 chrV:14487506-14487586 0.00026 69_[+3]_3 chrV:18069404-18069484 0.00026 50_[+3]_22 chrX:17317143-17317223 0.00026 44_[+3]_28 chrI:2414204-2414284 0.00026 36_[+3]_36 chrV:13070333-13070413 0.00026 62_[+3]_10 chrI:8045379-8045459 0.00026 71_[+3]_1 chrIII:8229663-8229743 0.00026 45_[+3]_27 chrX:10763285-10763365 0.00026 57_[+3]_15 chrI:2676812-2676892 0.00026 29_[+3]_43 chrX:3520107-3520187 0.00028 45_[+3]_27 chrIII:6649797-6649877 0.00028 16_[+3]_56 chrX:2268951-2269031 0.00028 42_[+3]_30 chrI:5719085-5719165 0.00032 59_[+3]_13 chrII:7968266-7968346 0.00033 20_[+3]_52 chrI:7369070-7369150 0.00037 17_[+3]_55 chrIV:4584862-4584942 0.00037 34_[+3]_38 chrX:2266493-2266573 0.00037 31_[+3]_41 chrI:2415609-2415689 0.00042 47_[+3]_25 chrX:8354544-8354624 0.00042 8_[+3]_64 chrX:2645476-2645556 0.00042 61_[+3]_11 chrIII:29778-29858 0.00042 56_[+3]_16 chrIII:3216031-3216111 0.00042 25_[+3]_47 chrV:8912319-8912399 0.00042 64_[+3]_8 chrI:4484992-4485072 0.00047 38_[+3]_34 chrV:9107065-9107145 0.00047 13_[+3]_59 chrX:14838472-14838552 0.00056 72_[+3] chrX:4319150-4319230 0.00059 49_[+3]_23 chrIII:6139487-6139567 0.00059 1_[+3]_71 chrIII:3140759-3140839 0.00069 23_[+3]_49 chrV:12530351-12530431 0.00069 22_[+3]_50 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTTTTCT MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CTTTTTCT width=8 seqs=64 chrIV:6514876-6514956 ( 47) CTTTTTCT 1 chrII:14460546-14460626 ( 12) CTTTTTCT 1 chrIII:30559-30639 ( 64) CTTTTTCT 1 chrIV:11790736-11790816 ( 66) CTTTTTCT 1 chrIV:6834799-6834879 ( 66) CTTTTTCT 1 chrIV:6541572-6541652 ( 5) CTTTTTCT 1 chrIV:925931-926011 ( 32) CTTTTTCT 1 chrIV:6956865-6956945 ( 9) CTTCTTCT 1 chrV:16754044-16754124 ( 6) CTTCTTCT 1 chrIV:659693-659773 ( 52) CTTCTTCT 1 chrIV:6393559-6393639 ( 8) CTTCTTCT 1 chrX:3152428-3152508 ( 4) CTCTTTCT 1 chrIV:5337754-5337834 ( 10) CTTCTTCT 1 chrIII:8218311-8218391 ( 48) CTTCTTCT 1 chrV:6661796-6661876 ( 62) CTCCTTCT 1 chrX:6954809-6954889 ( 7) CTCCTTCT 1 chrX:6740689-6740769 ( 72) CTTTTTCC 1 chrIII:10608314-10608394 ( 32) CTTTTTCC 1 chrIII:6658148-6658228 ( 45) CTTTTTCC 1 chrI:14802468-14802548 ( 31) CTCTTTCC 1 chrV:8663103-8663183 ( 64) CTTCTTCC 1 chrII:10829173-10829253 ( 52) CTCTTTCC 1 chrIII:5626063-5626143 ( 26) CTTCTTCC 1 chrI:3650747-3650827 ( 17) CTTTTTTT 1 chrX:3669990-3670070 ( 68) CTTTTTTT 1 chrX:4633168-4633248 ( 69) CTTTTTTT 1 chrII:12382783-12382863 ( 46) CTTTCTCT 1 chrIII:7264013-7264093 ( 15) CTTTCTCT 1 chrX:16737593-16737673 ( 48) CTTTCTCT 1 chrX:16485995-16486075 ( 34) CTCCTTCC 1 chrIV:14837059-14837139 ( 72) CTCTTTTT 1 chrII:8834708-8834788 ( 49) CTCTTTTT 1 chrX:9691950-9692030 ( 35) CTTCTTTT 1 chrII:4134822-4134902 ( 31) CTTTTCCT 1 chrV:14487506-14487586 ( 70) CTTTTCCT 1 chrV:18069404-18069484 ( 51) CTTCTTTT 1 chrX:17317143-17317223 ( 45) CTCTTTTT 1 chrI:2414204-2414284 ( 37) CTCTTTTT 1 chrV:13070333-13070413 ( 63) CTCTTTTT 1 chrI:8045379-8045459 ( 72) CTCTTTTT 1 chrIII:8229663-8229743 ( 46) CTTTTCCT 1 chrX:10763285-10763365 ( 58) CTTTTCCT 1 chrI:2676812-2676892 ( 30) CTCTTTTT 1 chrX:3520107-3520187 ( 46) CTCTCTCT 1 chrIII:6649797-6649877 ( 17) CTTCCTCT 1 chrX:2268951-2269031 ( 43) CTCTCTCT 1 chrI:5719085-5719165 ( 60) CTCCTTTT 1 chrII:7968266-7968346 ( 21) CTCCCTCT 1 chrI:7369070-7369150 ( 18) CTTTTTTC 1 chrIV:4584862-4584942 ( 35) CTCCTCCT 1 chrX:2266493-2266573 ( 32) CTTTTTTC 1 chrI:2415609-2415689 ( 48) TTTTTTCT 1 chrX:8354544-8354624 ( 9) TTTTTTCT 1 chrX:2645476-2645556 ( 62) TTTTTTCT 1 chrIII:29778-29858 ( 57) TTTTTTCT 1 chrIII:3216031-3216111 ( 26) TTTTTTCT 1 chrV:8912319-8912399 ( 65) TTTTTTCT 1 chrI:4484992-4485072 ( 39) CTTCTTTC 1 chrV:9107065-9107145 ( 14) CTCTTTTC 1 chrX:14838472-14838552 ( 73) TTCTTTCT 1 chrX:4319150-4319230 ( 50) CTTCTCCC 1 chrIII:6139487-6139567 ( 2) CTCTTCCC 1 chrIII:3140759-3140839 ( 24) CTTCCTTT 1 chrV:12530351-12530431 ( 23) CTTCCTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTTTTCT MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 9.89106 E= 4.0e-004 -1264 218 -1264 -145 -1264 -1264 -1264 174 -1264 74 -1264 117 -1264 74 -1264 117 -1264 -48 -1264 152 -1264 -84 -1264 158 -1264 184 -1264 -1 -1264 16 -1264 139 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTTTTCT MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 64 E= 4.0e-004 0.000000 0.890625 0.000000 0.109375 0.000000 0.000000 0.000000 1.000000 0.000000 0.328125 0.000000 0.671875 0.000000 0.328125 0.000000 0.671875 0.000000 0.140625 0.000000 0.859375 0.000000 0.109375 0.000000 0.890625 0.000000 0.703125 0.000000 0.296875 0.000000 0.218750 0.000000 0.781250 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTTTTCT MEME-3 regular expression -------------------------------------------------------------------------------- CT[TC][TC]TT[CT][TC] -------------------------------------------------------------------------------- Time 18.53 secs. ******************************************************************************** ******************************************************************************** MOTIF GCGCGCGC MEME-4 width = 8 sites = 14 llr = 136 E-value = 1.8e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCGCGCGC MEME-4 Description -------------------------------------------------------------------------------- Simplified A :1::11:: pos.-specific C 291919:a probability G 6:917:a: matrix T 2::::::: bits 2.4 ** 2.1 ** 1.9 ** *** 1.6 *** *** Relative 1.4 *** *** Entropy 1.2 ******* (14.0 bits) 0.9 ******* 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GCGCGCGC consensus C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCGCGC MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrII:14036902-14036982 20 2.61e-06 TGTGAGGGGC GCGCGCGC CTCAAATGTG chrX:15668842-15668922 46 2.61e-06 ATGATCCATC GCGCGCGC GATGCTTTCA chrIV:659693-659773 24 5.10e-06 CTTATATTCT CCGCGCGC GTGCGCCCTt chrIV:10340771-10340851 37 8.90e-06 ACGCCGGAGC TCGCGCGC TTCAAGCACA chrII:4134822-4134902 51 8.90e-06 ATCTGATTCG TCGCGCGC TTCCCGTCCG chrX:5122850-5122930 40 1.14e-05 GTACGCGAAA GCGCCCGC AGTGGATTCT chrIV:16658880-16658960 56 1.79e-05 CGAGGTATGA GCGCACGC AGGCAGTGAG chrIII:10282659-10282739 33 1.79e-05 GAGATGGGTC GCGCACGC GAATGTGATG chrX:12534635-12534715 32 2.03e-05 TGGGCTAGGT CCGCCCGC AAGGTCATTC chrIII:4483148-4483228 13 2.28e-05 AAAGAGAGAT GCCCGCGC TATCTGGGAT chrI:2415609-2415689 27 2.54e-05 aCTGGAAATT CCGGGCGC CTCTTGTTGT chrI:8581625-8581705 35 4.07e-05 CTGGAAAAAT GCGCGAGC ACGACTAATT chrIII:29778-29858 30 4.07e-05 CTCGTCCCCC GAGCGCGC AGAGTTCTTG chrIII:6139487-6139567 41 4.47e-05 TTATTCATGT TCGGGCGC AGCGGTGTAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCGCGC MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrII:14036902-14036982 2.6e-06 19_[+4]_53 chrX:15668842-15668922 2.6e-06 45_[+4]_27 chrIV:659693-659773 5.1e-06 23_[+4]_49 chrIV:10340771-10340851 8.9e-06 36_[+4]_36 chrII:4134822-4134902 8.9e-06 50_[+4]_22 chrX:5122850-5122930 1.1e-05 39_[+4]_33 chrIV:16658880-16658960 1.8e-05 55_[+4]_17 chrIII:10282659-10282739 1.8e-05 32_[+4]_40 chrX:12534635-12534715 2e-05 31_[+4]_41 chrIII:4483148-4483228 2.3e-05 12_[+4]_60 chrI:2415609-2415689 2.5e-05 26_[+4]_46 chrI:8581625-8581705 4.1e-05 34_[+4]_38 chrIII:29778-29858 4.1e-05 29_[+4]_43 chrIII:6139487-6139567 4.5e-05 40_[+4]_32 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCGCGC MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCGCGCGC width=8 seqs=14 chrII:14036902-14036982 ( 20) GCGCGCGC 1 chrX:15668842-15668922 ( 46) GCGCGCGC 1 chrIV:659693-659773 ( 24) CCGCGCGC 1 chrIV:10340771-10340851 ( 37) TCGCGCGC 1 chrII:4134822-4134902 ( 51) TCGCGCGC 1 chrX:5122850-5122930 ( 40) GCGCCCGC 1 chrIV:16658880-16658960 ( 56) GCGCACGC 1 chrIII:10282659-10282739 ( 33) GCGCACGC 1 chrX:12534635-12534715 ( 32) CCGCCCGC 1 chrIII:4483148-4483228 ( 13) GCCCGCGC 1 chrI:2415609-2415689 ( 27) CCGGGCGC 1 chrI:8581625-8581705 ( 35) GCGCGAGC 1 chrIII:29778-29858 ( 30) GAGCGCGC 1 chrIII:6139487-6139567 ( 41) TCGGGCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCGCGC MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.9532 E= 1.8e+002 -1045 13 148 -48 -207 224 -1045 -1045 -1045 -145 218 -1045 -1045 213 -52 -1045 -107 -46 180 -1045 -207 224 -1045 -1045 -1045 -1045 229 -1045 -1045 235 -1045 -1045 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCGCGC MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 14 E= 1.8e+002 0.000000 0.214286 0.571429 0.214286 0.071429 0.928571 0.000000 0.000000 0.000000 0.071429 0.928571 0.000000 0.000000 0.857143 0.142857 0.000000 0.142857 0.142857 0.714286 0.000000 0.071429 0.928571 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGCGCGC MEME-4 regular expression -------------------------------------------------------------------------------- [GCT]CGCGCGC -------------------------------------------------------------------------------- Time 21.90 secs. ******************************************************************************** ******************************************************************************** MOTIF TGCGTCTC MEME-5 width = 8 sites = 5 llr = 58 E-value = 1.9e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGCGTCTC MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C ::a::a:a probability G :a:a:::: matrix T a:::a:a: bits 2.4 *** * * 2.1 *** * * 1.9 *** * * 1.6 ******** Relative 1.4 ******** Entropy 1.2 ******** (16.9 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TGCGTCTC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCGTCTC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrIII:7193379-7193459 36 8.46e-06 GTCATATGTC TGCGTCTC TCTGTCTATA chrV:7762594-7762674 23 8.46e-06 GCGATCACGC TGCGTCTC TCGATTCCAT chrIII:3220468-3220548 31 8.46e-06 AGAAATCCTC TGCGTCTC TCGCCTCACC chrI:14276671-14276751 60 8.46e-06 TTTTGTACTC TGCGTCTC ACCTTTTTGA chrI:4404692-4404772 55 8.46e-06 TAACAATGTC TGCGTCTC TCAGAGTTAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCGTCTC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrIII:7193379-7193459 8.5e-06 35_[+5]_37 chrV:7762594-7762674 8.5e-06 22_[+5]_50 chrIII:3220468-3220548 8.5e-06 30_[+5]_42 chrI:14276671-14276751 8.5e-06 59_[+5]_13 chrI:4404692-4404772 8.5e-06 54_[+5]_18 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCGTCTC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGCGTCTC width=8 seqs=5 chrIII:7193379-7193459 ( 36) TGCGTCTC 1 chrV:7762594-7762674 ( 23) TGCGTCTC 1 chrIII:3220468-3220548 ( 31) TGCGTCTC 1 chrI:14276671-14276751 ( 60) TGCGTCTC 1 chrI:4404692-4404772 ( 55) TGCGTCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCGTCTC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 11.2675 E= 1.9e+003 -897 -897 -897 174 -897 -897 229 -897 -897 235 -897 -897 -897 -897 229 -897 -897 -897 -897 174 -897 235 -897 -897 -897 -897 -897 174 -897 235 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCGTCTC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 1.9e+003 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCGTCTC MEME-5 regular expression -------------------------------------------------------------------------------- TGCGTCTC -------------------------------------------------------------------------------- Time 25.27 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrV:8912319-8912399 1.42e-01 80 chrIV:10189299-10189379 3.01e-01 80 chrIII:6139487-6139567 7.38e-04 27_[+1(4.47e-05)]_5_[+4(4.47e-05)]_\ 32 chrX:12532572-12532652 2.02e-02 80 chrIII:3216031-3216111 5.63e-02 2_[+1(8.97e-05)]_70 chrII:14196108-14196188 9.83e-01 80 chrIII:8217412-8217492 1.55e-01 80 chrX:3517311-3517391 1.60e-01 3_[+2(3.13e-05)]_69 chrIV:636540-636620 4.79e-02 80 chrI:2676812-2676892 3.89e-01 80 chrX:17322618-17322698 5.39e-01 80 chrI:13007714-13007794 1.52e-02 80 chrI:4404692-4404772 3.83e-02 54_[+5(8.46e-06)]_18 chrIII:8219308-8219388 9.67e-01 80 chrIII:8211703-8211783 7.40e-04 55_[+2(3.13e-05)]_17 chrX:3883371-3883451 3.56e-01 80 chrX:12534635-12534715 2.52e-03 31_[+4(2.03e-05)]_41 chrX:6954809-6954889 1.99e-02 6_[+3(7.52e-05)]_66 chrII:2198739-2198819 8.13e-02 80 chrI:296308-296388 5.30e-01 80 chrX:3038303-3038383 7.57e-01 80 chrIII:8216378-8216458 2.38e-01 80 chrX:8591987-8592067 1.06e-01 80 chrX:2268951-2269031 6.99e-03 18_[+1(4.47e-05)]_54 chrIII:42279-42359 2.06e-01 80 chrX:2955782-2955862 4.38e-02 80 chrX:16778576-16778656 4.31e-01 80 chrX:2266493-2266573 2.23e-01 80 chrX:4633168-4633248 7.52e-03 14_[+1(4.47e-05)]_58 chrIII:10282659-10282739 1.05e-02 32_[+4(1.79e-05)]_40 chrX:10763285-10763365 6.86e-02 80 chrV:4229867-4229947 3.91e-01 80 chrIII:8218311-8218391 6.08e-02 47_[+3(6.34e-05)]_25 chrX:12198428-12198508 5.98e-02 80 chrIII:9311800-9311880 7.07e-02 80 chrIII:8220205-8220285 4.10e-01 80 chrIII:8215104-8215184 5.36e-02 80 chrX:12100152-12100232 1.72e-02 29_[+2(7.38e-05)]_43 chrX:15215461-15215541 1.41e-03 65_[+1(8.97e-05)]_7 chrIII:5626063-5626143 3.06e-02 80 chrI:8387099-8387179 8.01e-01 80 chrIII:6697196-6697276 2.98e-01 80 chrIII:4483148-4483228 1.63e-02 12_[+4(2.28e-05)]_60 chrI:7363660-7363740 8.22e-01 80 chrIV:7784947-7785027 9.05e-01 80 chrIII:5998827-5998907 7.52e-02 80 chrV:5089891-5089971 3.06e-01 80 chrI:7409772-7409852 4.08e-01 80 chrX:3669990-3670070 1.45e-01 80 chrIV:3821643-3821723 1.82e-01 80 chrII:7955686-7955766 3.05e-01 80 chrII:4505104-4505184 2.83e-02 32_[+1(4.47e-05)]_40 chrIV:925931-926011 2.92e-03 31_[+3(2.74e-05)]_41 chrIII:8229663-8229743 5.77e-02 80 chrV:11850959-11851039 3.58e-02 42_[+1(8.97e-05)]_30 chrX:9956623-9956703 1.32e-01 80 chrX:7776767-7776847 4.79e-01 80 chrII:10997445-10997525 8.71e-02 80 chrII:5305266-5305346 7.16e-01 80 chrX:737136-737216 6.27e-01 80 chrX:15555061-15555141 1.81e-01 80 chrX:4091686-4091766 1.83e-01 80 chrIV:647691-647771 6.63e-01 80 chrIII:5757794-5757874 1.05e-01 80 chrII:10746220-10746300 3.32e-02 11_[+1(8.97e-05)]_61 chrIV:5337754-5337834 1.93e-02 6_[+3(6.34e-05)]_17_[+3(7.52e-05)]_\ 41 chrI:14276671-14276751 6.16e-03 59_[+5(8.46e-06)]_13 chrIV:4052863-4052943 3.86e-01 80 chrX:12513607-12513687 3.11e-01 80 chrV:8767280-8767360 2.45e-01 80 chrX:14838472-14838552 3.75e-03 42_[+1(8.97e-05)]_30 chrI:8045379-8045459 2.39e-01 80 chrIV:10507711-10507791 2.29e-01 80 chrIII:6352609-6352689 7.66e-01 80 chrX:5027643-5027723 8.43e-01 80 chrX:13364958-13365038 9.48e-02 80 chrIII:5824715-5824795 2.29e-01 80 chrII:8618999-8619079 7.76e-01 80 chrV:13070333-13070413 1.02e-03 80 chrI:2414204-2414284 1.41e-01 80 chrIII:12613387-12613467 3.40e-01 80 chrX:9141400-9141480 3.13e-01 80 chrV:13401497-13401577 1.93e-02 19_[+1(8.97e-05)]_53 chrII:8951311-8951391 1.70e-01 80 chrX:12569923-12570003 5.65e-01 80 chrI:878285-878365 3.92e-02 80 chrI:11939036-11939116 3.41e-01 80 chrX:12960161-12960241 2.60e-01 80 chrX:2729349-2729429 3.97e-01 80 chrX:15668842-15668922 9.59e-03 45_[+4(2.61e-06)]_27 chrIII:5643538-5643618 4.27e-02 51_[+1(8.97e-05)]_21 chrIII:4127471-4127551 1.38e-01 6_[+2(7.38e-05)]_66 chrIV:14773576-14773656 4.10e-01 80 chrIII:29778-29858 3.79e-03 29_[+4(4.07e-05)]_43 chrIV:5292170-5292250 6.14e-02 62_[+1(4.47e-05)]_10 chrX:2645476-2645556 7.29e-02 80 chrIII:6649797-6649877 7.54e-03 36_[+2(5.25e-05)]_36 chrX:15008860-15008940 2.84e-01 80 chrX:10838786-10838866 1.55e-01 16_[+2(5.25e-05)]_56 chrIV:6836093-6836173 1.29e-01 80 chrX:2441301-2441381 7.42e-01 80 chrIII:6658148-6658228 1.01e-02 44_[+3(9.32e-05)]_15_[+1(4.47e-05)]_\ 5 chrX:8354544-8354624 4.40e-01 80 chrII:1808368-1808448 7.98e-01 80 chrX:6887927-6888007 4.88e-01 80 chrII:10829173-10829253 2.46e-02 80 chrIII:12780699-12780779 2.51e-01 80 chrI:6437560-6437640 1.16e-02 14_[+1(4.47e-05)]_58 chrI:6394395-6394475 1.54e-01 67_[+2(3.13e-05)]_5 chrII:9755627-9755707 4.75e-01 80 chrX:12512625-12512705 2.26e-01 80 chrIV:2859756-2859836 1.94e-01 80 chrV:8169304-8169384 3.80e-01 80 chrI:9494660-9494740 2.10e-01 80 chrII:13503829-13503909 2.54e-01 80 chrIII:10574787-10574867 6.97e-01 80 chrX:4229596-4229676 1.17e-01 80 chrV:1303532-1303612 1.43e-01 55_[+2(5.25e-05)]_17 chrX:12204497-12204577 6.93e-01 80 chrX:7233147-7233227 2.10e-02 20_[+1(4.47e-05)]_52 chrX:2084201-2084281 5.66e-01 80 chrIV:15814226-15814306 6.48e-02 80 chrIII:3220468-3220548 3.13e-03 30_[+5(8.46e-06)]_42 chrX:11646179-11646259 3.03e-02 63_[+1(4.47e-05)]_9 chrII:601458-601538 7.79e-01 80 chrIV:6541572-6541652 3.43e-03 4_[+3(2.74e-05)]_68 chrI:10756554-10756634 8.45e-02 61_[+2(5.25e-05)]_11 chrIV:7623992-7624072 1.08e-02 25_[+1(4.47e-05)]_47 chrIII:13042981-13043061 7.74e-02 57_[+5(6.80e-05)]_15 chrV:8663103-8663183 8.17e-02 80 chrI:3650747-3650827 6.19e-02 80 chrI:7398956-7399036 4.05e-02 61_[+1(4.47e-05)]_11 chrX:3152428-3152508 9.17e-04 3_[+3(6.34e-05)]_40_[+2(3.13e-05)]_\ 21 chrIII:9971501-9971581 2.66e-01 80 chrII:7968266-7968346 6.01e-02 80 chrV:3837558-3837638 1.09e-01 20_[+1(8.97e-05)]_52 chrI:4406176-4406256 8.24e-01 80 chrIV:6393559-6393639 6.91e-02 7_[+3(6.34e-05)]_65 chrIII:7357528-7357608 2.51e-01 80 chrI:7342571-7342651 3.26e-01 80 chrII:11382346-11382426 7.70e-01 80 chrIV:8583131-8583211 4.29e-01 80 chrX:7012004-7012084 2.76e-01 80 chrX:11607571-11607651 4.07e-01 80 chrIV:7224750-7224830 8.00e-01 80 chrX:16737593-16737673 2.72e-01 80 chrII:11306258-11306338 1.08e-01 80 chrX:15355771-15355851 9.76e-03 69_[+2(3.13e-05)]_3 chrIV:11450923-11451003 5.71e-01 80 chrV:12530351-12530431 3.18e-01 80 chrIII:7264013-7264093 7.60e-02 80 chrX:5031926-5032006 6.13e-01 80 chrX:3520107-3520187 9.66e-04 65_[+1(4.47e-05)]_7 chrI:14802468-14802548 7.58e-04 44_[+1(8.97e-05)]_28 chrI:5719085-5719165 2.20e-02 67_[+1(4.47e-05)]_5 chrII:12691024-12691104 7.45e-02 80 chrIV:2858885-2858965 2.34e-01 80 chrII:14036902-14036982 4.20e-03 17_[+4(2.61e-06)]_55 chrII:9121114-9121194 3.64e-01 80 chrX:17317143-17317223 1.26e-01 80 chrX:2830410-2830490 1.23e-01 22_[+2(7.38e-05)]_50 chrX:4859789-4859869 6.43e-02 65_[+2(3.13e-05)]_7 chrI:8581625-8581705 1.64e-03 34_[+4(4.07e-05)]_21_[+2(3.13e-05)]_\ 9 chrX:11668219-11668299 7.51e-02 14_[+1(8.97e-05)]_58 chrIV:659693-659773 1.31e-03 23_[+4(5.10e-06)]_14_[+3(6.34e-05)]_\ 27 chrV:9107065-9107145 1.73e-01 80 chrIV:4584862-4584942 1.17e-01 80 chrII:10284890-10284970 2.06e-01 80 chrX:16485995-16486075 3.04e-01 80 chrIV:6834799-6834879 5.69e-02 29_[+3(2.74e-05)]_28_[+3(2.74e-05)]_\ 7 chrIII:764577-764657 1.74e-02 80 chrIV:10461955-10462035 6.26e-01 80 chrV:17784948-17785028 1.02e-01 5_[+2(3.13e-05)]_67 chrV:7727072-7727152 7.53e-01 80 chrIV:11790736-11790816 4.38e-02 65_[+3(2.74e-05)]_7 chrV:12030761-12030841 9.82e-03 80 chrV:10516623-10516703 6.43e-01 80 chrV:7762594-7762674 8.10e-03 22_[+5(8.46e-06)]_50 chrIV:1978201-1978281 6.13e-01 80 chrII:6766669-6766749 1.99e-01 80 chrI:2960667-2960747 2.63e-01 18_[+2(5.25e-05)]_54 chrI:9385527-9385607 6.14e-02 80 chrIII:1797060-1797140 4.95e-02 80 chrIV:6954683-6954763 2.64e-02 80 chrX:12175252-12175332 1.87e-01 80 chrV:18069404-18069484 2.22e-02 80 chrI:7369070-7369150 1.40e-01 80 chrX:5122850-5122930 2.57e-03 16_[+1(8.97e-05)]_15_[+4(1.14e-05)]_\ 33 chrIII:10579021-10579101 1.80e-02 56_[+2(3.13e-05)]_16 chrV:6867426-6867506 3.79e-01 80 chrV:9128749-9128829 1.58e-01 80 chrIV:7660897-7660977 6.60e-01 80 chrIII:8395095-8395175 4.33e-01 80 chrV:14487506-14487586 3.31e-04 15_[+2(3.13e-05)]_57 chrII:4134822-4134902 6.91e-04 50_[+4(8.90e-06)]_22 chrIII:3140759-3140839 1.85e-02 80 chrII:14052106-14052186 1.08e-02 80 chrV:13029031-13029111 7.81e-01 80 chrV:16754044-16754124 7.87e-04 5_[+3(6.34e-05)]_67 chrX:17158396-17158476 2.28e-01 80 chrX:6249117-6249197 5.04e-02 46_[+1(8.97e-05)]_26 chrX:3901829-3901909 6.02e-02 80 chrIV:4482986-4483066 8.33e-01 80 chrIII:3559131-3559211 3.90e-02 80 chrI:3101010-3101090 1.13e-02 16_[+2(3.13e-05)]_56 chrI:4484992-4485072 7.06e-03 1_[+2(5.25e-05)]_71 chrIII:30559-30639 3.27e-03 26_[+2(3.13e-05)]_29_[+3(2.74e-05)]_\ 9 chrIII:7193379-7193459 1.98e-02 35_[+5(8.46e-06)]_37 chrII:2962650-2962730 4.93e-01 80 chrII:5042591-5042671 5.96e-01 80 chrX:4319150-4319230 3.14e-02 80 chrIII:1743670-1743750 5.12e-02 6_[+2(5.25e-05)]_66 chrX:9691950-9692030 2.35e-02 4_[+1(4.47e-05)]_68 chrI:7848975-7849055 7.54e-02 80 chrIV:7223266-7223346 2.43e-01 80 chrII:12382783-12382863 1.51e-03 52_[+5(8.46e-06)]_20 chrII:8834708-8834788 3.66e-02 80 chrII:4453629-4453709 2.16e-01 80 chrII:14460546-14460626 2.00e-03 11_[+3(2.74e-05)]_31_[+1(4.47e-05)]_\ 22 chrIV:6956865-6956945 4.69e-02 2_[+3(6.34e-05)]_70 chrIII:761350-761430 7.28e-01 80 chrIII:3560356-3560436 6.36e-02 18_[+2(5.25e-05)]_54 chrIV:10340771-10340851 1.67e-02 36_[+4(8.90e-06)]_36 chrIII:3622689-3622769 6.35e-01 80 chrV:1494297-1494377 9.48e-01 80 chrI:2415609-2415689 2.42e-04 26_[+4(2.54e-05)]_46 chrI:9454314-9454394 6.60e-01 80 chrX:8157255-8157335 2.96e-01 80 chrX:9673089-9673169 2.34e-01 80 chrIII:3943871-3943951 7.59e-01 80 chrIII:11673164-11673244 4.25e-01 80 chrII:7625352-7625432 1.00e-01 32_[+1(8.97e-05)]_40 chrIII:5689922-5690002 4.38e-01 80 chrIV:13272608-13272688 9.01e-01 80 chrIV:9774546-9774626 4.49e-02 67_[+1(4.47e-05)]_5 chrV:8418161-8418241 6.29e-01 80 chrX:11403982-11404062 2.19e-01 80 chrIII:5639992-5640072 4.27e-02 80 chrI:9090545-9090625 5.42e-01 80 chrIV:6514876-6514956 5.45e-02 46_[+3(2.74e-05)]_26 chrIII:10608314-10608394 1.14e-02 24_[+3(9.32e-05)]_48 chrII:6465835-6465915 2.68e-01 80 chrV:6661796-6661876 2.65e-02 61_[+3(7.52e-05)]_11 chrII:11032192-11032272 9.25e-01 80 chrII:7188556-7188636 1.02e-01 80 chrX:6740689-6740769 1.08e-01 71_[+3(9.32e-05)]_1 chrIV:16658880-16658960 1.72e-03 10_[+2(3.13e-05)]_37_[+4(1.79e-05)]_\ 17 chrX:3703774-3703854 4.32e-01 80 chrIV:11867963-11868043 4.49e-02 80 chrIV:14837059-14837139 1.39e-03 15_[+5(8.46e-06)]_57 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c27n07.farnam.hpc.yale.internal ********************************************************************************