******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.12.0 (Release date: Tue Jun 27 16:22:50 2017 -0700) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme-suite.org . This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://meme-suite.org . ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** DATAFILE= /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeK562eGFPComparisons/DDX20-Antibody.IDR0.05.filt.narrowPeak.summitPlusMinus250bp.MemeChipResultsDefaultMax/seqs-sampled ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr17:27602706-27602806 1.0000 100 chr15:43330539-43330639 1.0000 100 chr1:26126332-26126432 1.0000 100 chr11:64304550-64304650 1.0000 100 chrX:1072586-1072686 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chr11:74011434-74011534 1.0000 100 chr1:236524497-236524597 1.0000 100 chr2:200963493-200963593 1.0000 100 chr6:10519044-10519144 1.0000 100 chr7:92886007-92886107 1.0000 100 chr7:111562517-111562617 1.0000 100 chr17:44557029-44557129 1.0000 100 chr17_GL000205v2_random: 1.0000 100 chr6:31651687-31651787 1.0000 100 chr10:77874692-77874792 1.0000 100 chr6:35343413-35343513 1.0000 100 chr1:70354761-70354861 1.0000 100 chr1:25247144-25247244 1.0000 100 chr6:27519378-27519478 1.0000 100 chr1:37595383-37595483 1.0000 100 chr17:56985554-56985654 1.0000 100 chr1:225881705-225881805 1.0000 100 chr1:89895990-89896090 1.0000 100 chr1:198159121-198159221 1.0000 100 chr17:57379413-57379513 1.0000 100 chr11:94767936-94768036 1.0000 100 chr6:30720083-30720183 1.0000 100 chr2:202033401-202033501 1.0000 100 chr4:147708992-147709092 1.0000 100 chr1:28884871-28884971 1.0000 100 chr7:98131851-98131951 1.0000 100 chr18:37669996-37670096 1.0000 100 chr4:7042850-7042950 1.0000 100 chr15:67125146-67125246 1.0000 100 chr11:34603477-34603577 1.0000 100 chr9:126914486-126914586 1.0000 100 chr2:27663598-27663698 1.0000 100 chr1:167635251-167635351 1.0000 100 chr17:28598448-28598548 1.0000 100 chr8:141415749-141415849 1.0000 100 chr11:73598425-73598525 1.0000 100 chr17:19112065-19112165 1.0000 100 chr9:40939231-40939331 1.0000 100 chr16:21261444-21261544 1.0000 100 chr4:184339304-184339404 1.0000 100 chr5:154835041-154835141 1.0000 100 chr22:35299951-35300051 1.0000 100 chr1:116679456-116679556 1.0000 100 chr2:177242485-177242585 1.0000 100 chr1:21904952-21905052 1.0000 100 chr1:50873422-50873522 1.0000 100 chr1:179882000-179882100 1.0000 100 chr6:41460847-41460947 1.0000 100 chr1:31296645-31296745 1.0000 100 chr5:132526665-132526765 1.0000 100 chr11:118688309-11868840 1.0000 100 chr19:4815615-4815715 1.0000 100 chr1:112462835-112462935 1.0000 100 chr20:37178953-37179053 1.0000 100 chr16:85569373-85569473 1.0000 100 chr7:106986689-106986789 1.0000 100 chr2:98508293-98508393 1.0000 100 chr10:74827054-74827154 1.0000 100 chr14:100446668-10044676 1.0000 100 chr15:89893823-89893923 1.0000 100 chr14:20332950-20333050 1.0000 100 chr6:158704452-158704552 1.0000 100 chr19:50376097-50376197 1.0000 100 chr4:98801117-98801217 1.0000 100 chr13:95270982-95271082 1.0000 100 chr15:75198605-75198705 1.0000 100 chr11:60194025-60194125 1.0000 100 chr2:6893783-6893883 1.0000 100 chr19:19192102-19192202 1.0000 100 chr2:65432465-65432565 1.0000 100 chr15:78306299-78306399 1.0000 100 chr12:131860207-13186030 1.0000 100 chr6:143164458-143164558 1.0000 100 chr17:44288279-44288379 1.0000 100 chr17:38861369-38861469 1.0000 100 chr6:83974564-83974664 1.0000 100 chr1:248691384-248691484 1.0000 100 chr3:136752029-136752129 1.0000 100 chr6:43723735-43723835 1.0000 100 chr13:79405983-79406083 1.0000 100 chr19:35744816-35744916 1.0000 100 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeK562eGFPComparisons/DDX20-Antibody.IDR0.05.filt.narrowPeak.summitPlusMinus250bp.MemeChipResultsDefaultMax/seqs-sampled -oc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeK562eGFPComparisons/DDX20-Antibody.IDR0.05.filt.narrowPeak.summitPlusMinus250bp.MemeChipResultsDefaultMax/meme_out -mod zoops -nmotifs 3 -minw 5 -maxw 50 -bfile /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeK562eGFPComparisons/DDX20-Antibody.IDR0.05.filt.narrowPeak.summitPlusMinus250bp.MemeChipResultsDefaultMax/background -dna -revcomp -nostatus model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 5 maxw= 50 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 600 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 60000 N= 600 shuffle= -1 strands: + - sample: seed= 0 ctfrac= -1 maxwords= -1 Letter frequencies in dataset: A 0.240 C 0.260 G 0.260 T 0.240 Background letter frequencies (from /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeK562eGFPComparisons/DDX20-Antibody.IDR0.05.filt.narrowPeak.summitPlusMinus250bp.MemeChipResultsDefaultMax/background): A 0.243 C 0.257 G 0.257 T 0.243 ******************************************************************************** ******************************************************************************** MOTIF TCATGARTTTTCYRGGAAAGGGGYGGGVAWTT MEME-1 width = 32 sites = 14 llr = 400 E-value = 8.6e-057 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCATGARTTTTCYRGGAAAGGGGYGGGVAWTT MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::9119411:::15:19a92211:232295:: pos.-specific C :71:111::1194::::::::::4:::4:1:: probability G ::::7:61:::::4a91:1779918764:::: matrix T a3191::8999161:::::11:16::1:14aa bits 2.0 * * * ** 1.8 * * * ** 1.6 * * * * * ** * * ** 1.4 * * * **** ***** * * ** Relative 1.2 * ** * **** ***** ** * * ** Entropy 1.0 **** * ***** ***** ** ** * ** (41.2 bits) 0.8 **** ******** ************ * ** 0.6 *************************** **** 0.4 ******************************** 0.2 ******************************** 0.0 -------------------------------- Multilevel TCATGAGTTTTCTAGGAAAGGGGTGGGCAATT consensus T A CG AA CAAAG T sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCATGARTTTTCYRGGAAAGGGGYGGGVAWTT MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------------------------------- chr17:48825343-48825443 + 33 6.82e-19 ggtggataat tcatgagttttctaggaaaggggtgggaaatt cctggaaatg chr4:184339304-184339404 + 27 2.62e-18 ggtgacttat tcatgagttttctaggaaagaggtgggcaatt cctggaactg chr12:118582186-11858228 + 23 2.67e-17 agtggattat tcatgagttttctaggaaaggggcagggattt cctggaaatg chr4:122906769-122906869 - 28 2.67e-17 GTTGGCTTAT TCATGAGTTTTCCAGGAAAGGGGCAGGCAATT CCCGGAACTG chr4:147708992-147709092 - 33 2.76e-16 GGTGGATTAT TTATAAATTTTCCGGGAAAGGGGTGGGCAATT CCCAGAATTG chr16:26969845-26969945 - 65 2.76e-16 TTAT TCATGAGTTTTCTGGGAAAGGGTTGAGCAATT CCCAGAACTG chr12:107110022-10711012 - 43 2.76e-16 GGTGGATTAT TCATGAGTTTTCTGGGAAATGGGTGGACAATT CCCAGAACTG chr17:59167396-59167496 + 41 3.57e-16 ggtggattat tcatgagttttctggggaaagggtggggattt cccagaactg chr7:106534325-106534425 - 52 4.68e-13 AGTGAATTAG TCATCAGTTTTCCAGGGAAGGGACAAGGATTT CCCAGAACAG chrX:70988318-70988418 + 32 1.15e-12 gagtgggtta tttagaattttctaggaaagaggcgataactt ccaggttatt chr1:12657434-12657534 + 42 5.59e-12 ggcggaatat tcatgaaaattcctggaaaatggcggagtttt ctcagaactg chr20:63506961-63507061 + 33 1.39e-11 agtggaatat tcataaagatttctggaaaaaggtgaagattt ctaggaactg chr1:143867486-143867586 + 43 9.16e-11 gggtggatta ttattcctttccaggaaagggggggggcaatt ccaggaactg chr1:50873422-50873522 - 20 1.19e-10 GCACAGGTTT TTCAGAAATCCCTAGAAAAGGAGTGGTAACTT CTGAGTTGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCATGARTTTTCYRGGAAAGGGGYGGGVAWTT MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr17:48825343-48825443 6.8e-19 32_[+1]_36 chr4:184339304-184339404 2.6e-18 26_[+1]_42 chr12:118582186-11858228 2.7e-17 22_[+1]_46 chr4:122906769-122906869 2.7e-17 27_[-1]_41 chr4:147708992-147709092 2.8e-16 32_[-1]_36 chr16:26969845-26969945 2.8e-16 64_[-1]_4 chr12:107110022-10711012 2.8e-16 42_[-1]_26 chr17:59167396-59167496 3.6e-16 40_[+1]_28 chr7:106534325-106534425 4.7e-13 51_[-1]_17 chrX:70988318-70988418 1.1e-12 31_[+1]_37 chr1:12657434-12657534 5.6e-12 41_[+1]_27 chr20:63506961-63507061 1.4e-11 32_[+1]_36 chr1:143867486-143867586 9.2e-11 42_[+1]_26 chr1:50873422-50873522 1.2e-10 19_[-1]_49 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCATGARTTTTCYRGGAAAGGGGYGGGVAWTT MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TCATGARTTTTCYRGGAAAGGGGYGGGVAWTT width=32 seqs=14 chr17:48825343-48825443 ( 33) TCATGAGTTTTCTAGGAAAGGGGTGGGAAATT 1 chr4:184339304-184339404 ( 27) TCATGAGTTTTCTAGGAAAGAGGTGGGCAATT 1 chr12:118582186-11858228 ( 23) TCATGAGTTTTCTAGGAAAGGGGCAGGGATTT 1 chr4:122906769-122906869 ( 28) TCATGAGTTTTCCAGGAAAGGGGCAGGCAATT 1 chr4:147708992-147709092 ( 33) TTATAAATTTTCCGGGAAAGGGGTGGGCAATT 1 chr16:26969845-26969945 ( 65) TCATGAGTTTTCTGGGAAAGGGTTGAGCAATT 1 chr12:107110022-10711012 ( 43) TCATGAGTTTTCTGGGAAATGGGTGGACAATT 1 chr17:59167396-59167496 ( 41) TCATGAGTTTTCTGGGGAAAGGGTGGGGATTT 1 chr7:106534325-106534425 ( 52) TCATCAGTTTTCCAGGGAAGGGACAAGGATTT 1 chrX:70988318-70988418 ( 32) TTTAGAATTTTCTAGGAAAGAGGCGATAACTT 1 chr1:12657434-12657534 ( 42) TCATGAAAATTCCTGGAAAATGGCGGAGTTTT 1 chr20:63506961-63507061 ( 33) TCATAAAGATTTCTGGAAAAAGGTGAAGATTT 1 chr1:143867486-143867586 ( 43) TTATTCCTTTCCAGGAAAGGGGGGGGGCAATT 1 chr1:50873422-50873522 ( 20) TTCAGAAATCCCTAGAAAAGGAGTGGTAACTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCATGARTTTTCYRGGAAAGGGGYGGGVAWTT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 32 n= 41400 bayes= 10.5085 E= 8.6e-057 -1045 -1045 -1045 204 -1045 148 -1045 23 182 -184 -1045 -177 -77 -1045 -1045 182 -77 -184 148 -177 193 -184 -1045 -1045 55 -184 115 -1045 -77 -1045 -184 169 -77 -1045 -1045 182 -1045 -184 -1045 193 -1045 -84 -1045 182 -1045 185 -1045 -177 -177 48 -1045 123 104 -1045 48 -77 -1045 -1045 196 -1045 -77 -1045 174 -1045 182 -1045 -84 -1045 204 -1045 -1045 -1045 193 -1045 -184 -1045 -18 -1045 148 -177 -18 -1045 148 -177 -177 -1045 185 -1045 -177 -1045 174 -177 -1045 48 -184 123 -18 -1045 161 -1045 23 -1045 148 -1045 -18 -1045 132 -77 -18 74 48 -1045 193 -1045 -1045 -177 104 -84 -1045 55 -1045 -1045 -1045 204 -1045 -1045 -1045 204 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCATGARTTTTCYRGGAAAGGGGYGGGVAWTT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 32 nsites= 14 E= 8.6e-057 0.000000 0.000000 0.000000 1.000000 0.000000 0.714286 0.000000 0.285714 0.857143 0.071429 0.000000 0.071429 0.142857 0.000000 0.000000 0.857143 0.142857 0.071429 0.714286 0.071429 0.928571 0.071429 0.000000 0.000000 0.357143 0.071429 0.571429 0.000000 0.142857 0.000000 0.071429 0.785714 0.142857 0.000000 0.000000 0.857143 0.000000 0.071429 0.000000 0.928571 0.000000 0.142857 0.000000 0.857143 0.000000 0.928571 0.000000 0.071429 0.071429 0.357143 0.000000 0.571429 0.500000 0.000000 0.357143 0.142857 0.000000 0.000000 1.000000 0.000000 0.142857 0.000000 0.857143 0.000000 0.857143 0.000000 0.142857 0.000000 1.000000 0.000000 0.000000 0.000000 0.928571 0.000000 0.071429 0.000000 0.214286 0.000000 0.714286 0.071429 0.214286 0.000000 0.714286 0.071429 0.071429 0.000000 0.928571 0.000000 0.071429 0.000000 0.857143 0.071429 0.000000 0.357143 0.071429 0.571429 0.214286 0.000000 0.785714 0.000000 0.285714 0.000000 0.714286 0.000000 0.214286 0.000000 0.642857 0.142857 0.214286 0.428571 0.357143 0.000000 0.928571 0.000000 0.000000 0.071429 0.500000 0.142857 0.000000 0.357143 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCATGARTTTTCYRGGAAAGGGGYGGGVAWTT MEME-1 regular expression -------------------------------------------------------------------------------- T[CT]ATGA[GA]TTTTC[TC][AG]GGAAA[GA][GA]GG[TC][GA][GA][GA][CGA]A[AT]TT -------------------------------------------------------------------------------- Time 487.29 secs. ******************************************************************************** ******************************************************************************** MOTIF ACTGCAAYCTCMRCCTCCYRRGTTCAAGYGATTCTCCTGCCTCAGCCTC MEME-2 width = 49 sites = 8 llr = 364 E-value = 3.7e-041 ******************************************************************************** -------------------------------------------------------------------------------- Motif ACTGCAAYCTCMRCCTCCYRRGTTCAAGYGATTCTCCTGCCTCAGCCTC MEME-2 Description -------------------------------------------------------------------------------- Simplified A 9::1:88::::343:1:::44:1::a61:19:::3:::1::1:8::1:: pos.-specific C :8:38:15a:95:8a:9a5::33:a:1:511:39:a9138a191:a9:9 probability G :336:311::116:::1::668::::39:8::::::::61:::19:::: matrix T 1:8:3::4:a:1:::9::5:::6a::::5::a818:19:1:81:1::a1 bits 2.0 ** * * *** * * * * * 1.8 ** * * *** * * * * * 1.6 ** * * *** * * * * * 1.4 * *** **** *** * ** * *** * * ***** Relative 1.2 *** ** *** ***** * *** * ******** * * ***** Entropy 1.0 *** *** *** ********** *** ** ******** ********* (65.6 bits) 0.8 *** *** *** ************** *********** ********** 0.6 *********** ************************************* 0.4 *********** ************************************* 0.2 ************************************************* 0.0 ------------------------------------------------- Multilevel ACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTC consensus GGCTG T AAA TAACC G T C A C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACTGCAAYCTCMRCCTCCYRRGTTCAAGYGATTCTCCTGCCTCAGCCTC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------------------------------------------- chr6:2845925-2846025 + 52 8.06e-29 gactctgctc actgcaacctccgcctcccaggttcaagcgattctcctgcctcagcctc chr11:6379438-6379538 + 2 1.76e-26 t actgcaacctccgcctcccaagttcaagcaattctcctgcctcagcctc cggagtagct chr2:85993324-85993424 - 51 2.35e-24 C ACTGCAACCTGCGCCTCCTGGGTTCAAGTGATTCTCCTAGCTCAGCCTC ACGAGTAGCT chr1:26636751-26636851 + 3 2.04e-23 tc actgcaagctccgcctcctgggttcacgccattctcctgcctcagcctt ccgagtagct chr6:150071211-150071311 + 39 1.03e-22 atctcagctc actacaatctctgccacccgggttcaagcgattctcttccctcagcctc ccgagtagct chr9:272237-272337 + 20 6.22e-20 atctcagctc actgcaacctcaacctcccaggatcagatgattctcctcccacctcatc ctcccaagta chr3:20321633-20321733 - 2 8.08e-18 CCATGTTGGC TGGCTGGTCTCAAACTGCTGACCTCAAGTGATCCACCCGTCTCAGCCTC C chr11:33015353-33015453 + 11 5.53e-17 catgtaggcc aggctgctctcgaactcctgacctcaggtgctctacctgccctggcctc ccaaagtgct -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACTGCAAYCTCMRCCTCCYRRGTTCAAGYGATTCTCCTGCCTCAGCCTC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:2845925-2846025 8.1e-29 51_[+2] chr11:6379438-6379538 1.8e-26 1_[+2]_50 chr2:85993324-85993424 2.4e-24 50_[-2]_1 chr1:26636751-26636851 2e-23 2_[+2]_49 chr6:150071211-150071311 1e-22 38_[+2]_13 chr9:272237-272337 6.2e-20 19_[+2]_32 chr3:20321633-20321733 8.1e-18 1_[-2]_50 chr11:33015353-33015453 5.5e-17 10_[+2]_41 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACTGCAAYCTCMRCCTCCYRRGTTCAAGYGATTCTCCTGCCTCAGCCTC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ACTGCAAYCTCMRCCTCCYRRGTTCAAGYGATTCTCCTGCCTCAGCCTC width=49 seqs=8 chr6:2845925-2846025 ( 52) ACTGCAACCTCCGCCTCCCAGGTTCAAGCGATTCTCCTGCCTCAGCCTC 1 chr11:6379438-6379538 ( 2) ACTGCAACCTCCGCCTCCCAAGTTCAAGCAATTCTCCTGCCTCAGCCTC 1 chr2:85993324-85993424 ( 51) ACTGCAACCTGCGCCTCCTGGGTTCAAGTGATTCTCCTAGCTCAGCCTC 1 chr1:26636751-26636851 ( 3) ACTGCAAGCTCCGCCTCCTGGGTTCACGCCATTCTCCTGCCTCAGCCTT 1 chr6:150071211-150071311 ( 39) ACTACAATCTCTGCCACCCGGGTTCAAGCGATTCTCTTCCCTCAGCCTC 1 chr9:272237-272337 ( 20) ACTGCAACCTCAACCTCCCAGGATCAGATGATTCTCCTCCCACCTCATC 1 chr3:20321633-20321733 ( 2) TGGCTGGTCTCAAACTGCTGACCTCAAGTGATCCACCCGTCTCAGCCTC 1 chr11:33015353-33015453 ( 11) AGGCTGCTCTCGAACTCCTGACCTCAGGTGCTCTACCTGCCCTGGCCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACTGCAAYCTCMRCCTCCYRRGTTCAAGYGATTCTCCTGCCTCAGCCTC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 49 n= 31200 bayes= 11.0806 E= 3.7e-041 185 -965 -965 -96 -965 155 -4 -965 -965 -965 -4 162 -96 -4 128 -965 -965 155 -965 4 162 -965 -4 -965 162 -104 -104 -965 -965 96 -104 62 -965 196 -965 -965 -965 -965 -965 204 -965 177 -104 -965 4 96 -104 -96 62 -965 128 -965 4 155 -965 -965 -965 196 -965 -965 -96 -965 -965 185 -965 177 -104 -965 -965 196 -965 -965 -965 96 -965 104 62 -965 128 -965 62 -965 128 -965 -965 -4 155 -965 -96 -4 -965 136 -965 -965 -965 204 -965 196 -965 -965 204 -965 -965 -965 136 -104 -4 -965 -96 -965 177 -965 -965 96 -965 104 -96 -104 155 -965 185 -104 -965 -965 -965 -965 -965 204 -965 -4 -965 162 -965 177 -965 -96 4 -965 -965 162 -965 196 -965 -965 -965 177 -965 -96 -965 -104 -965 185 -96 -4 128 -965 -965 155 -104 -96 -965 196 -965 -965 -96 -104 -965 162 -965 177 -965 -96 162 -104 -104 -965 -965 -965 177 -96 -965 196 -965 -965 -96 177 -965 -965 -965 -965 -965 204 -965 177 -965 -96 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACTGCAAYCTCMRCCTCCYRRGTTCAAGYGATTCTCCTGCCTCAGCCTC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 49 nsites= 8 E= 3.7e-041 0.875000 0.000000 0.000000 0.125000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.250000 0.750000 0.125000 0.250000 0.625000 0.000000 0.000000 0.750000 0.000000 0.250000 0.750000 0.000000 0.250000 0.000000 0.750000 0.125000 0.125000 0.000000 0.000000 0.500000 0.125000 0.375000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.875000 0.125000 0.000000 0.250000 0.500000 0.125000 0.125000 0.375000 0.000000 0.625000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.125000 0.000000 0.000000 0.875000 0.000000 0.875000 0.125000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.375000 0.000000 0.625000 0.000000 0.375000 0.000000 0.625000 0.000000 0.000000 0.250000 0.750000 0.000000 0.125000 0.250000 0.000000 0.625000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.625000 0.125000 0.250000 0.000000 0.125000 0.000000 0.875000 0.000000 0.000000 0.500000 0.000000 0.500000 0.125000 0.125000 0.750000 0.000000 0.875000 0.125000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.875000 0.000000 0.125000 0.250000 0.000000 0.000000 0.750000 0.000000 1.000000 0.000000 0.000000 0.000000 0.875000 0.000000 0.125000 0.000000 0.125000 0.000000 0.875000 0.125000 0.250000 0.625000 0.000000 0.000000 0.750000 0.125000 0.125000 0.000000 1.000000 0.000000 0.000000 0.125000 0.125000 0.000000 0.750000 0.000000 0.875000 0.000000 0.125000 0.750000 0.125000 0.125000 0.000000 0.000000 0.000000 0.875000 0.125000 0.000000 1.000000 0.000000 0.000000 0.125000 0.875000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.875000 0.000000 0.125000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACTGCAAYCTCMRCCTCCYRRGTTCAAGYGATTCTCCTGCCTCAGCCTC MEME-2 regular expression -------------------------------------------------------------------------------- A[CG][TG][GC][CT][AG]A[CT]CTC[CA][GA][CA]CTCC[CT][GA][GA][GC][TC]TCA[AG]G[CT]GAT[TC]C[TA]CCT[GC]CCTCAGCCTC -------------------------------------------------------------------------------- Time 913.32 secs. ******************************************************************************** ******************************************************************************** MOTIF AGKWGCTGGGAYTACAGGCAYSHGCCACCACGCCCGGCTAATT MEME-3 width = 43 sites = 8 llr = 333 E-value = 3.2e-037 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGKWGCTGGGAYTACAGGCAYSHGCCACCACGCCCGGCTAATT MEME-3 Description -------------------------------------------------------------------------------- Simplified A 831611:::1a::a1a:1:8::33:19::8:3:1:11::88:: pos.-specific C ::1::9:::::4::8:::9:644:a9:aa:9:899::a3111: probability G 363:9::aa9::::::a9:3:6:8::1::3:6:::99:::1:3 matrix T :154::a::::6a:1:::1:4:4:::::::113:1:::81:98 bits 2.0 *** * ** ** * ** * 1.8 *** * ** ** * ** * 1.6 *** * ** ** * ** * 1.4 ******* ** **** ***** * ***** * Relative 1.2 * ******* ** ***** ******** ******* ** Entropy 1.0 * ******************* ******** *********** (60.1 bits) 0.8 * ******************* ******** *********** 0.6 ** ******************* ******************** 0.4 ** **************************************** 0.2 ******************************************* 0.0 ------------------------------------------- Multilevel AGTAGCTGGGATTACAGGCACGCGCCACCACGCCCGGCTAATT consensus GAGT C GTCTA G AT C G sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGKWGCTGGGAYTACAGGCAYSHGCCACCACGCCCGGCTAATT MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------------------------------------------- chr11:6379438-6379538 + 54 1.82e-24 cagcctccgg agtagctgggattacaggcatgcaccaccacgcccggctaatt ttgt chr2:85993324-85993424 - 5 2.66e-23 CAGCCTCACG AGTAGCTGGGACTACAGGCGCGTACCACCACGCCCGGCTAATT TTTT chr3:196143356-196143456 + 29 7.65e-23 cagcctccgg agtagctgggattacagacacccgccaccacacccggctaatt gttgtatttt chr2:86189150-86189250 + 11 1.80e-22 cagcctcccg ggcagctgggattacaggcacctgccaccacacccggctaatt tttgtatttt chr1:26636751-26636851 + 55 1.62e-20 cagccttccg agtagctggaactacaggcacccgccaccatgcccagctaatt ttt chr21:22209864-22209964 + 16 3.77e-19 cggcctctca aagtgctgggattacaggcgtgagccaccgcgcccgaccTATT GGtttctttt chr7:130009708-130009808 + 35 1.11e-16 agcctcccta gtataatgggactataggcacgtgccaccacttctggcTAGTG AGCTGGTGCT chr8:98045443-98045543 - 46 1.07e-15 CAACCTCCGA AAGTGCTGGGATTAAAGGTATGAGCAGCCGCGTACGGCCCCCG CAGCCATTCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGKWGCTGGGAYTACAGGCAYSHGCCACCACGCCCGGCTAATT MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr11:6379438-6379538 1.8e-24 53_[+3]_4 chr2:85993324-85993424 2.7e-23 4_[-3]_53 chr3:196143356-196143456 7.7e-23 28_[+3]_29 chr2:86189150-86189250 1.8e-22 10_[+3]_47 chr1:26636751-26636851 1.6e-20 54_[+3]_3 chr21:22209864-22209964 3.8e-19 15_[+3]_42 chr7:130009708-130009808 1.1e-16 34_[+3]_23 chr8:98045443-98045543 1.1e-15 45_[-3]_12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGKWGCTGGGAYTACAGGCAYSHGCCACCACGCCCGGCTAATT MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AGKWGCTGGGAYTACAGGCAYSHGCCACCACGCCCGGCTAATT width=43 seqs=8 chr11:6379438-6379538 ( 54) AGTAGCTGGGATTACAGGCATGCACCACCACGCCCGGCTAATT 1 chr2:85993324-85993424 ( 5) AGTAGCTGGGACTACAGGCGCGTACCACCACGCCCGGCTAATT 1 chr3:196143356-196143456 ( 29) AGTAGCTGGGATTACAGACACCCGCCACCACACCCGGCTAATT 1 chr2:86189150-86189250 ( 11) GGCAGCTGGGATTACAGGCACCTGCCACCACACCCGGCTAATT 1 chr1:26636751-26636851 ( 55) AGTAGCTGGAACTACAGGCACCCGCCACCATGCCCAGCTAATT 1 chr21:22209864-22209964 ( 16) AAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGACCTATT 1 chr7:130009708-130009808 ( 35) GTATAATGGGACTATAGGCACGTGCCACCACTTCTGGCTAGTG 1 chr8:98045443-98045543 ( 46) AAGTGCTGGGATTAAAGGTATGAGCAGCCGCGTACGGCCCCCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGKWGCTGGGAYTACAGGCAYSHGCCACCACGCCCGGCTAATT MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 43 n= 34800 bayes= 12.0865 E= 3.2e-037 162 -965 -4 -965 4 -965 128 -96 -96 -104 -4 104 136 -965 -965 62 -96 -965 177 -965 -96 177 -965 -965 -965 -965 -965 204 -965 -965 196 -965 -965 -965 196 -965 -96 -965 177 -965 204 -965 -965 -965 -965 55 -965 136 -965 -965 -965 204 204 -965 -965 -965 -96 155 -965 -96 204 -965 -965 -965 -965 -965 196 -965 -96 -965 177 -965 -965 177 -965 -96 162 -965 -4 -965 -965 128 -965 62 -965 55 128 -965 4 55 -965 62 4 -965 155 -965 -965 196 -965 -965 -96 177 -965 -965 185 -965 -104 -965 -965 196 -965 -965 -965 196 -965 -965 162 -965 -4 -965 -965 177 -965 -96 4 -965 128 -96 -965 155 -965 4 -96 177 -965 -965 -965 177 -965 -96 -96 -965 177 -965 -96 -965 177 -965 -965 196 -965 -965 -965 -4 -965 162 162 -104 -965 -96 162 -104 -104 -965 -965 -104 -965 185 -965 -965 -4 162 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGKWGCTGGGAYTACAGGCAYSHGCCACCACGCCCGGCTAATT MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 43 nsites= 8 E= 3.2e-037 0.750000 0.000000 0.250000 0.000000 0.250000 0.000000 0.625000 0.125000 0.125000 0.125000 0.250000 0.500000 0.625000 0.000000 0.000000 0.375000 0.125000 0.000000 0.875000 0.000000 0.125000 0.875000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.125000 0.000000 0.875000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.375000 0.000000 0.625000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.125000 0.750000 0.000000 0.125000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.125000 0.000000 0.875000 0.000000 0.000000 0.875000 0.000000 0.125000 0.750000 0.000000 0.250000 0.000000 0.000000 0.625000 0.000000 0.375000 0.000000 0.375000 0.625000 0.000000 0.250000 0.375000 0.000000 0.375000 0.250000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.125000 0.875000 0.000000 0.000000 0.875000 0.000000 0.125000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 0.875000 0.000000 0.125000 0.250000 0.000000 0.625000 0.125000 0.000000 0.750000 0.000000 0.250000 0.125000 0.875000 0.000000 0.000000 0.000000 0.875000 0.000000 0.125000 0.125000 0.000000 0.875000 0.000000 0.125000 0.000000 0.875000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.750000 0.125000 0.000000 0.125000 0.750000 0.125000 0.125000 0.000000 0.000000 0.125000 0.000000 0.875000 0.000000 0.000000 0.250000 0.750000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGKWGCTGGGAYTACAGGCAYSHGCCACCACGCCCGGCTAATT MEME-3 regular expression -------------------------------------------------------------------------------- [AG][GA][TG][AT]GCTGGGA[TC]TACAGGC[AG][CT][GC][CTA][GA]CCACC[AG]C[GA][CT]CCGGC[TC]AAT[TG] -------------------------------------------------------------------------------- Time 1338.47 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr17:27602706-27602806 8.33e-02 100 chr15:43330539-43330639 8.36e-02 100 chr1:26126332-26126432 3.43e-01 100 chr11:64304550-64304650 2.24e-01 100 chrX:1072586-1072686 3.66e-05 64_[-1(3.56e-08)]_4 chr19:6109626-6109726 3.54e-01 100 chr10:63236189-63236289 4.69e-01 100 chr20:33720156-33720256 9.74e-01 100 chr2:30191756-30191856 6.29e-01 100 chr19:12835083-12835183 5.10e-01 100 chr5:74767033-74767133 5.38e-01 100 chr17:59784174-59784274 6.98e-02 100 chr1:207322196-207322296 9.24e-01 100 chr19:28544629-28544729 5.88e-01 100 chr17:48825343-48825443 1.68e-15 32_[+1(6.82e-19)]_36 chr11:76825828-76825928 6.03e-01 100 chr11:117224210-11722431 4.05e-01 100 chr16:85322874-85322974 6.70e-01 100 chr15:89243739-89243839 8.70e-02 100 chr17:42017008-42017108 7.92e-01 100 chr9:36215780-36215880 2.53e-01 100 chr22:45313930-45314030 2.14e-01 100 chr8:100723235-100723335 3.63e-01 100 chr21:44025863-44025963 1.06e-01 100 chr10:72297911-72298011 7.94e-01 100 chr7:100478990-100479090 4.15e-01 100 chr3:38137038-38137138 2.22e-01 100 chr19:11094889-11094989 3.84e-01 100 chr16:22282242-22282342 7.20e-01 100 chr19:4867487-4867587 5.13e-01 100 chr15:75640090-75640190 6.55e-01 100 chr9:272237-272337 1.87e-15 19_[+2(6.22e-20)]_32 chr17:28812309-28812409 8.70e-01 100 chr1:219883311-219883411 5.54e-01 100 chr11:33015353-33015453 1.18e-12 10_[+2(5.53e-17)]_41 chr4:70903136-70903236 1.70e-01 100 chr1:156693260-156693360 6.86e-01 100 chrX:2890874-2890974 1.93e-01 100 chr7:36198851-36198951 9.32e-02 100 chr7:126701022-126701122 5.65e-01 100 chr17:14309229-14309329 7.57e-01 100 chr7:129769119-129769219 2.44e-01 100 chr2:55048904-55049004 7.20e-01 100 chr5:43064621-43064721 4.92e-01 100 chr11:123062266-12306236 3.95e-01 100 chr4:78732467-78732567 1.74e-01 100 chr2:46616924-46617024 2.05e-01 100 chr3:46976497-46976597 5.48e-01 100 chr16:15988398-15988498 6.56e-01 100 chr11:75814873-75814973 7.59e-02 100 chr11:12149752-12149852 4.36e-01 100 chr13:50084947-50085047 1.83e-01 100 chr6:20401502-20401602 2.74e-01 100 chr6:95519147-95519247 5.33e-01 100 chr10:69308148-69308248 6.44e-01 100 chr12:57744898-57744998 4.03e-01 100 chr11:63689229-63689329 6.83e-01 100 chr6:13941907-13942007 1.42e-01 13_[-1(7.08e-05)]_55 chr4:122906769-122906869 1.78e-12 27_[-1(2.67e-17)]_41 chr1:17248771-17248871 1.87e-01 100 chr15:57322189-57322289 3.72e-01 100 chr19:43596540-43596640 5.69e-01 100 chr6:167690532-167690632 2.36e-01 100 chr7:25862146-25862246 6.69e-01 100 chr2:233225575-233225675 6.92e-01 100 chr7:32892428-32892528 1.71e-01 100 chr5:132495538-132495638 5.74e-01 100 chr14:75069154-75069254 5.05e-01 100 chr7:73431437-73431537 5.22e-01 100 chr1:28736361-28736461 7.86e-01 100 chr12:122886975-12288707 1.74e-01 100 chr7:38335580-38335680 2.62e-01 100 chr11:34105132-34105232 3.77e-02 100 chr19:49877401-49877501 2.81e-01 100 chr7:5457844-5457944 1.16e-01 9_[-1(7.79e-05)]_59 chr13:94601502-94601602 1.02e-01 100 chr18:57819908-57820008 7.09e-01 100 chr1:47231506-47231606 1.76e-01 100 chr12:47215501-47215601 2.41e-02 100 chr22:46604284-46604384 9.87e-03 27_[+2(8.05e-05)]_24 chr12:101696956-10169705 6.09e-01 100 chr16:3003773-3003873 6.96e-01 100 chr5:56288875-56288975 9.51e-02 100 chrX:70988318-70988418 3.77e-08 31_[+1(1.15e-12)]_[+1(5.51e-05)]_5 chr7:70569458-70569558 1.22e-01 100 chr11:112025044-11202514 2.43e-01 100 chr7:102748558-102748658 2.15e-01 100 chr6:151229465-151229565 8.90e-01 100 chr2:216880613-216880713 1.69e-02 53_[+1(3.94e-05)]_15 chr19:48962326-48962426 8.16e-01 100 chr11:117160802-11716090 2.39e-01 100 chr15:39782821-39782921 8.67e-01 100 chr2:64751077-64751177 5.57e-01 100 chr6:154675472-154675572 5.27e-01 100 chr7:98218261-98218361 5.38e-03 29_[+2(1.65e-05)]_22 chr6:107459161-107459261 5.68e-01 100 chr12:107110022-10711012 6.64e-12 42_[-1(2.76e-16)]_26 chr6:33789138-33789238 4.40e-01 100 chr1:12657434-12657534 1.06e-07 8_[+1(7.64e-05)]_1_[+1(5.59e-12)]_\ 27 chr19:48784591-48784691 2.69e-01 100 chr9:128204383-128204483 3.45e-02 37_[-2(4.02e-05)]_14 chr3:196143356-196143456 6.78e-19 28_[+3(7.65e-23)]_29 chr9:136849034-136849134 9.20e-01 100 chr3:38165184-38165284 8.31e-01 100 chr8:2788072-2788172 3.07e-01 100 chr16:74666766-74666866 5.45e-01 100 chr20:38563676-38563776 1.63e-01 100 chr1:151281878-151281978 3.08e-01 100 chr11:19240781-19240881 7.73e-01 100 chr6:17843216-17843316 7.58e-01 100 chr5:80204849-80204949 9.21e-01 100 chr2:85993324-85993424 2.93e-39 4_[-3(2.66e-23)]_3_[-2(2.35e-24)]_1 chr6:107116000-107116100 1.07e-01 100 chr7:67301460-67301560 4.42e-01 100 chr1:158819561-158819661 9.42e-01 100 chr19:7829765-7829865 2.12e-01 100 chr8:102391829-102391929 2.39e-04 32_[-1(7.13e-08)]_36 chr2:74454741-74454841 6.85e-01 100 chr14:100141934-10014203 8.38e-01 100 chr19:13152853-13152953 6.62e-01 100 chr7:97144874-97144974 6.36e-01 100 chr10:125816469-12581656 3.40e-01 100 chr10:101587913-10158801 3.37e-01 100 chr20:45857242-45857342 6.66e-03 100 chr19:47334481-47334581 9.25e-01 100 chr11:69449678-69449778 4.80e-01 100 chr2:39141942-39142042 1.18e-01 100 chr19:11374865-11374965 2.97e-01 100 chr2:197804238-197804338 7.59e-01 100 chr14:23056104-23056204 9.27e-02 100 chr2:55236255-55236355 8.62e-01 100 chr6:107980224-107980324 3.67e-02 21_[+2(5.83e-05)]_30 chr1:46132882-46132982 9.07e-01 100 chr11:2303553-2303653 2.09e-01 100 chr3:187745267-187745367 4.37e-01 100 chr17:7214304-7214404 3.07e-01 100 chr1:17119308-17119408 5.91e-01 100 chr2:64830950-64831050 8.20e-01 100 chr12:118582186-11858228 6.61e-13 22_[+1(2.67e-17)]_46 chr6:135325463-135325563 3.74e-02 100 chr19:55166665-55166765 8.11e-01 100 chr6:26553581-26553681 1.62e-01 100 chr1:155193228-155193328 6.43e-01 100 chr14:91202212-91202312 7.69e-02 25_[+1(7.50e-05)]_43 chr17:68511960-68512060 7.93e-01 100 chr9:105647433-105647533 5.71e-02 2_[+1(9.42e-05)]_66 chr19:12733325-12733425 8.27e-01 100 chr1:1401931-1402031 4.51e-01 100 chr1:89823485-89823585 2.49e-01 100 chr6:146889092-146889192 3.27e-01 100 chr20:45415789-45415889 4.44e-01 100 chr4:123564669-123564769 4.31e-01 100 chr10:17428514-17428614 2.18e-01 100 chr1:54764512-54764612 5.80e-01 100 chr6:67885019-67885119 1.11e-01 100 chr8:143293897-143293997 3.53e-01 100 chr7:101192418-101192518 1.40e-01 100 chr8:67055020-67055120 6.77e-01 100 chr9:130712523-130712623 1.97e-01 100 chr3:4533746-4533846 4.15e-01 100 chr18:3037471-3037571 5.10e-01 100 chr15:66679640-66679740 2.85e-01 100 chr2:130342144-130342244 1.84e-01 100 chr6:37257725-37257825 5.88e-01 100 chr1:92956915-92957015 6.09e-01 100 chr14:76257017-76257117 1.27e-01 100 chr5:54313442-54313542 6.86e-01 100 chr9:19748541-19748641 1.74e-01 100 chr17:59565119-59565219 4.03e-01 100 chr7:1768762-1768862 9.02e-01 100 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38_[-1(3.94e-05)]_30 chr15:89893823-89893923 9.31e-01 100 chr14:20332950-20333050 4.06e-01 100 chr6:158704452-158704552 8.40e-01 100 chr19:50376097-50376197 6.35e-01 100 chr4:98801117-98801217 4.03e-01 100 chr13:95270982-95271082 3.02e-01 100 chr15:75198605-75198705 2.68e-01 100 chr11:60194025-60194125 5.53e-01 100 chr2:6893783-6893883 8.24e-01 100 chr19:19192102-19192202 1.60e-01 100 chr2:65432465-65432565 6.69e-01 100 chr15:78306299-78306399 5.00e-01 100 chr12:131860207-13186030 7.08e-02 1_[-1(2.79e-05)]_67 chr6:143164458-143164558 3.76e-01 100 chr17:44288279-44288379 3.79e-01 100 chr17:38861369-38861469 3.21e-01 100 chr6:83974564-83974664 5.06e-02 43_[+1(8.73e-05)]_25 chr1:248691384-248691484 4.77e-01 100 chr3:136752029-136752129 1.96e-01 100 chr6:43723735-43723835 1.62e-01 100 chr13:79405983-79406083 3.30e-01 100 chr19:35744816-35744916 5.40e-01 100 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (3) found. ******************************************************************************** CPU: kali ********************************************************************************