******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.10.0 (Release date: Wed May 21 10:35:36 2014 +1000) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net. 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.nbcr.net. ******************************************************************************** ******************************************************************************** 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= motifs/4/4.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10150 1.0000 500 10229 1.0000 500 10446 1.0000 500 10453 1.0000 500 10942 1.0000 500 11226 1.0000 500 11287 1.0000 500 11503 1.0000 500 11793 1.0000 500 11975 1.0000 500 12100 1.0000 500 12103 1.0000 500 1214 1.0000 500 12163 1.0000 500 20605 1.0000 500 23929 1.0000 500 24791 1.0000 500 25278 1.0000 500 261312 1.0000 500 262941 1.0000 500 264008 1.0000 500 264396 1.0000 500 3174 1.0000 500 3508 1.0000 500 3553 1.0000 500 6097 1.0000 500 6678 1.0000 500 6765 1.0000 500 7889 1.0000 500 8036 1.0000 500 9674 1.0000 500 bd1439 1.0000 500 bd1823 1.0000 500 bd635 1.0000 500 ThpsCp086 1.0000 500 ThpsCp130 1.0000 500 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme motifs/4/4.seqs.fa -oc motifs/4 -dna -minw 12 -maxw 21 -nmotifs 3 -maxsize 500000 model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 12 maxw= 21 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 36 wnsites= 0.8 theta: prob= 1 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= 18000 N= 36 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.276 C 0.213 G 0.235 T 0.276 Background letter frequencies (from dataset with add-one prior applied): A 0.276 C 0.213 G 0.235 T 0.276 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 28 llr = 303 E-value = 7.4e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :96261278336812:3461 pos.-specific C a136:381:65423421316 probability G :::::2:11:::::1242:3 matrix T ::1244::111::625123: bits 2.2 * 2.0 * 1.8 * 1.6 * * Relative 1.3 ** * Entropy 1.1 ** * ** (15.6 bits) 0.9 ** ** **** ** * 0.7 ** ** **** *** ** 0.4 ***** ******** * ** 0.2 ***************** ** 0.0 -------------------- Multilevel CAACATCAACCAATCTGAAC consensus C TC AAC CACACTG sequence G TG G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- ThpsCp130 103 1.81e-09 TAAACGGTTT CAACTTCAACCAATCTGTAG TTGATTCTCA ThpsCp086 169 1.81e-09 TAAACGGTTT CAACTTCAACCAATCTGTAG TTGATTCTCA bd1439 104 1.81e-09 TAAACGGTTT CAACTTCAACCAATCTGTAG TTGATTCTCA 1214 162 9.31e-09 GAGAGAGGAA CAACATCAACACATTTGAAG GTGCTGTCAA 11503 467 1.48e-07 GTTCACTTCA CAACAACAAATCATCTGCAC CAACTCCAAC 11287 348 2.56e-07 CGAAGCCTCC CAACACCCACCAACATAGCC AACCAACAAC 8036 311 8.90e-07 AGAACAACCC CAACTCCAACCAACTCTGTG GTGGTTCCAC 3553 231 9.98e-07 CAAGCTTCGG CATCTGCAACCAATACGGTG AAGGCTCATC 10453 377 1.12e-06 TCCATTCCAT CAATATCAATACATCGGCAC ACGCCTATGA 10446 377 1.12e-06 TCCATTCCAT CAATATCAATACATCGGCAC ACGCCTATGA 7889 481 1.74e-06 ACCACCGCAT CCACACCAACACAATTGATC 262941 466 2.14e-06 CTTTCCGGTA CATCAGAAACACATCTCCTC GTTACCAACA 25278 426 2.38e-06 TTTGGTGGAC CACCAACCACCACCACAAAC CGTCGTCCGT 10229 219 2.63e-06 GGGAACAGTC CACCAGCAACCACCGGCACC GAGAACAACT 3508 470 3.55e-06 GTCTCTTCCT CCAAACCAAACACTCGAATC CAGCCATCAC 24791 85 5.70e-06 GGGATGATGT CATCAGCAGCCAACTGAGAG GCAGAGATTC 261312 116 9.68e-06 AGTCCCATTC CCCCTCCAACCAATCAGGAA AGTAGAGATT 12103 368 1.05e-05 GCCAATACAG CACTAGACACACACGTGAAC AGAGTAGAGA bd1823 103 1.14e-05 CTGTGAACGT CAACTTCGTACAACATTGAC ATTGTTTTGA 264396 159 1.99e-05 GCAGTGTGAG CACCACCATATAATGCACTG TGGCTTGACG 12163 339 1.99e-05 TAATGAATGA CAAAATCAGACACTGTTATC CCCCTTTTTT 23929 220 2.31e-05 TAGTGTCAAA CAAAACAAAAAAATCTCTAA TTCAATTAGA 11975 92 2.31e-05 AGGTGAAGGC CAGATCCAAACAAACGAAAC AGAAGGCCAC 10150 480 3.53e-05 ATCACGACAT CCATTTCCTCAAACATACAC C bd635 448 4.04e-05 CACAGCGTTT CACAATAGACTCATTTCATC GCAAAGAACA 264008 151 4.04e-05 TCCAAAGATT CACCAACGAACCTTCTGCCG AACTTCCCCA 11226 390 4.31e-05 CAAAAGAGTT CACCATCAGCGACCTCATTC GATCCAGAAC 6097 271 4.60e-05 ATATATAATT CAATTGAGAAACATACAAAC ACGTTCTTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ThpsCp130 1.8e-09 102_[+1]_378 ThpsCp086 1.8e-09 168_[+1]_312 bd1439 1.8e-09 103_[+1]_377 1214 9.3e-09 161_[+1]_319 11503 1.5e-07 466_[+1]_14 11287 2.6e-07 347_[+1]_133 8036 8.9e-07 310_[+1]_170 3553 1e-06 230_[+1]_250 10453 1.1e-06 376_[+1]_104 10446 1.1e-06 376_[+1]_104 7889 1.7e-06 480_[+1] 262941 2.1e-06 465_[+1]_15 25278 2.4e-06 425_[+1]_55 10229 2.6e-06 218_[+1]_262 3508 3.6e-06 469_[+1]_11 24791 5.7e-06 84_[+1]_396 261312 9.7e-06 115_[+1]_365 12103 1.1e-05 367_[+1]_113 bd1823 1.1e-05 102_[+1]_378 264396 2e-05 158_[+1]_322 12163 2e-05 338_[+1]_142 23929 2.3e-05 219_[+1]_261 11975 2.3e-05 91_[+1]_389 10150 3.5e-05 479_[+1]_1 bd635 4e-05 447_[+1]_33 264008 4e-05 150_[+1]_330 11226 4.3e-05 389_[+1]_91 6097 4.6e-05 270_[+1]_210 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=28 ThpsCp130 ( 103) CAACTTCAACCAATCTGTAG 1 ThpsCp086 ( 169) CAACTTCAACCAATCTGTAG 1 bd1439 ( 104) CAACTTCAACCAATCTGTAG 1 1214 ( 162) CAACATCAACACATTTGAAG 1 11503 ( 467) CAACAACAAATCATCTGCAC 1 11287 ( 348) CAACACCCACCAACATAGCC 1 8036 ( 311) CAACTCCAACCAACTCTGTG 1 3553 ( 231) CATCTGCAACCAATACGGTG 1 10453 ( 377) CAATATCAATACATCGGCAC 1 10446 ( 377) CAATATCAATACATCGGCAC 1 7889 ( 481) CCACACCAACACAATTGATC 1 262941 ( 466) CATCAGAAACACATCTCCTC 1 25278 ( 426) CACCAACCACCACCACAAAC 1 10229 ( 219) CACCAGCAACCACCGGCACC 1 3508 ( 470) CCAAACCAAACACTCGAATC 1 24791 ( 85) CATCAGCAGCCAACTGAGAG 1 261312 ( 116) CCCCTCCAACCAATCAGGAA 1 12103 ( 368) CACTAGACACACACGTGAAC 1 bd1823 ( 103) CAACTTCGTACAACATTGAC 1 264396 ( 159) CACCACCATATAATGCACTG 1 12163 ( 339) CAAAATCAGACACTGTTATC 1 23929 ( 220) CAAAACAAAAAAATCTCTAA 1 11975 ( 92) CAGATCCAAACAAACGAAAC 1 10150 ( 480) CCATTTCCTCAAACATACAC 1 bd635 ( 448) CACAATAGACTCATTTCATC 1 264008 ( 151) CACCAACGAACCTTCTGCCG 1 11226 ( 390) CACCATCAGCGACCTCATTC 1 6097 ( 271) CAATTGAGAAACATACAAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 17316 bayes= 9.87665 E= 7.4e-008 -1145 223 -1145 -1145 164 -57 -1145 -1145 105 42 -272 -136 -63 159 -1145 -63 122 -1145 -1145 37 -136 42 -14 51 -63 195 -1145 -1145 137 -57 -72 -1145 151 -1145 -113 -136 22 151 -1145 -195 22 133 -272 -136 122 75 -1145 -1145 151 -25 -1145 -295 -195 59 -1145 114 -36 101 -72 -36 -295 1 -14 96 22 -57 86 -136 37 23 -14 -63 105 -99 -1145 22 -195 151 45 -1145 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 28 E= 7.4e-008 0.000000 1.000000 0.000000 0.000000 0.857143 0.142857 0.000000 0.000000 0.571429 0.285714 0.035714 0.107143 0.178571 0.642857 0.000000 0.178571 0.642857 0.000000 0.000000 0.357143 0.107143 0.285714 0.214286 0.392857 0.178571 0.821429 0.000000 0.000000 0.714286 0.142857 0.142857 0.000000 0.785714 0.000000 0.107143 0.107143 0.321429 0.607143 0.000000 0.071429 0.321429 0.535714 0.035714 0.107143 0.642857 0.357143 0.000000 0.000000 0.785714 0.178571 0.000000 0.035714 0.071429 0.321429 0.000000 0.607143 0.214286 0.428571 0.142857 0.214286 0.035714 0.214286 0.214286 0.535714 0.321429 0.142857 0.428571 0.107143 0.357143 0.250000 0.214286 0.178571 0.571429 0.107143 0.000000 0.321429 0.071429 0.607143 0.321429 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CA[AC]C[AT][TCG]CAA[CA][CA][AC]A[TC][CAT][TCG][GA][ACG][AT][CG] -------------------------------------------------------------------------------- Time 10.48 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 6 llr = 135 E-value = 3.1e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A a:a2:5:3a5:232:aa:::: pos.-specific C :a:3a:87::a:2:5::a:a: probability G :::5::2::5::5:::::5:: matrix T :::::5:::::8:85:::5:a bits 2.2 * * * * * 2.0 * * * * * 1.8 *** * * * *** ** 1.6 *** * * * * *** ** Relative 1.3 *** * * * * *** ** Entropy 1.1 *** * *** ** ***** ** (32.5 bits) 0.9 *** ******** ******** 0.7 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel ACAGCACCAACTGTCAACGCT consensus C T A G A T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- ThpsCp130 263 1.12e-12 AGTTGCTTTC ACAGCTCCAGCTGTTAACGCT TAATTTTAAG ThpsCp086 329 1.12e-12 AGTTGCTTTC ACAGCTCCAGCTGTTAACGCT TAATTTTAAG bd1439 264 1.12e-12 AGTTGCTTTC ACAGCTCCAGCTGTTAACGCT TAATTTTAAG 10453 474 4.42e-11 CGATACACAG ACACCACAAACTATCAACTCT TCAACT 10446 474 4.42e-11 CGATACACAG ACACCACAAACTATCAACTCT TCAACT 11287 376 4.84e-10 CCAACCAACA ACAACAGCAACACACAACTCT CTCTCTCTCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ThpsCp130 1.1e-12 262_[+2]_217 ThpsCp086 1.1e-12 328_[+2]_151 bd1439 1.1e-12 263_[+2]_216 10453 4.4e-11 473_[+2]_6 10446 4.4e-11 473_[+2]_6 11287 4.8e-10 375_[+2]_104 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=6 ThpsCp130 ( 263) ACAGCTCCAGCTGTTAACGCT 1 ThpsCp086 ( 329) ACAGCTCCAGCTGTTAACGCT 1 bd1439 ( 264) ACAGCTCCAGCTGTTAACGCT 1 10453 ( 474) ACACCACAAACTATCAACTCT 1 10446 ( 474) ACACCACAAACTATCAACTCT 1 11287 ( 376) ACAACAGCAACACACAACTCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 17280 bayes= 11.1502 E= 3.1e-006 186 -923 -923 -923 -923 223 -923 -923 186 -923 -923 -923 -73 65 109 -923 -923 223 -923 -923 86 -923 -923 86 -923 197 -50 -923 27 165 -923 -923 186 -923 -923 -923 86 -923 109 -923 -923 223 -923 -923 -73 -923 -923 159 27 -35 109 -923 -73 -923 -923 159 -923 123 -923 86 186 -923 -923 -923 186 -923 -923 -923 -923 223 -923 -923 -923 -923 109 86 -923 223 -923 -923 -923 -923 -923 186 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6 E= 3.1e-006 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.333333 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.833333 0.166667 0.000000 0.333333 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.166667 0.000000 0.000000 0.833333 0.333333 0.166667 0.500000 0.000000 0.166667 0.000000 0.000000 0.833333 0.000000 0.500000 0.000000 0.500000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- ACA[GC]C[AT]C[CA]A[AG]CT[GA]T[CT]AAC[GT]CT -------------------------------------------------------------------------------- Time 20.85 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 22 llr = 268 E-value = 4.4e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :12:2:6:::3::3312:75: pos.-specific C :1:41:11::2:1::::1:1: probability G 9:85:a234745714447146 matrix T 18::7::663152625512:4 bits 2.2 2.0 1.8 * 1.6 * * Relative 1.3 * * * Entropy 1.1 *** * * * (17.6 bits) 0.9 *** * ** ** ** * 0.7 ********** ** ** * 0.4 ********** *** ****** 0.2 ********************* 0.0 --------------------- Multilevel GTGGTGATTGGGGTGTTGAAG consensus AC GGGTATTAAGG GT sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- ThpsCp130 171 1.81e-09 ATCATTAACC GTGCTGATTTAGGTATGGAAG TAATGCACGA ThpsCp086 237 1.81e-09 ATCATTAACC GTGCTGATTTAGGTATGGAAG TAATGCACGA bd1439 172 1.81e-09 ATCATTAACC GTGCTGATTTAGGTATGGAAG TAATGCACGA 3174 303 4.49e-08 GGATGCCATT GTGGTGCTGGCTGTATTGTAG AGGAAGCTAT bd635 100 6.57e-08 GTGTCGGGTT GTGGTGGGTGGTGGAGAGAGG CAGTGTTGTG 264396 5 2.62e-07 GAAC GTGCTGATTGAGTTGGATAGT TGCAGAATTG 10446 2 3.24e-07 T GAGGAGATTGGTTTGGTGAAT AAGAATTATG 24791 330 7.18e-07 TATAAGGGAT GTGGTGATGTATTAGTTCAGT TGTACCAATA 20605 161 7.89e-07 GGTGTGGGTG GTGGTGATGGGTGATAGCACT TAAAAACTCC 25278 227 9.49e-07 GTTGTTGAGA GCGGTGAGTGCGTTGTTGTCG TCGGTGGAGG 261312 360 1.04e-06 TGCCGCGTGG GTAGCGAGTGTGGTAAGGAAG AAAAGAGGTC 23929 97 1.04e-06 GATGAGTTCA GCAGAGGTTGGGGTGTTGTAG CTTTGGTGCT 6678 397 1.36e-06 CTAACGCTTT GTGCTAGTGGATGTGTAGACG TCGCCAGTAA 10942 282 1.36e-06 ATTTTGAGTT GTGATGCTTGGGCTAGGGAGT ATGTTGCGGA 12100 279 1.91e-06 TCATGGTACA GAGGCGAGTGATGATGAGAAG TGTTTGACTT 10229 85 2.86e-06 GTCTTCGTTT GTAGTGACGGCGGAGTTGATT GGAGAGACGG 10150 194 3.09e-06 ATGTAGATAT GTGCTGCCTTGTGTTTGTAGT CCAACAATAG 11503 187 5.22e-06 AGAATGAATG GTGGAGGGGGGGGGCGTTAGG GATCGGCGTT 8036 63 5.60e-06 CGCCATTTTG TTGTTGGTTTGTGTGGTGTGG TACCAGAGAG bd1823 214 6.90e-06 TACGACTGAC GTGCTGATGGCGTGTGTCGAT GAATAGTAAT 11287 127 6.90e-06 TGGGATGCTG TTACCGAGGGGTGAGAGGAGG AGGGATAGTA 3508 224 1.32e-05 GACTTGGAGA GTAGAGATTGTTCATTTGGAG AGAACACTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- ThpsCp130 1.8e-09 170_[+3]_309 ThpsCp086 1.8e-09 236_[+3]_243 bd1439 1.8e-09 171_[+3]_308 3174 4.5e-08 302_[+3]_177 bd635 6.6e-08 99_[+3]_380 264396 2.6e-07 4_[+3]_475 10446 3.2e-07 1_[+3]_478 24791 7.2e-07 329_[+3]_150 20605 7.9e-07 160_[+3]_319 25278 9.5e-07 226_[+3]_253 261312 1e-06 359_[+3]_120 23929 1e-06 96_[+3]_383 6678 1.4e-06 396_[+3]_83 10942 1.4e-06 281_[+3]_198 12100 1.9e-06 278_[+3]_201 10229 2.9e-06 84_[+3]_395 10150 3.1e-06 193_[+3]_286 11503 5.2e-06 186_[+3]_293 8036 5.6e-06 62_[+3]_417 bd1823 6.9e-06 213_[+3]_266 11287 6.9e-06 126_[+3]_353 3508 1.3e-05 223_[+3]_256 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=22 ThpsCp130 ( 171) GTGCTGATTTAGGTATGGAAG 1 ThpsCp086 ( 237) GTGCTGATTTAGGTATGGAAG 1 bd1439 ( 172) GTGCTGATTTAGGTATGGAAG 1 3174 ( 303) GTGGTGCTGGCTGTATTGTAG 1 bd635 ( 100) GTGGTGGGTGGTGGAGAGAGG 1 264396 ( 5) GTGCTGATTGAGTTGGATAGT 1 10446 ( 2) GAGGAGATTGGTTTGGTGAAT 1 24791 ( 330) GTGGTGATGTATTAGTTCAGT 1 20605 ( 161) GTGGTGATGGGTGATAGCACT 1 25278 ( 227) GCGGTGAGTGCGTTGTTGTCG 1 261312 ( 360) GTAGCGAGTGTGGTAAGGAAG 1 23929 ( 97) GCAGAGGTTGGGGTGTTGTAG 1 6678 ( 397) GTGCTAGTGGATGTGTAGACG 1 10942 ( 282) GTGATGCTTGGGCTAGGGAGT 1 12100 ( 279) GAGGCGAGTGATGATGAGAAG 1 10229 ( 85) GTAGTGACGGCGGAGTTGATT 1 10150 ( 194) GTGCTGCCTTGTGTTTGTAGT 1 11503 ( 187) GTGGAGGGGGGGGGCGTTAGG 1 8036 ( 63) TTGTTGGTTTGTGTGGTGTGG 1 bd1823 ( 214) GTGCTGATGGCGTGTGTCGAT 1 11287 ( 127) TTACCGAGGGGTGAGAGGAGG 1 3508 ( 224) GTAGAGATTGTTCATTTGGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 17280 bayes= 9.97104 E= 4.4e-006 -1110 -1110 195 -160 -160 -123 -1110 157 -28 -1110 171 -1110 -260 77 121 -260 -60 -64 -1110 130 -260 -1110 202 -1110 121 -64 -5 -1110 -1110 -123 21 121 -1110 -1110 63 121 -1110 -1110 163 -2 21 -23 80 -160 -1110 -1110 109 86 -1110 -123 153 -28 -2 -1110 -79 110 21 -222 80 -28 -102 -1110 63 86 -60 -1110 63 72 -1110 -64 163 -102 140 -1110 -137 -60 72 -64 63 -260 -1110 -1110 143 40 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 22 E= 4.4e-006 0.000000 0.000000 0.909091 0.090909 0.090909 0.090909 0.000000 0.818182 0.227273 0.000000 0.772727 0.000000 0.045455 0.363636 0.545455 0.045455 0.181818 0.136364 0.000000 0.681818 0.045455 0.000000 0.954545 0.000000 0.636364 0.136364 0.227273 0.000000 0.000000 0.090909 0.272727 0.636364 0.000000 0.000000 0.363636 0.636364 0.000000 0.000000 0.727273 0.272727 0.318182 0.181818 0.409091 0.090909 0.000000 0.000000 0.500000 0.500000 0.000000 0.090909 0.681818 0.227273 0.272727 0.000000 0.136364 0.590909 0.318182 0.045455 0.409091 0.227273 0.136364 0.000000 0.363636 0.500000 0.181818 0.000000 0.363636 0.454545 0.000000 0.136364 0.727273 0.136364 0.727273 0.000000 0.090909 0.181818 0.454545 0.136364 0.363636 0.045455 0.000000 0.000000 0.636364 0.363636 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GT[GA][GC]TG[AG][TG][TG][GT][GA][GT][GT][TA][GAT][TG][TG]GA[AG][GT] -------------------------------------------------------------------------------- Time 31.19 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10150 9.18e-04 193_[+3(3.09e-06)]_265_\ [+1(3.53e-05)]_1 10229 6.13e-05 84_[+3(2.86e-06)]_113_\ [+1(2.63e-06)]_262 10446 1.09e-12 1_[+3(3.24e-07)]_354_[+1(1.12e-06)]_\ 77_[+2(4.42e-11)]_6 10453 3.31e-09 376_[+1(1.12e-06)]_77_\ [+2(4.42e-11)]_6 10942 6.72e-03 281_[+3(1.36e-06)]_198 11226 7.12e-02 389_[+1(4.31e-05)]_91 11287 4.56e-11 126_[+3(6.90e-06)]_200_\ [+1(2.56e-07)]_8_[+2(4.84e-10)]_104 11503 1.27e-05 186_[+3(5.22e-06)]_259_\ [+1(1.48e-07)]_14 11793 9.33e-02 299_[+2(6.59e-05)]_180 11975 8.56e-02 91_[+1(2.31e-05)]_389 12100 1.49e-03 278_[+3(1.91e-06)]_201 12103 3.94e-02 367_[+1(1.05e-05)]_113 1214 7.67e-05 33_[+1(4.91e-05)]_108_\ [+1(9.31e-09)]_319 12163 4.32e-02 338_[+1(1.99e-05)]_142 20605 2.01e-03 160_[+3(7.89e-07)]_319 23929 1.35e-04 96_[+3(1.04e-06)]_102_\ [+1(2.31e-05)]_261 24791 3.66e-06 16_[+3(3.22e-05)]_47_[+1(5.70e-06)]_\ 225_[+3(7.18e-07)]_119_[+2(4.66e-05)]_10 25278 1.34e-05 226_[+3(9.49e-07)]_178_\ [+1(2.38e-06)]_55 261312 9.36e-05 115_[+1(9.68e-06)]_224_\ [+3(1.04e-06)]_120 262941 9.60e-03 465_[+1(2.14e-06)]_15 264008 1.48e-01 150_[+1(4.04e-05)]_330 264396 4.53e-05 4_[+3(2.62e-07)]_133_[+1(1.99e-05)]_\ 322 3174 4.84e-04 212_[+3(4.32e-05)]_69_\ [+3(4.49e-08)]_177 3508 4.22e-04 223_[+3(1.32e-05)]_102_\ [+1(5.23e-05)]_103_[+1(3.55e-06)]_11 3553 4.02e-03 230_[+1(9.98e-07)]_250 6097 6.04e-02 270_[+1(4.60e-05)]_210 6678 3.98e-03 396_[+3(1.36e-06)]_83 6765 8.83e-01 500 7889 6.59e-03 376_[+1(1.84e-05)]_84_\ [+1(1.74e-06)] 8036 7.45e-06 62_[+3(5.60e-06)]_227_\ [+1(8.90e-07)]_170 9674 1.71e-01 500 bd1439 5.10e-19 103_[+1(1.81e-09)]_48_\ [+3(1.81e-09)]_71_[+2(1.12e-12)]_216 bd1823 4.43e-05 102_[+1(1.14e-05)]_91_\ [+3(6.90e-06)]_235_[+2(4.07e-05)]_10 bd635 1.33e-05 43_[+3(7.96e-05)]_35_[+3(6.57e-08)]_\ 327_[+1(4.04e-05)]_33 ThpsCp086 5.10e-19 168_[+1(1.81e-09)]_48_\ [+3(1.81e-09)]_71_[+2(1.12e-12)]_151 ThpsCp130 5.10e-19 102_[+1(1.81e-09)]_48_\ [+3(1.81e-09)]_71_[+2(1.12e-12)]_217 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************