AlignACE version 2.2 July 7, 1998 AlignACE -jARP.orf -y -e Parameter values: expect = 10 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 YDL029W 300 bp YDL029W ARP2 1-22, 146-1299 actin-related protein #2 YDR106W 300 bp YDR106W ARP10 1-855 Actin-related protein #3 YHR129C 600 bp YHR129C ARP1 1-1155 Centractin #4 YJL081C 300 bp YJL081C ARP4 1-1470 54.8 kDa actin-related protein #5 YJR065C 300 bp YJR065C ARP3 1-1350 actin-related gene #6 YLR085C 300 bp YLR085C ARP6 1-1317 Actin-related protein #7 YMR033W 480 bp YMR033W ARP9 1-30, 117-1490 actin related protein, subunit of the chromatin remodeling Snf\/Swi complex #8 YNL059C 600 bp YNL059C ARP5 1-2268 Actin-related protein #9 YOR141C 469 bp YOR141C ARP8 1-2646 Actin-related protein #10 YPR034W 505 bp YPR034W ARP7 1-1434 actin related protein, subunit of the chromatin remodeling Snf\/Swi complex Motif number 1 ATTAGAACTAGAAGAAGAAGACGAAGAAGGA 1 16 1 GAAAAGAAGA 0.753685 -285 AGATTCTAACAAAAAAGAGAACTGTTTTTGA 2 166 0 AAAAAGAGAA 0.939019 -135 CGAGAGACATAAACAAAAGAGGTACAAATAC 2 221 1 AAAAAAAGAG 0.862362 -80 TAATTCCAAAGAATAAAAGAAATACCTGTTT 3 175 1 GAAAAAAGAA 0.949769 -426 AATACAAACGGAAAAAGAGAAGGCAATAGGA 3 381 0 GAAAAGAGAA 0.964911 -220 ACGAATTGAGGAATTAGAAAGAAAGTTAGCC 3 579 1 GAATAGAAAG 0.827793 -22 GAAACAGCGAGAAGAAAAAAAAGAAAACAAG 4 212 1 GAAAAAAAAA 0.952018 -89 GGGCCAAGAAGAACAAGAGAATTAATGCAAG 6 234 1 GAAAAGAGAA 0.964911 -67 TTTTCTGATAAAAGAAAAAAAGTATAATGTC 7 36 1 AAAAAAAAAA 0.917427 -445 TTGTTAAGTAGAAATAGAAAGATATACGCTG 7 73 1 GAATAGAAAG 0.827793 -408 TCATATTTTCAAAAAAAAAAAAAGTTTTCTT 7 167 1 AAAAAAAAAA 0.917427 -314 CAATATTGCGGAATTAGAAAAAATGTACCAC 7 419 1 GAATAGAAAA 0.890391 -62 ATAAAAACAGAAACAAAAAAGGCGTTTCTCG 9 261 0 AAAAAAAAAG 0.86798 -209 TAGAATTGAAGAAAAAAAAAAACTTGATAAA 10 117 1 GAAAAAAAAA 0.952018 -389 AAAAAATTTCAAACAAAAAAATTATCGCCTT 10 145 1 AAAAAAAAAA 0.917427 -361 GAGTGATCCTGAAAAAAAAAAATGATGGCCG 10 342 1 GAAAAAAAAA 0.952018 -164 CGTTTCGAAGAAAATAAAGAAAAAATAAAGC 10 373 1 AAATAAAGAA 0.748787 -133 AGCAAACCTCAAACAAGAAAACAAAGCGGAA 10 401 1 AAAAAGAAAA 0.94172 -105 GGAAAATGGTAAACAAGAGAGATAGAACAGA 10 428 1 AAAAAGAGAG 0.901108 -78 *** ******* Masking position 6 Map Score: 21.2749 Number of sites scoring better than the average of aligned sites = 5189 Number in coding regions = 1955 Number in noncoding regions = 3234 Number of orfs with sites within 600 bp upstream = 1945 Fraction of orfs with sites within 600 bp upstream = 0.3124 Motif number 2 GCAATGCCTCTAATTTCAAACAAGCAACATAA 3 84 1 TAATCAAACA 0.934379 -517 TATCGTCTGGTAATTCCAAAGAATAAAAGAAA 3 165 1 TAATCAAAGA 0.718954 -436 TGCACATCAATAATGATAAACACCTTTATTGA 3 458 1 TAATTAAACA 0.898712 -143 CCCTTTTCAAAAGTTTCAAACAAAAATATATG 5 213 1 AAGTCAAACA 0.957247 -88 GCATCACCTTAAACACTAACCACGTGCAACCA 6 72 0 AAACTAACCA 0.718658 -229 ATTGTGTCAAAAATGGTAAAGAAAACTTTTTT 7 184 0 AAATTAAAGA 0.844884 -297 GGTATCTACAAAATTCTAACCACAAGTACTGA 8 188 1 AAATTAACCA 0.897961 -413 ATCCGCGTATAAATATTAAACACTTTTGCCTT 8 246 1 AAATTAAACA 0.968069 -355 GAAACGAGATAAATGCTAAACGCTAATTATAG 8 441 0 AAATTAAACG 0.815586 -160 ATAGAGTGGTAAGTAACAAACAGAACAACAAT 9 68 1 AAGTCAAACA 0.957247 -402 AACGCCCACGAAGTAGCAAACACTTTCAGGTA 9 400 1 AAGTCAAACA 0.957247 -70 ACTTGATAAAAAATTTCAAACAAAAAAATTAT 10 138 1 AAATCAAACA 0.979861 -368 AAAATAAAGCAAACCTCAAACAAGAAAACAAA 10 394 1 AAACCAAACA 0.933874 -112 ACAAAGCGGAAAATGGTAAACAAGAGAGATAG 10 421 1 AAATTAAACA 0.968069 -85 **** ****** Masking position 8 Map Score: 8.91519 Number of sites scoring better than the average of aligned sites = 598 Number in coding regions = 400 Number in noncoding regions = 198 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 3 TTCATTTTTCCAGTTTATATTTCAATTTAA 3 49 1 CAGTTTATAT 0.915888 -552 CAACATAATACAGTATTTATTGATCAACGT 3 108 1 CAGTATTTAT 0.908242 -493 CCATGATAAACAGTGTTTATTATACCACGT 3 208 1 CAGTGTTTAT 0.973179 -393 TCTCCCACGGCAGCGTATATCTTTCTATTT 7 84 0 CAGCGTATAT 0.952397 -397 GACAGTTCTACTGTGTTTATATCATTAGAG 7 308 1 CTGTGTTTAT 0.968288 -173 CTGAGAACCGCTGCTTATATTGATTATTAT 8 527 0 CTGCTTATAT 0.895501 -74 TGTCTCCTTCCAGCTTTTATATCGCTTGAT 9 111 1 CAGCTTTTAT 0.94527 -359 TCACAGCACACTGCGTATATATAGGCTTAC 9 155 0 CTGCGTATAT 0.943935 -315 TTTTTTGTTTCTGTTTTTATAGCAGCAACT 9 272 1 CTGTTTTTAT 0.939545 -198 GATTGTATCCCTGTATTTATGTACTATTGA 9 441 0 CTGTATTTAT 0.892814 -29 CAAGAGAGAACAGTGATTATAAGGAAAGAA 10 206 1 CAGTGATTAT 0.821758 -300 ********** Masking position 9 Map Score: 8.07332 Number of sites scoring better than the average of aligned sites = 410 Number in coding regions = 226 Number in noncoding regions = 184 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 4 CTCAAATTGTTTTTCGCCTTTCAATTCTACAAG 1 185 0 TTTCCCTTCA 0.994755 -116 AAAGTGGCCATTTTCGCGATGCACATCAATAAT 3 439 1 TTTCCGATCA 0.943228 -162 CCCTTCTATATTGTCACCTTCCATTTATGAAGA 8 287 0 TTTCCCTTCA 0.994755 -314 CGTTTAGCATTTATCTCGTTTCGTAGACTATGA 8 451 1 TTTCCGTTCG 0.960975 -150 TAGGGGAAACTTGTCTCCTTCCAGCTTTTATAT 9 100 1 TTTCCCTTCA 0.994755 -370 AACAAAAAAATTATCGCCTTACACGGAAACGAA 10 156 1 TTTCCCTTCA 0.994755 -350 TCGGCAAGTCTTCACACCTTTCAATACTTAGAC 10 298 1 TTACCCTTCA 0.975231 -208 ** ** **** ** Masking position 10 Map Score: 6.36093 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 26 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 TGATGGGTATTTTGATATGAAGTAAATCTGT 2 97 1 TTTGATAGAA 0.767037 -204 AAATCTGTTGTTTGATTATAAACTTCGTTTT 2 120 1 TTTGATTTAA 0.628408 -181 CAGTTCTCTTTTTTGTTAGAATCTAATTGTC 2 173 1 TTTTGTTGAA 0.898586 -128 TTGATCAACGTTTGATTAGAAGTTGAATTTT 3 127 1 TTTGATTGAA 0.910243 -474 TACTGTGTCCTTTGCTTTGAGCTCTTGTTCA 3 330 0 TTTGCTTGAG 0.963279 -271 GAAATGAACTTTTTCTTGAAAAGATTAATAC 3 407 0 TTTTCTTAAA 0.766756 -194 TTACATTAGTTTTTCTTTGAAAAGTTCCCAT 4 127 1 TTTTCTTGAA 0.965876 -174 AGACTCTTTTTTTGCCTAAAATCCTTGGTTT 4 252 0 TTTGCCTAAA 0.580432 -49 TCTCATATATTTTTGTTTGAAACTTTTGAAA 5 217 0 TTTTGTTGAA 0.898591 -84 AAAACTTTTTTTTTTTTTGAAAATATGAAGG 7 164 0 TTTTTTTGAA 0.690427 -317 AATGTTGAAATTTGCTTTTAGCCACTGCGCG 7 365 0 TTTGCTTTAG 0.81363 -116 ATTAAACACTTTTGCCTTGAAGTGCTGTCTT 8 260 1 TTTGCCTGAA 0.922599 -341 CAATGAACAGTTTGCTAAGAGCAATGACAAT 8 358 1 TTTGCTAGAG 0.894675 -243 GCAAAAGAAATTTTCTATGAAATCGAACGTA 9 36 1 TTTTCTAGAA 0.90163 -434 GCGATAATTTTTTTGTTTGAAATTTTTTATC 10 142 0 TTTTGTTGAA 0.898591 -364 TTTTTCTTTATTTTCTTCGAAACGCGGCCAT 10 366 0 TTTTCTTGAA 0.965867 -140 TTCTCGCGCTTTTGCTAATAGCCTACTACTC 10 457 0 TTTGCTATAG 0.585695 -49 ******* *** Masking position 3 Map Score: 7.70083 Number of sites scoring better than the average of aligned sites = 2591 Number in coding regions = 1919 Number in noncoding regions = 672 Number of orfs with sites within 600 bp upstream = 521 Fraction of orfs with sites within 600 bp upstream = 0.0836813 Motif number 6 CTTGCTTCTTAAGTTCATCGTAGACCTTCTTACT 1 56 0 AAGCACGAGA 0.948643 -245 CTACAGAAAAAAGCTCATAAAAGAATGCTAAGTA 3 285 1 AAGCAAAAGA 0.947168 -316 GCTCAAAGCAAAGGACACAGTACACCTGTGTGAC 3 339 1 AAGCAAGACA 0.963869 -262 GGAAAAAGAGAAGGCAATAGGAAACTCACCGTCA 3 369 0 AAGAAAGAAA 0.881363 -232 AATAATAGCGAAGCAAATAGCAGATATTCCCAAT 3 489 1 AAGAAAGAGA 0.979684 -112 AAATTAATAAAAGGGCATAGACCAAGGAGTACAT 3 531 1 AAGCAAGCCA 0.783528 -70 TTTGAAGTTGAAGTAACACGAACATAAGAAATGG 4 168 1 AAGACCGACA 0.806361 -133 CCAAGGATTTTAGGCAAAAAAAGAGTCTTCGTTA 4 255 1 TAGAAAAAGA 0.747115 -46 GTCATTGGTAAAGTGAAACATACATCAACCGGCT 5 71 0 AAGAACAACA 0.801654 -230 CATTGAGCAAAAGACAAAAGCGGAAGTCCGCCCA 6 11 0 AAGAAAGGGA 0.867422 -290 GAATTAATGCAAGACCAAAGGAGAAGAAGCGCAG 6 252 1 AAGCAAGAGA 0.979269 -49 AAGTAGTTCAAAGATCACAACAGAATTTTATCTT 8 23 0 AAGCAAAAGA 0.947168 -578 ATAGAGTGGTAAGTAACAAACAGAACAACAATTA 9 68 1 AAGACAAAGA 0.877401 -402 GGTAAATTACTAGTCAATAGTACATAAATACAGG 9 428 1 TAGAAAGACA 0.814681 -42 TAAGCAAGAGACGAGCAGAAAGGAACTAT 10 6 1 AAGACAGAGA 0.949639 -500 GTTAGAATTGAAGAAAAAAAAAAACTTGATAAAA 10 115 1 AAGAAAAAAA 0.738189 -391 *** ** ** *** Masking position 2 Map Score: 7.029 Number of sites scoring better than the average of aligned sites = 2390 Number in coding regions = 1519 Number in noncoding regions = 871 Number of orfs with sites within 600 bp upstream = 725 Fraction of orfs with sites within 600 bp upstream = 0.116447 Motif number 7 AATATAAACTGGAAAAATGAAGCGAAAATAA 3 39 0 GGAAAATGAA 0.972941 -562 TTTGTTAAATTGAAATATAAACTGGAAAAAT 3 52 0 TGAAAATAAA 0.517375 -549 AAAAAGAGAAGGCAATAGGAAACTCACCGTC 3 370 0 GGCAAAGGAA 0.70318 -231 ACTTTTTCTTGAAAAGATTAATACAAACGGA 3 400 0 GAAAAATTAA 0.744 -201 TCTGATAAAAGAAAAAAAGTATAATGTCAGA 7 39 1 GAAAAAAGTA 0.748149 -442 TTTTTTTTTTGAAAATATGAAGGAAAGACGT 7 156 0 GAAAAATGAA 0.962998 -325 GCCACTGCGCGGAAATATGTAGTATTCGTAA 7 345 0 GGAAAATGTA 0.920279 -136 TGCGGAATTAGAAAAAATGTACCACGCGAAG 7 425 1 GAAAAATGTA 0.89311 -56 ATGGTAATTGGAAAGATAAAATTCTGTTGT 8 10 1 GGAAAATAAA 0.942115 -591 ATTTGAGAATGGCAATATGAATAAATGGAGA 9 364 1 GGCAAATGAA 0.919092 -106 TAGAATTGAAGAAAAAAAAAAACTTGATAAA 10 117 1 GAAAAAAAAA 0.807257 -389 GAGTGATCCTGAAAAAAAAAAATGATGGCCG 10 342 1 GAAAAAAAAA 0.807257 -164 AGAAAATAAAGAAAAAATAAAGCAAACCTCA 10 381 1 GAAAAATAAA 0.921754 -125 ***** ***** Masking position 5 Map Score: 3.73297 Number of sites scoring better than the average of aligned sites = 2291 Number in coding regions = 1279 Number in noncoding regions = 1012 Number of orfs with sites within 600 bp upstream = 768 Fraction of orfs with sites within 600 bp upstream = 0.123354 Motif number 8 AAGACGAAGAAGGAAATGTAATGAGTAAGAAGGTCTA 1 33 1 AAAATTAAAA 0.745332 -268 CTATCTATCAAACAAATATACATATCACAGAGAGATT 1 101 0 AAAATTACAA 0.967589 -200 GGACGTGAAAGTTAAATATACGTACCAGAAGACAAAT 1 240 1 GAAATTACAA 0.861609 -61 ATAATCAAACAACAGATTTACTTCATATCAAAATACC 2 102 0 AAGATTACCA 0.935852 -199 GAAATGATAAAAAAAATCTACCCAGGAAACCCTATGA 2 270 1 AAAATTACAA 0.967589 -31 CGAAGCAAATAGCAGATATTCCCAATAAAACAGCAAA 3 497 1 AAGATTTCAA 0.907777 -104 AAAAAAGAAAACAAGATGTACAGAAAACCAAGGATTT 4 228 1 AAGATTACAA 0.985907 -73 TTTGGACGCAATAAGATATACATATTATTTAATGTGC 7 265 1 AAGATTACAA 0.985907 -216 CACGGAAACGAATAGATTTACTTATTACACAAGAGAG 10 177 1 AAGATTACAA 0.985907 -329 TAAGGAAAGAAAGAGATATATACAATATTTCCATCAA 10 225 1 AAGATTATAA 0.872741 -281 * **** *** * * Masking position 9 Map Score: 2.09589 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 144 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 9 TATTATGTTGCTTGTTTGAAATTAGAGGCA 3 88 0 CTTGTTTGAA 0.849136 -513 TGATAAACACCTTTATTGAATAATAGCGAA 3 471 1 CTTTATTGAA 0.888363 -130 AAGCCAAAATCTATATTGAAAAAAATTGGT 4 39 0 CTATATTGAA 0.948165 -262 TGTAATCTAACTATTTTAAAAACGTACACA 4 102 0 CTATTTTAAA 0.845059 -199 CCATTTAAAGCTATTTTGAAGTTGAAGTAA 4 154 1 CTATTTTGAA 0.97677 -147 GGGGTTCTCGCCATTTTGAAGCCGCGGACA 5 186 0 CCATTTTGAA 0.965864 -115 TCTTCTTGGCCCATTTTGAAATGCATTTGT 6 216 0 CCATTTTGAA 0.965864 -85 ********** Masking position 9 Map Score: 0.707842 Number of sites scoring better than the average of aligned sites = 466 Number in coding regions = 337 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 10 ********** No masking Map Score: -5.04242e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 11 TTTGATAGATAGCAGTTGTATGTATTTATACTATTC 1 126 1 ACATGATTAT 0.983258 -175 GTAATAAACTAACAAAACTATATAATAATA 1 281 1 ACAACATTAT 0.941363 -20 TTCGTGGTATAGCATTAGCATGTACTCCTTGGTCTA 3 548 0 ACAAGATTAT 0.968689 -53 ACCACGTGCAACCAACAGAATATATTTGATGTCTGA 6 50 0 ACAAGATTAT 0.96892 -251 TAGTATTCGTAACAAGTGACTCTAATGATATAAACA 7 321 0 ACATGCTTAT 0.932823 -160 GTACGGAAAGATCACATGTATATATTTAACAAAGAA 8 98 0 ACATGATTAT 0.982221 -503 ATAGGCTTACCACAGTTGGATTTAATCAAGCGATAT 9 129 0 CCATGATTAT 0.932722 -341 GTGGGCGTTCATCATCTCCATTTATTCATATTGCCA 9 373 0 ACATCATTAT 0.96691 -97 ACTCAAGGTGAACAAGTCTAAGTATTGAAAGGTGTG 10 310 0 ACATCAATAT 0.828389 -196 * ** ** ** ** * Masking position 4 Map Score: 1.20414 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 105 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 12 ********** No masking Map Score: -5.04242e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 13 ********** No masking Map Score: -5.04242e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 14 ********** No masking Map Score: -5.04242e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0