AlignACE version 2.2 July 7, 1998 AlignACE -jKAR.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 YCL055W 569 bp YCL055W KAR4 1-1008 May assist Ste12p in pheromone-dependent expression of KAR3 and CIK1 #2 YJL034W 325 bp YJL034W KAR2 1-2049 Homologue of mammalian BiP (GPR78) protein\; member of the HSP70 gene family #3 YMR065W 300 bp YMR065W KAR5 1-1515 appears to be required for the completion of nuclear membrane fusion and may play a role in the organization of the membrane fusion complex #4 YNL188W 419 bp YNL188W kar1 1-1302 involved in spindle pole body duplication and karyogamy, interacts with Cdc31p, localizes to the spindle pole body #5 YPL269W 300 bp YPL269W KAR9 1-1935 Cortical protein required for cytoplasmic microtubule orientation\; localizes to the tip of shmoo projections and to the tip of budding cells in a cell-cycle dependent manner #6 YPR141C 300 bp YPR141C kar3 1-2190 kinesin-like nuclear fusion protein Motif number 1 GTAAAGGAAGAAGAAAAGAAAGTTGA 1 7 0 AAGAAAAGAA 0.866167 -563 GGAGATGAATAAAAGTAAAGGAAGAAGAAA 1 21 0 AAAAGTAAAG 0.85862 -549 AAGAAGCAATAAGAGCAAAGGGGCGAAATG 1 131 1 AAGAGCAAAG 0.847229 -439 TGCTTTGCAAAAGGGTAAAACAGCGTTTAC 1 262 1 AAGGGTAAAA 0.875396 -308 TAGGATAGCCAAAAGTAAAAAAAAAAAAAA 1 294 1 AAAAGTAAAA 0.935439 -276 AAGTAAAAAAAAAAAAAAAAAAAAAAAGAA 1 306 1 AAAAAAAAAA 0.930303 -264 AAAAAAAAAAAAAAAAAGAAGGAAGTTAGT 1 316 1 AAAAAAAGAA 0.800535 -254 TATGTCCAGCAAAACTAAAATTGTTTGAGC 1 351 0 AAAACTAAAA 0.794847 -219 CAGCCATTATAAAACAAAAGAGAAGTGAGA 1 539 1 AAAACAAAAG 0.760084 -31 GGGACTTTAAAAAAGTAAAACAGTAACACG 2 267 0 AAAAGTAAAA 0.935439 -59 GAGTAGTCTCAAGGGAAAAAGCGTATCAAA 2 300 1 AAGGGAAAAA 0.931999 -26 TATATACATTAAAAGAAAAACTTAAAAATA 4 76 0 AAAAGAAAAA 0.965831 -344 TGCGAATTAAAAGATTAGAATTTCTTATAT 4 101 0 AAGATTAGAA 0.693813 -319 ACTTCTATAAAAGGGAAAAACCCCAGAGAA 4 170 0 AAGGGAAAAA 0.931999 -250 CGCCAAAAATAAGAAAAAAATTGGAAAGAC 4 261 1 AAGAAAAAAA 0.955604 -159 GGAAAGACACAAGAAAAAAGTAAGAATATC 4 283 1 AAGAAAAAAG 0.90022 -137 CGTTTCTTCGAAAATAAAAATACGCCTGTT 4 329 0 AAAATAAAAA 0.901158 -91 TCAAAAAAGAAAGATAAAAATGCCTATGCT 4 392 0 AAGATAAAAA 0.936315 -28 AAAATTTTGAAAGAAAAAAA 6 1 0 AAGAAAAAAA 0.955604 -300 AATCTCAAACAAAATCAAAACAAACACTGT 6 64 1 AAAATCAAAA 0.725756 -237 ********** Masking position 7 Map Score: 18.6372 Number of sites scoring better than the average of aligned sites = 15898 Number in coding regions = 3953 Number in noncoding regions = 11945 Number of orfs with sites within 600 bp upstream = 2956 Fraction of orfs with sites within 600 bp upstream = 0.474783 Motif number 2 CGCGGGAAATGATTTCAATGTTCGACTCTGA 1 66 0 GTTTCAATGT 0.868583 -504 TGCAACTTTCTATTTTAATAGAACCTTCTGG 2 111 1 TTTTTAATAG 0.876442 -215 ACTGTTTTACTTTTTTAAAGTCCCCAAGAGT 2 273 1 TTTTTAAAGT 0.907309 -53 ATGCTGCCTTTTTTTTAATATAGACGATTTA 3 66 0 TTTTTAATAT 0.96067 -235 TCAAAGTTTTTGAATAGAAACAGTTGT 3 284 0 TTTTGAATAG 0.800572 -17 TTTAAGTTTTTCTTTTAATGTATATAAGAAA 4 80 1 TTTTTAATGT 0.971209 -340 CGCACAATAGTATTTTCATGTACTAGTTCGT 4 127 1 TTTTTCATGT 0.831228 -293 TATTGCTGGGTTTTTTAATCTATTTTGCGGA 4 227 1 TTTTTAATCT 0.866487 -193 GTTCGACAGATTTTTCAATATCATCTGAATT 5 12 0 TTTTCAATAT 0.97036 -289 ATATAGTATATATTTAAATGTGCGAGATAAG 5 127 0 TTTTAAATGT 0.875144 -174 ACTTTGTTATTGTTTCAATGTTATTTGTTTA 5 221 0 TTTTCAATGT 0.978393 -80 TTTTTTTCTTTCAAAATTTTCCAATAA 6 7 1 TTTTCAAAAT 0.902689 -294 CTTATTATTCTATTTGAATATACCAGAACAA 6 205 1 TTTTGAATAT 0.932602 -96 CTAAGTCCTTTATTTCAAAATCTACCTTTTT 6 256 0 TTTTCAAAAT 0.90555 -45 * ********* Masking position 8 Map Score: 9.66665 Number of sites scoring better than the average of aligned sites = 1351 Number in coding regions = 864 Number in noncoding regions = 487 Number of orfs with sites within 600 bp upstream = 320 Fraction of orfs with sites within 600 bp upstream = 0.0513974 Motif number 3 GTTATGTCGCAAGATGAAACTCGGAAATGACG 1 447 0 AAATGAACTC 0.838956 -123 CTTAATAGTATTCTCACTTCTCTTT 1 555 0 AAAGTATCTC 0.988378 -15 CGGTAAAAACTAGAGGACTCACACT 2 4 0 TAAGGATCAC 0.893092 -322 AAAGGACACGAAAAGGGTTCTCTGGAAGATAT 2 206 1 AAAGGGTCTC 0.975133 -120 TAAAGTCCCCAAGAGTAGTCTCAAGGGAAAAA 2 288 1 AAAGTATCTC 0.986481 -38 TAATTCGCACAATAGTATTTTCATGTACTAGT 4 122 1 AAAGTATTTC 0.94384 -298 TACTAGTTCGTACAGTATTCTCTTTCTCTGGG 4 147 1 TAAGTATCTC 0.96423 -273 ATGCCAAATAAAAAGGATTTTCATTACCCGAA 5 171 1 AAAGGATTTC 0.970617 -130 GAGATACACCAAAATGAATCTCAAACAAAATC 6 48 1 AAATGATCTC 0.970526 -253 ** **** **** Masking position 4 Map Score: 5.61285 Number of sites scoring better than the average of aligned sites = 619 Number in coding regions = 460 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 4 TTAATGCCTTAAGTCAAAAAATAGTTTTTGG 1 212 1 AGTCAAAAAA 0.972057 -358 CACAAGATATATCCCAAAAACTATTTTTTGA 1 225 0 ACCCAAAAAC 0.928616 -345 GGATAGCCAAAAGTAAAAAAAAAAAAAAAAA 1 296 1 AGTAAAAAAA 0.85742 -274 GTTAGTATCGAGCTCAAACAATTTTAGTTTT 1 340 1 ACTCAAACAA 0.976953 -230 TTCAGGATTAATCCCAAACAATTATGATAAA 3 192 0 ACCCAAACAA 0.97869 -109 TTTGCGGAAGACGCCAAAAATAAGAAAAAAA 4 250 1 AGCCAAAAAT 0.855934 -170 TCATGAACTCAAAAAAGAAAGATAAA 4 404 0 ACTCAAAAAA 0.980913 -16 ATACTGTTAAATGCCAAATAAAAAGGATTTT 5 161 1 AGCCAAATAA 0.886678 -140 ACCAAAATGAATCTCAAACAAAATCAAAACA 6 55 1 ACTCAAACAA 0.976953 -246 TGAGTATTACAGCTAAAAAAATTATCGAATA 6 130 1 ACTAAAAAAA 0.898827 -171 * ********* Masking position 6 Map Score: 6.75651 Number of sites scoring better than the average of aligned sites = 882 Number in coding regions = 609 Number in noncoding regions = 273 Number of orfs with sites within 600 bp upstream = 222 Fraction of orfs with sites within 600 bp upstream = 0.0356569 Motif number 5 TCAACTTTCTTTTCTTCTTCCTTTACTTTTATTCATCT 1 7 1 TTTCTTTTCT 0.87673 -563 TTGAGCTCGATACTAACTTCCTTCTTTTTTTTTTTTTTTTTT 1 315 0 TTCCTTTTTT 0.887339 -255 ACAATTTTAGTTTTGCTGGACATATTTTCAGTTTCATTACTG 1 357 1 TTTCATTTAT 0.948128 -213 TCATTACTGTATATTTGCAGCTTGGTTTTTGTCGCTCTGTAG 1 390 1 ATGCTTTTTT 0.811758 -180 TGCAGTGAGTTGCTCTTATGCTGCCTTTTTTTTAATATAGAC 3 72 0 TTTCTTTTTT 0.974205 -229 ACAGTACGTATTCTTATTTACATTGTTTATTTGCGTGGAATG 3 126 0 TTTCATTTTT 0.987891 -175 TGTTTGGGATTAATCCTGAACAAATTTTCTATATATAAACAC 3 203 1 TTTCATTTTT 0.987891 -98 ACTTCATTGGTATTCCGAACCAGTGTTTATATATAGAAAATT 3 225 0 TTGCATTTTT 0.978544 -76 TAAATCTTCATTATCTGATCCATTATTTTTAAGTTTTTCTTT 4 53 1 TTGCATTTTA 0.829159 -367 ACTTTTTTCTTGTGTCTTTCCAATTTTTTTCTTATTTTTGGC 4 262 0 TGTCATTTTT 0.927887 -158 GAGGCGCATCAAATTGTAAACAGTGTTTGTTTTGATTTTGTT 6 71 0 ATTCATTTTT 0.943382 -230 TTAGCTGTAATACTCATCATCATATTTTGATTCGAGGCGCAT 6 104 0 TTTCATTTAT 0.948128 -197 AGTTTAATAGTTGCCAGAATTTCTCTAAGTCCTTTA 6 275 0 TTTCATTTTT 0.987891 -26 * * * ** *** * * Masking position 16 Map Score: 6.34197 Number of sites scoring better than the average of aligned sites = 1266 Number in coding regions = 599 Number in noncoding regions = 667 Number of orfs with sites within 600 bp upstream = 500 Fraction of orfs with sites within 600 bp upstream = 0.0803084 Motif number 6 ATTGAAATCATTTCCCGCGAATTTTTCGATTATA 1 78 1 TTTCCGGTTT 0.990256 -492 GTTTTACCCTTTTGCAAAGCATTTGATCACAAGA 1 249 0 TTTGCAGTTT 0.88604 -321 CAATTTTAGTTTTGCTGGACATATTTTCAGTTTC 1 358 1 TTTGCGATAT 0.802048 -212 TTTTGCTATGTTAGCTGCAACTTTCTATTTTAAT 2 96 1 TTAGCGATTT 0.801976 -230 CCGGGTGAAATTTCCAGAAGGTTCTATTAAAATA 2 121 0 TTTCCGATTC 0.849103 -205 GAGTTGCTCTTATGCTGCCTTTTTTTTAATATAG 3 74 0 TATGCGCTTT 0.859114 -227 CGCAATTCCCTTTGCAGTGAGTTGCTCTTATGCT 3 92 0 TTTGCGGTTG 0.952973 -209 GTATTCTCTTTCTCTGGGGTTTTTCCCTTTTATA 4 161 1 TCTCTGGTTT 0.808408 -259 TTATATATGTATTGCTGGGTTTTTTAATCTATTT 4 218 1 ATTGCGGTTT 0.926264 -202 TTCTTACTTTTTTCTTGTGTCTTTCCAATTTTTT 4 275 0 TTTCTGGTTT 0.952902 -145 ATTAGCCTCCTTTGCCGCGTCTTTCAGGAGATGT 5 41 0 TTTGCGGTTT 0.991599 -260 TACCCATTCTTATCTCGCACATTTAAATATATAC 5 119 1 TATCTGATTT 0.698807 -182 CCAGAACAACTATCCGGAGTCTTTGTTTAAAAAA 6 227 1 TATCCGGTTT 0.973068 -74 ***** * * *** Masking position 12 Map Score: 2.99661 Number of sites scoring better than the average of aligned sites = 2063 Number in coding regions = 1455 Number in noncoding regions = 608 Number of orfs with sites within 600 bp upstream = 509 Fraction of orfs with sites within 600 bp upstream = 0.0817539 Motif number 7 AAAGCCAAAGTATGGGACAAGCATTTCGCCCCTTT 1 147 0 TTGGAAGCAT 0.960906 -423 TTGGCTATCCTATTGTAAACGCTGTTTTACCCTTT 1 271 0 TTTTAAGCTT 0.97751 -299 TTCTCTTTTGTTTTATAATGGCTGTTCTACTTTCT 1 528 0 TTTTATGCTT 0.932134 -42 AAAAGCAACTTTTTCGACACGCTGTCCAGTTCCTC 2 165 0 TTTGAAGCTT 0.988425 -161 GGTATGTTTGATACGCTTTTTCCCTTGAG 2 307 0 TTTGAAGCTT 0.988425 -19 CATCGAGAAATATTTGAATTGCACTGAACGAGAAG 3 20 1 TTTGATGCAT 0.9708 -281 GTTCTATAGTTGTTATATATGTATTGCTGGGTTTT 4 206 1 TTTTAAGTAT 0.839991 -214 GTTTTGATTTTGTTTGAGATTCATTTTGGTGTATC 6 50 0 TTTGAATCAT 0.911614 -251 AATTATCGAATATTATATAAGCATTAAAGCTATCA 6 149 1 TTTTAAGCAT 0.981667 -152 * ** ** * *** * Masking position 7 Map Score: 3.18321 Number of sites scoring better than the average of aligned sites = 502 Number in coding regions = 353 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 8 TAAAGGAAGAAGAAAAGAAAGTTGA 1 6 0 AGAAAAGAAA 0.822329 -564 TTCGACTCTGAGGTAAGAAGTAAAGAGGAG 1 47 0 AGGTAAGAAG 0.896369 -523 GGATAGCCAAAAGTAAAAAAAAAAAAAAAA 1 296 1 AAGTAAAAAA 0.790179 -274 AAAAAAAAAAAAAAAAGAAGGAAGTTAGTA 1 317 1 AAAAAAGAAG 0.88321 -253 AACAAAAGAGAAGTGAGAATACTATTAAG 1 551 1 AAGTGAGAAT 0.718304 -19 TAAACAATGTAAATAAGAATACGTACTGTA 3 139 1 AAATAAGAAT 0.963454 -162 CTTTTAATGTATATAAGAAATTCTAATCTT 4 91 1 ATATAAGAAA 0.799216 -329 AAGACGCCAAAAATAAGAAAAAAATTGGAA 4 257 1 AAATAAGAAA 0.969066 -163 CACAAGAAAAAAGTAAGAATATCCACAGCT 4 290 1 AAGTAAGAAT 0.945889 -130 GTTTCTTCGAAAATAAAAATACGCCTGTTA 4 328 0 AAATAAAAAT 0.826973 -92 TCATGAACTCAAAAAAGAAAGATAAAAATG 4 400 0 AAAAAAGAAA 0.901655 -20 TAAATGTGCGAGATAAGAATGGGTATATGC 5 114 0 AGATAAGAAT 0.930111 -187 GTTAAATGCCAAATAAAAAGGATTTTCATT 5 166 1 AAATAAAAAG 0.824089 -135 TCAAATAGAATAATAAGAAACACAAAGAGC 6 192 0 TAATAAGAAA 0.7551 -109 ********** Masking position 6 Map Score: 8.31421 Number of sites scoring better than the average of aligned sites = 3187 Number in coding regions = 1414 Number in noncoding regions = 1773 Number of orfs with sites within 600 bp upstream = 1246 Fraction of orfs with sites within 600 bp upstream = 0.200128 Motif number 9 TCGCCCCTTTGCTCTTATTGCTTCTTGTTA 1 127 0 GCTCTTATTG 0.987632 -443 AGGAGATAAGGCTCCTAATGTCACATCCAA 1 181 0 GCTCCTAATG 0.972953 -389 AGCCTTATCTCCTCTTAATGCCTTAAGTCA 1 198 1 CCTCTTAATG 0.982084 -372 TCTCCATTACCCTCTTATTGGAAAATTTTG 6 22 0 CCTCTTATTG 0.982085 -279 CAATTTTTCCGCTCTTTGTGTTTCTTATTA 6 182 1 GCTCTTTGTG 0.953271 -119 ********** Masking position 6 Map Score: 0.958506 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 71 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 10 ********** No masking Map Score: 1.64379e-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 CGAAAAATTCGCGGGAAATGATTTCAATGT 1 76 0 GCGGGAAATG 0.983452 -494 GTTAAGTAGAAAGGGTAATTATAATCGAAA 1 101 0 AAGGGTAATT 0.883376 -469 ACTCACTGCAAAGGGAATTGCGCATTCCAC 3 104 1 AAGGGAATTG 0.866627 -197 TTGTTTATTTGCGTGGAATGCGCAATTCCC 3 116 0 GCGTGGAATG 0.931632 -185 AAGTATCGATTCGGGTAATGAAAATCCTTT 5 182 0 TCGGGTAATG 0.965409 -119 AACAATAACAAAGTGTAATGTGGCCGCACG 5 238 1 AAGTGTAATG 0.940934 -63 TTTCCAATAAGAGGGTAATGGAGATACACC 6 28 1 GAGGGTAATG 0.989227 -273 ********** Masking position 7 Map Score: 0.178534 Number of sites scoring better than the average of aligned sites = 495 Number in coding regions = 295 Number in noncoding regions = 200 Number of orfs with sites within 600 bp upstream = 188 Fraction of orfs with sites within 600 bp upstream = 0.030196 Motif number 12 ********** No masking Map Score: 1.64379e-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: 1.64379e-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: 1.64379e-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