AlignACE version 2.2 July 7, 1998 AlignACE -jQCR.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 YDR529C 300 bp YDR529C QCR7 1-384 ubiquinol-cytochrome c oxidoreductase subunit 7 (14 kDa) #2 YFR033C 300 bp YFR033C QCR6 1-444 ubiquinol-cytochrome c oxidoreductase subunit 6 (17 kDa) #3 YGR183C 424 bp YGR183C qcr9 1-3, 217-414 7.3 kDa subunit 9 of the ubiquinol cytochrome c oxidoreductase complex #4 YHR001W-A 457 bp YHR001W-A QCR10 1-6, 70-297 8.5 kDa subunit of the ubiqunol-cytochrome c oxidoreductase complex #5 YJL166W 361 bp YJL166W QCR8 1-285 Ubiquinol cytochrome-c reductase subunit 8 (11 kDa protein) #6 YPR191W 339 bp YPR191W QCR2 1-1107 40 kDa ubiquinol cytochrome-c reductase core protein 2 Motif number 1 ACTGCAATGCGGTTTCCCCAACAC 1 1 1 ACGCAGGGTT 0.957095 -300 TAGATGTGTAACTGCGCTGTGATCTTGTTTTGAC 1 97 1 ACGCGGGATC 0.930879 -204 TCGGGTCACCCCGGCGGGGGGCCTGACAATTTAC 1 155 1 CCGCGGGCCT 0.996579 -146 GACGGATGTACCGGCAGGCCGCCT 2 1 0 CCGCACGCCT 0.95088 -300 GTCCGATATGCCCGGAACGTGCTTCCCATTGGTG 2 66 0 CCGGAGGCTT 0.987148 -235 GGCATATCGGACTGGGGCGCGCCTCCCCTGCGCG 2 88 1 ACGGGGGCCT 0.988676 -213 GCGCGCCTCCCCTGCGCGGTGCTTGTTATAAGAG 2 104 1 CCGCGGGCTT 0.997184 -197 GGGCCACTTTCCAGCAAAGCGCCTCTTATAACAA 2 126 0 CCGCAGGCCT 0.994537 -175 AATAATAGGAAAAGCAACGACCTCATCTCTCGAA 5 246 1 AAGCAGCCTC 0.761267 -116 TTTTTCCTTCAATGCGATGAGCTTTTGAAAAATT 6 112 1 AAGCGGGCTT 0.977 -228 CGGATATAAGACGGGGCGGGCCTTCTATTGGTTC 6 162 0 ACGGGGCCTT 0.956935 -178 AAGGTTTTTAACAGCAGTGTGCTCGAACGATTAG 6 272 1 ACGCAGGCTC 0.990723 -68 ** *** * **** Masking position 4 Map Score: 12.7933 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 273 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 2 GATAAAAAGCGCGTCGCTCCTGATTGGTCA 1 127 0 GCGTCGCTCC 0.908516 -174 GCTTTTTATCGGGTCACCCCGGCGGGGGGC 1 147 1 GGGTCACCCC 0.971435 -154 GGACTGGGGCGCGCCTCCCCTGCGCGGTGC 2 96 1 GCGCCTCCCC 0.995992 -205 TTCCAGCAAAGCGCCTCTTATAACAAGCAC 2 122 0 GCGCCTCTTA 0.935714 -179 AACCCGGTGTGGGCCACTTTCCAGCAAAGC 2 140 0 GGGCCACTTT 0.852762 -161 GTGCAAATAAGCGCCAACCAATACTGCCCT 2 197 0 GCGCCAACCA 0.896487 -104 CTCAATCCTTGGGCCTTTCCCTAATGACAT 3 281 1 GGGCCTTTCC 0.984564 -144 AAGGAAACTTGAGCCACCCCCCAAATTTTA 5 209 1 GAGCCACCCC 0.974611 -153 AAGACGGGGCGGGCCTTCTATTGGTTCGTT 6 159 0 GGGCCTTCTA 0.904055 -181 TAAAGAACAAGGGCCTTTCCTCAGAGCGTT 6 217 1 GGGCCTTTCC 0.984564 -123 ********** Masking position 5 Map Score: 5.5947 Number of sites scoring better than the average of aligned sites = 686 Number in coding regions = 515 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 3 ACATTAACAGAAGCACACATATACACTTACACCTACACA 2 246 1 ACAATAACTA 0.803032 -55 TTACACCTACACACACGGATAAAGAAAAAGAAATAGAAA 2 272 1 ACAATAAAAA 0.980001 -29 TTTATAGTTGACATATTTGTATATAAAAACTTATACATT 3 31 1 ATAGTAAAAA 0.828063 -394 ATTGACTTTTATTTATTATTAACAAAGAAGTAATACCAA 3 89 1 ATATTAAAAA 0.764673 -336 TTTAATGTCCTGTCACGGATAGTCAATAATCGTTGAAGG 3 341 1 TCAATAAAAA 0.901916 -84 TAGGTGCATATTACACTGATATTAAATTACAGAGTGAGA 4 46 0 TCAATAAATA 0.839862 -412 CGCACTTGAAAACTATGTAAATATAAGTATATATTCAAA 4 189 0 ATAAAAAATA 0.879234 -269 CGTGATTTTGATCCAATTAAAACTAAATATGGTTCAACC 4 257 1 ACAAAAAATA 0.921158 -201 TTATTCCAGAAGATATCTATAACAAATTATGCATTCAAA 4 358 0 ATAATAAATA 0.945698 -100 ATTTTTTTTAAGCCAATGAAAATGAAGAAATGCGTGATC 5 149 1 ACAAAAAAAA 0.953456 -213 GTCGTACGTTAAATACAAATAATCAACAAAACACTACAC 5 317 1 ATAATAAAAA 0.968289 -45 AGAATTGCTGACACAGGAATAGGGAAAAATTTTTGTTGA 6 22 0 ACAATAAAAA 0.980001 -318 AGCCTACCAAATATATATATAAAGAACAAGGGCCTTTCC 6 198 1 ATAATAAAAA 0.968289 -142 GGAGAGTTAAAATTATTAAAAGGAAAAAAGAAGAACGTT 6 310 1 ATAAAAAAAA 0.927351 -30 * ** *** ** ** Masking position 11 Map Score: 6.45427 Number of sites scoring better than the average of aligned sites = 1646 Number in coding regions = 647 Number in noncoding regions = 999 Number of orfs with sites within 600 bp upstream = 637 Fraction of orfs with sites within 600 bp upstream = 0.102313 Motif number 4 CTACTCAGTCTTAAGGGCAGTATTGGTTGGC 2 184 1 TTAGGGCAGT 0.98703 -117 TAATGTCCTGTCACGGATAGTCAATAATCGT 3 343 1 TCAGGATAGT 0.948756 -82 ATGCACCTAGTTATGGGTAGTTTTTGCTAAC 4 76 1 TTAGGGTAGT 0.993618 -382 GTGGTGAAGATTGAGGACAGTTTCGCGGCTC 4 112 0 TTGGGACAGT 0.92259 -346 TCTTCAGTCATTAGAGGTAGTGGTGAAGATT 4 131 0 TTAAGGTAGT 0.968411 -327 GTTTTAAGTCTTATGGATTGTATTTATCGAT 4 429 0 TTAGGATTGT 0.925881 -29 TAGTATAAGCTTTAAGATAGTATCTCTCGAT 5 91 1 TTTAGATAGT 0.85102 -271 TGATCGGAAATTACGGGTAGTACGAGAAGGA 5 183 1 TTAGGGTAGT 0.993618 -179 TCGTAGAAGTTTTTGTGTAGTGTTTTGTTGA 5 339 0 TTTGTGTAGT 0.848196 -23 *** ******* Masking position 1 Map Score: 5.18556 Number of sites scoring better than the average of aligned sites = 455 Number in coding regions = 360 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 5 AAATTGTCCAACAACAACCTTTACTGCTATTTT 1 233 0 ACAACACTTA 0.841938 -68 AGCGCCAACCAATACTGCCCTTAAGACTGAGTA 2 185 0 AATACGCCTA 0.978503 -116 ACAAAGAAGTAATACCAACCTAATTACAAATAC 3 110 1 AATACACCTA 0.984599 -315 AAGGATATGAAAATCAACCTTCAACGATTATTG 3 364 0 AAATCACTTA 0.782322 -61 CAACAATAGCAATACGGACTAAA 3 412 1 AATACGCTAA 0.905055 -13 AACGTTAGCAAAAACTACCCATAACTAGGTGCA 4 77 0 AAAACACCAA 0.955414 -381 TACGAGCCGCGAAACTGTCCTCAATCTTCACCA 4 109 1 GAAACGCCTA 0.93631 -349 TTGCAATAGTAATACGCACTTGAAAACTATGTA 4 209 0 AATACCCTTA 0.899269 -249 TATATCGATAAATACAATCCATAAGACTTAAAA 4 426 1 AATACACCAA 0.962213 -32 CATAAGACTTAAAACTAACCTCA 4 445 1 AAAACACCTA 0.981751 -13 TAGATCGAGAGATACTATCTTAAAGCTTATACT 5 92 0 GATACACTTA 0.928058 -270 ***** * *** * Masking position 13 Map Score: 4.09976 Number of sites scoring better than the average of aligned sites = 730 Number in coding regions = 555 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 6 GGGTTTTCGAGATTAGGACCTACTCAGTCT 2 165 1 GATTAGGACC 0.991472 -136 CCCCGCGTTTGATTGGGTCGTGTATAATGA 3 214 0 GATTGGGTCG 0.981569 -211 TTTCAAACTAGATAAGGACCATGTATAAGA 5 39 1 GATAAGGACC 0.978734 -323 ATGTTCGAGAGATGAGGTCGTTGCTTTTCC 5 253 0 GATGAGGTCG 0.985785 -109 GTGCTCGAACGATTAGGACGGGAGAGTTAA 6 290 1 GATTAGGACG 0.994131 -50 ********** Masking position 3 Map Score: 2.41738 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 87 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 7 TCGCTCCTGATTGGTCAAAACAAGATCACAGCG 1 111 0 TTGTCAAAAA 0.986243 -190 TTCTGATAAATTGTCCAACAACAACCTTTACTG 1 240 0 TTGCCAAACA 0.94064 -61 TAGTTTTAATTGGATCAAAATCACGTGACAAAA 4 249 0 TGGTCAAACA 0.984104 -209 TCATTTTCATTGGCTTAAAAAAAATCCTTGGAC 5 141 0 TGGTTAAAAA 0.922699 -221 TTAATCGGACTTGCTCAAGTAAACAATGTTCGA 5 275 0 TTGTCAATAA 0.940808 -87 TTGGATCTTGCTCAACAAAAATTTTTCCCT 6 8 1 TTGTCAAAAA 0.987107 -332 AAAATAATTTTGGATCAAAATAATAATAGTGGA 6 81 0 TGGTCAAAAA 0.989235 -259 *** **** * ** Masking position 7 Map Score: 1.81322 Number of sites scoring better than the average of aligned sites = 421 Number in coding regions = 332 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 8 GTCACCTACAGCAGAACGTGAGCACGTGACCG 2 32 1 GAGACGTGAG 0.909439 -269 CTGCTAAGCTAAAGTTTGAGAGGGGATGTCAT 3 304 0 AAGTTGAGAG 0.973636 -121 TATAATTAAAATAGAATGAGAAGC 4 3 0 AAGATGAGAA 0.970329 -455 ATATTAAATTACAGAGTGAGAAATCGTACTAG 4 35 0 AAGATGAGAA 0.970329 -423 AGGTAGTGGTGAAGATTGAGGACAGTTTCGCG 4 116 0 GAGATGAGGA 0.892063 -342 GTATATATTCAAAGTGCGACAGCGTTATATCG 4 170 0 AAGTCGACAG 0.852676 -288 ACGTGGAACGGTAGATCGAGAGATACTATCTT 5 104 0 GAGACGAGAG 0.987505 -258 GAAATTACGGGTAGTACGAGAAGGAAACTTGA 5 189 1 GAGTCGAGAA 0.980222 -173 TCAAGTAAACAATGTTCGAGAGATGAGGTCGT 5 262 0 ATGTCGAGAG 0.862962 -100 ATAGTGGAAGAAATATTGAGAACAATAGAGAA 6 57 0 AATATGAGAA 0.720416 -283 GTTTGCTGACGAAGTTTTAGAAGTTAATAAGG 6 244 1 GAGTTTAGAA 0.744241 -96 * *** ****** Masking position 9 Map Score: 2.57618 Number of sites scoring better than the average of aligned sites = 1644 Number in coding regions = 1158 Number in noncoding regions = 486 Number of orfs with sites within 600 bp upstream = 364 Fraction of orfs with sites within 600 bp upstream = 0.0584645 Motif number 9 AACCAACAGAGTATCACTATTAAGGTCTAT 1 46 1 GTATCACTAT 0.972538 -255 TTGTTAATATGTATCATTATACACGACCCA 3 201 1 GTATCATTAT 0.957541 -224 TTTAGTCCGTATTGCTATTGTTGCTTTA 3 407 0 GTATTGCTAT 0.939822 -18 TTTCAAGTGCGTATTACTATTGCAAAGTAG 4 217 1 GTATTACTAT 0.976936 -241 GTTGCTTTTCCTATTATTATATGAATAAAA 5 234 0 CTATTATTAT 0.934175 -128 ATTTCTTCCACTATTATTATTTTGATCCAA 6 75 1 CTATTATTAT 0.934175 -265 ********** Masking position 4 Map Score: 1.60288 Number of sites scoring better than the average of aligned sites = 343 Number in coding regions = 213 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 10 CACATCTATAGACAATGTACATATGGCTAA 1 75 0 GACAATGTAC 0.979948 -226 CGGGGGGCCTGACAATTTACTTTCATAGAG 1 169 1 GACAATTTAC 0.983253 -132 GTTGTTGTTGGACAATTTATCAGAATATTA 1 248 1 GACAATTTAT 0.974238 -53 CAAAAAACCATACCATTTATCAAGGGGACG 4 310 1 TACCATTTAT 0.829105 -148 ACTAGATAAGGACCATGTATAAGAACTATA 5 45 1 GACCATGTAT 0.962957 -317 TTTAACGTACGACAACTTACTCTTAATCGG 5 300 0 GACAACTTAC 0.956032 -62 ********** Masking position 5 Map Score: 1.43372 Number of sites scoring better than the average of aligned sites = 209 Number in coding regions = 158 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 11 CAGGAGCGACGCGCTTTTTATCGGGTCACC 1 135 1 GCGCTTTTTA 0.943667 -166 CTAGCGAAGGCAACTTTTGAACTCCCCAGT 3 172 1 CAACTTTTGA 0.847752 -253 ATTGACTTCCCCGCGTTTGATTGGGTCGTG 3 222 0 CCGCGTTTGA 0.979132 -203 TATTCGACTTGCGCTTTTGCTGTGAAGATT 4 395 0 GCGCTTTTGC 0.98898 -63 TCAATGCGATGAGCTTTTGAAAAATTTCTG 6 120 1 GAGCTTTTGA 0.985686 -220 CCTTTCCTCAGAGCGTTTGCTGACGAAGTT 6 230 1 GAGCGTTTGC 0.979309 -110 ********** Masking position 6 Map Score: 0.821415 Number of sites scoring better than the average of aligned sites = 464 Number in coding regions = 359 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 12 ACACACACGGATAAAGAAAAAGAAATAGAA 2 280 1 ATAAAGAAAA 0.85722 -21 GTATAAGTTTTTATATACAAATATGTCAAC 3 37 0 TTATATACAA 0.765384 -388 TTTGTTAATAATAAATAAAAGTCAATCGAC 3 85 0 ATAAATAAAA 0.957624 -340 TGACAGGACATTAAATACAACTGCTAAGCT 3 326 0 TTAAATACAA 0.955456 -99 TCGTACTAGTATAATTAAAATAGAATGAGA 4 14 0 ATAATTAAAA 0.802012 -444 TAATATATCGATAAATACAATCCATAAGAC 4 423 1 ATAAATACAA 0.9728 -35 CTATTATTATATGAATAAAATTTGGGGGGT 5 224 0 ATGAATAAAA 0.857018 -138 TTGTCGTACGTTAAATACAAATAATCAACA 5 315 1 TTAAATACAA 0.955456 -47 ********** Masking position 7 Map Score: 1.8742 Number of sites scoring better than the average of aligned sites = 679 Number in coding regions = 268 Number in noncoding regions = 411 Number of orfs with sites within 600 bp upstream = 249 Fraction of orfs with sites within 600 bp upstream = 0.0399936 Motif number 13 AGTGATACTCTGTTGGTTTTTGGCCTGCTG 1 34 0 TGTTGGTTTT 0.959829 -267 TTTGTAATTAGGTTGGTATTACTTCTTTGT 3 110 0 GGTTGGTATT 0.974292 -315 AATCGTTGAAGGTTGATTTTCATATCCTTC 3 368 1 GGTTGATTTT 0.959829 -57 ACCTAGTTATGGGTAGTTTTTGCTAACGTT 4 80 1 GGGTAGTTTT 0.961435 -378 TGAGGTTAGTTTTAAGTCTTATG 4 445 0 GGTTAGTTTT 0.982251 -13 ********** Masking position 4 Map Score: 0.0206039 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 230 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 14 ********** No masking Map Score: -3.67107e-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 15 ********** No masking Map Score: -3.67107e-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