AlignACE version 2.2 July 7, 1998 AlignACE -jTIM.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 YDL217C 390 bp YDL217C TIM22 1-624 Mitochondrial inner membrane protein involved in import of proteins of the ADP\/ATP carrier (AAC) family #2 YDR322C-A 300 bp YDR322C-A TIM11 1-291 subunit e of mitochondrial F1F0-ATPase #3 YEL020W-A 300 bp YEL020W-A TIM9 1-264 Translocase in inner membrane of mitochondria involved in mitochondrial protein import #4 YIL022W 600 bp YIL022W TIM44 1-1296 48.8 kDa protein involved in mitochondrial protein import #5 YJL143W 427 bp YJL143W TIM17 1-477 16.5 kDa inner membrane protein required for import of mitochondrial precursor proteins #6 YJL054W 300 bp YJL054W TIM54 1-1437 Translocase for the insertion of proteins into the mitochondrial inner membrane. Motif number 1 ATCAAGAAATTGTGATTTTAAATACTTTATACGAAG 1 365 1 TTGATTTTTT 0.704749 -26 TAAGGGTATAAATTTTTCTTTAGTTTTTTTGACTTTTCAC 2 197 1 ATTTTTTTTT 0.8345 -104 ATATAATACTTCCTTTTATCTAAAATTTCTGTGTGAAAAG 2 229 0 TCTTTTTTTT 0.976786 -72 TCTTTCCAATTTTTTTTTTTTCGTCATTATAGAAATCATT 3 164 0 TTTTTTTTTT 0.980854 -137 TACAGTCCTGTCTTATTGTTCTTGATTTGTGCCCCGTAAA 3 268 0 TTTATTTTTT 0.898902 -33 GTTCAGATATTTCGTTTCTGAATTTCTTCTAATACACAAT 4 66 0 TCGTTTTTTT 0.918673 -535 CCTACTTTAGTATTTTTATATGATAACTTTTTGAGTTGTA 4 109 1 TTTTTTTCTT 0.889872 -492 TTGAGTTGTATCCTTTTCTTCATTTATTTTTAGAAACTTT 4 139 1 TCTTTTTTTT 0.976786 -462 TTAGAAACTTTCTTTTTTTGGCCATAACATAAAATTTAAA 4 168 1 TTTTTTTACT 0.720737 -433 GGTGTTCTTTTCTTTTTGTTTCAGCGTCGTTATTTAAATT 4 200 0 TTTTTTTTCT 0.932219 -401 CCCGGCCGGGTGTTTTTTTCTCTTTCTTTTTCGCCCACTG 4 380 1 TTTTTTTTTT 0.980854 -221 TAGTGTTTCGTTTTTTTATTCCTGAATTTTTCACTACCGC 4 551 1 TTTTTTTTTT 0.980854 -50 TTCATCGGACGCCTTTTTTACTGCTATTGTTCAACAAAGT 5 251 1 GCTTTTTTTT 0.859905 -177 ATGAGAATAGTGCTTTTATCCTCTGGATTTGGCATAAAAA 5 324 0 TCTTTTTATT 0.88759 -104 CCGTGTACTCTATTTTTCTTAACGCTTTCTTCTGAACTTG 5 391 0 TTTTTTTTTT 0.980854 -37 * ***** * ** * Masking position 9 Map Score: 10.4987 Number of sites scoring better than the average of aligned sites = 3960 Number in coding regions = 758 Number in noncoding regions = 3202 Number of orfs with sites within 600 bp upstream = 1241 Fraction of orfs with sites within 600 bp upstream = 0.199325 Motif number 2 AAACATAAGCTATTGCAGCGTCATTGGAGC 1 23 0 TATTGCAGCG 0.909129 -368 TCTCCACGCTAATTGGTCCGCGGAGCCAAT 2 157 1 AATTGGTCCG 0.939443 -144 TTTTATCTAAAATTTCTGTGTGAAAAGTCA 2 226 0 AATTTCTGTG 0.963272 -75 TTGAAGCTCTAATTTGTGAGTTTAGTATAC 3 96 0 AATTTGTGAG 0.9014 -205 AATTTAGTAGAATTTCTGCGGAGAACCAAA 4 28 0 AATTTCTGCG 0.989706 -573 CTGAAATAGCAATTGCTGCGGTAGTGAAAA 4 578 0 AATTGCTGCG 0.993485 -23 TCAAATCATTAATTTCTGTGCATAAAGTGT 5 152 1 AATTTCTGTG 0.963272 -276 TTTCAATTTGAATTGGAGCGACGAAGGTCA 6 86 1 AATTGGAGCG 0.971683 -215 ********** Masking position 2 Map Score: 5.54254 Number of sites scoring better than the average of aligned sites = 326 Number in coding regions = 251 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 3 GATGCATCAGTCAACTTAATTCTCTAATAAAACAGACAG 1 204 1 TACTTCCATA 0.942791 -187 TTTCCTCGGATCCATTTCGTACATATAAAATCCGAAGCT 1 245 1 TATTTCTAAA 0.923812 -146 AAAACTAAAGAAAAATTTATACCCTTAAATAGATCTGAT 2 185 0 AAATTCCAAA 0.851241 -116 TTTAGTTTTTTTGACTTTTCACACAGAAATTTTAGATAA 2 215 1 TACTTCCAAA 0.991534 -86 CTTATTGTTCTTGATTTGTGCCCCGTAAAATACTGTTAC 3 258 0 TATTTCCAAA 0.958355 -43 AACATAAAATTTAAATAACGACGCTGAAACAAAAAGAAA 4 193 1 TAATACCAAA 0.851241 -408 TTACGATAAGTAAACTTCTCACCTGTAAATACTAGTAAC 4 308 1 TACTTCTAAA 0.98402 -293 GCGGGCTTATTATACTTGGTACTTTCAAACCTGGTTCCG 4 471 0 TACTTCTAAA 0.984002 -130 GAATATACTATACACTTTATGCACAGAAATTAATGATTT 5 154 0 TACTTCCAAA 0.991534 -274 AGAGGATAAAAGCACTATTCTCATCAAAAGATGGAAAAG 5 340 1 AACTACTAAA 0.791274 -88 CGCTTTCTTCTGAACTTGACTCTTTCACAGCTTTTCCAT 5 370 0 TACTTCTACA 0.927755 -58 * **** * * *** Masking position 4 Map Score: 4.20381 Number of sites scoring better than the average of aligned sites = 546 Number in coding regions = 373 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 4 TCAAATTGTCACCCGGTATAGATATACTTATA 1 94 0 ACCCGGTAGA 0.894015 -297 CTTACTGATAAAATGGCATCGAGCTTACAACT 1 160 1 AAATGGCAGA 0.787528 -231 TGTCACTACTAAACGGGATAGTACTAAACGGG 1 308 1 AAACGGGAGT 0.984194 -83 GGATAGTACTAAACGGGATAGTAGAGATAGCT 1 323 1 AAACGGGAGT 0.984194 -68 ATCAGTTATTACCCGGGAATCTCGGTCGTAAT 3 135 1 ACCCGGGACT 0.985852 -166 TGGAAGAACTGGCACAGTTTGGTTCTCC 4 7 1 AACTGGCAGT 0.95505 -594 ATGTTCAGTTACCCGGCCGGGTGTTTTTTTCT 4 369 1 ACCCGGCCGT 0.499931 -232 AAAGTGGGTAACCCGGCATTCTTGCGCCAAAG 5 286 1 ACCCGGCACT 0.987813 -142 AAAATAGAGTACACGGGAGCGTT 5 415 1 ACACGGGAGT 0.98897 -13 ATTCAAATTGAAACGGCCCTCTGGAACGACGT 6 67 0 AAACGGCCCT 0.935256 -234 ******** ** Masking position 1 Map Score: 6.62274 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 207 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 5 AATAACTATTAAAAGTACGTTGCAGATAAA 1 50 0 AAAAGTACGT 0.972891 -341 AATTTTAGATAAAAGGAAGTATTATATCGG 2 242 1 AAAAGGAAGT 0.943911 -59 GGCCTTTATAAAAAGGAACTATCCAATACC 3 215 1 AAAAGGAACT 0.919299 -86 ATAAAAATACTAAAGTAGGTCTGTTCAGAT 4 98 0 TAAAGTAGGT 0.834705 -503 TATGGCCAAAAAAAGAAAGTTTCTAAAAAT 4 164 0 AAAAGAAAGT 0.915822 -437 AGCGTACTGAAGAAGTACCTAATCATAATG 4 264 0 AGAAGTACCT 0.945344 -337 ACTTATCGTAAGAAGTAGCTTGAAAAGCGT 4 289 0 AGAAGTAGCT 0.945344 -312 GATAAAATAGAGAAGTACGTCGTTCCAGAG 6 51 1 AGAAGTACGT 0.962339 -250 TAAATAATAGAAACGTAAGTCATGTATCTA 6 134 1 AAACGTAAGT 0.861068 -167 CATTGTTCTCAAAAGAAGCTCAATAGACC 6 282 1 AAAAGAAGCT 0.89892 -19 ********** Masking position 7 Map Score: 3.95125 Number of sites scoring better than the average of aligned sites = 1175 Number in coding regions = 737 Number in noncoding regions = 438 Number of orfs with sites within 600 bp upstream = 343 Fraction of orfs with sites within 600 bp upstream = 0.0550916 Motif number 6 GCATCGTCTTTCTCTTCAGTTGTAAGCTCG 1 179 0 TCTCTTCAGT 0.872045 -212 AAAATCCGAAGCTTTTCAGGACAAAATACT 1 271 1 GCTTTTCAGG 0.95492 -120 CCCGTTTAGTACTATCCCGTTTAGTAGTGA 1 310 0 ACTATCCCGT 0.927331 -81 AGCTATCTCTACTATCCCGTTTAGTACTAT 1 325 0 ACTATCCCGT 0.927331 -66 TTCCCAGCCTGCTTTTCTGTAACGTTC 3 8 0 GCTTTTCTGT 0.91634 -293 TGAAGCTTTTTCTTTCCAATTTTTTTTTTT 3 184 0 TCTTTCCAAT 0.818076 -117 ATAAAAAGGAACTATCCAATACCTCGCCAG 3 222 1 ACTATCCAAT 0.814855 -79 TCTTCAGTACGCTTTTCAAGCTACTTCTTA 4 281 1 GCTTTTCAAG 0.872323 -320 AACTGAACATGGTTTTCCGTATGGTTGCTA 4 349 0 GGTTTTCCGT 0.85873 -252 TATGACTGAGGCTCTCCAGTGGGCGAAAAA 4 406 0 GCTCTCCAGT 0.975664 -195 CCGTGCGTGGGCTATTCAGTATAACCCGAA 5 45 0 GCTATTCAGT 0.976607 -383 CTCTTTCACAGCTTTTCCATCTTTTGATGA 5 360 0 GCTTTTCCAT 0.94855 -68 ********** Masking position 5 Map Score: 4.16859 Number of sites scoring better than the average of aligned sites = 1812 Number in coding regions = 1391 Number in noncoding regions = 421 Number of orfs with sites within 600 bp upstream = 345 Fraction of orfs with sites within 600 bp upstream = 0.0554128 Motif number 7 GTTACAGAAAAGCAGGCTGGGAAGCATATT 3 15 1 AGCAGGCTGG 0.985115 -286 ATCAAGAACAATAAGACAGGACTGTAAAG 3 282 1 ATAAGACAGG 0.874788 -19 TATATGTCAAAGAAGACTGGTTGAGTAGCA 4 434 1 AGAAGACTGG 0.982756 -167 AGTTGGGATAAGAGGGCAGGACCGAGCTTA 4 521 1 AGAGGGCAGG 0.986949 -80 GATATGCTTTATAATGCTGGAGT 5 4 0 ATAATGCTGG 0.928751 -424 CTTTGGCGCAAGAATGCCGGGTTACCCACT 5 288 0 AGAATGCCGG 0.979274 -140 ACGTCGTTCCAGAGGGCCGTTTCAATTTGA 6 67 1 AGAGGGCCGT 0.928889 -234 TTTCTAAGCCCGAAGGCTGGAAAAAATAGT 6 220 1 CGAAGGCTGG 0.985114 -81 ********** Masking position 7 Map Score: 3.35964 Number of sites scoring better than the average of aligned sites = 712 Number in coding regions = 584 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 8 GCAGCGTCATTGGAGCAACGTTAGGAAT 1 9 0 TGGAGCAACG 0.982619 -382 ATGTACGAAATGGATCCGAGGAAATGCTGT 1 239 0 TGGATCCGAG 0.927474 -152 TAGATCTGATTGGCTCCGCGGACCAATTAG 2 165 0 TGGCTCCGCG 0.985617 -136 CCACTGTCAGTGGCGCCACGGAAGGATAGC 5 113 1 TGGCGCCACG 0.994623 -315 AACGGCCCTCTGGAACGACGTACTTCTCTA 6 58 0 TGGAACGACG 0.974886 -243 CAATTTGAATTGGAGCGACGAAGGTCACGC 6 89 1 TGGAGCGACG 0.993521 -212 ********** Masking position 1 Map Score: 3.34694 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 94 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 ACGAAATGGATCCGAGGAAATGCTGTCTGT 1 235 0 TCCGAGGAAA 0.978906 -156 TAATAAGAACTTAGAAGAATTGCACTCAAG 2 49 1 TTAGAAGAAT 0.86788 -252 TATTCGATCATTCGCGGAATCTCCACGCTA 2 138 1 TTCGCGGAAT 0.917244 -163 AGTTTGGTTCTCCGCAGAAATTCTACTAAA 4 26 1 TCCGCAGAAA 0.985423 -575 AAATTGTGTATTAGAAGAAATTCAGAAACG 4 64 1 TTAGAAGAAA 0.91333 -537 AAAAAAGGCGTCCGATGAATGTTCGTTGTA 5 240 0 TCCGATGAAT 0.91384 -188 AGAGTCAAGTTCAGAAGAAAGCGTTAAGAA 5 386 1 TCAGAAGAAA 0.964233 -42 TTGCCTCCACTCCGCAGGAAGTTGTTGATA 6 25 1 TCCGCAGGAA 0.947239 -276 ********** Masking position 9 Map Score: 2.15391 Number of sites scoring better than the average of aligned sites = 914 Number in coding regions = 687 Number in noncoding regions = 227 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 10 TGACAGAAAAATAGTATTTTGTCCTGAAAA 1 283 0 ATAGTATTTT 0.968446 -108 AAATTTTTCTTTAGTTTTTTTGACTTTTCA 2 206 1 TTAGTTTTTT 0.947783 -95 TACTTATAATACAGTTTTTTAGTTTTGCTG 3 59 0 ACAGTTTTTT 0.940839 -242 GAACCAAGTAACAGTATTTTACGGGGCACA 3 251 1 ACAGTATTTT 0.953854 -50 CAGACCTACTTTAGTATTTTTATATGATAA 4 105 1 TTAGTATTTT 0.959403 -496 CTTATAGTGTTTCGTTTTTTTATTCCTGAA 4 547 1 TTCGTTTTTT 0.848139 -54 CATAAAGTGTATAGTATATTCATATAGATA 5 172 1 ATAGTATATT 0.864661 -256 ********** Masking position 5 Map Score: 1.3606 Number of sites scoring better than the average of aligned sites = 679 Number in coding regions = 355 Number in noncoding regions = 324 Number of orfs with sites within 600 bp upstream = 229 Fraction of orfs with sites within 600 bp upstream = 0.0367812 Motif number 11 TTGTCACCCGGTATAGATATACTTATAGAG 1 91 0 GTATAGATAT 0.934915 -300 GATCCATTTCGTACATATAAAATCCGAAGC 1 253 1 GTACATATAA 0.872099 -138 TATACGTTATGTTCCGATATAATACTTCCT 2 255 0 GTTCCGATAT 0.943995 -46 CACTCAGCTAGTTCCTATATACGTTATGTT 2 272 0 GTTCCTATAT 0.86829 -29 AAGTAGGTCTGTTCAGATATTTCGTTTCTG 4 86 0 GTTCAGATAT 0.96752 -515 TAGTATATTCATATAGATATGTATATATAT 5 183 1 ATATAGATAT 0.559149 -245 ATATAGATATGTATATATATCATTGAATAC 5 193 1 GTATATATAT 0.869284 -235 TAAACGATCTGTATAGATAATGTGGTGAAA 6 167 1 GTATAGATAA 0.90918 -134 ********** Masking position 7 Map Score: 0.64541 Number of sites scoring better than the average of aligned sites = 715 Number in coding regions = 468 Number in noncoding regions = 247 Number of orfs with sites within 600 bp upstream = 162 Fraction of orfs with sites within 600 bp upstream = 0.0260199 Motif number 12 ********** No masking Map Score: 5.14676e-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: 5.14676e-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: 5.14676e-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