AlignACE version 2.2 July 7, 1998 AlignACE -jCOX.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 YDL067C 438 bp YDL067C COX9 1-180 Subunit VIIa of cytochrome c oxidase #2 YER141W 300 bp YER141W COX15 1-1461 cytochrome oxidase assembly factor #3 YGL191W 600 bp YGL191W COX13 1-390 subunit VIa of cytochrome c oxidase, may specifically interact with ATP #4 YGL187C 600 bp YGL187C COX4 1-468 subunit IV of cytochrome c oxidase #5 YGR062C 300 bp YGR062C COX18 1-951 Cytochrome OXidase gene 18 #6 YHR051W 401 bp YHR051W COX6 1-447 subunit VI of cytochrome c oxidase #7 YIL111W 375 bp YIL111W COX5b 1-1, 90-544 Cytochrome-c oxidase chain Vb #8 YLL009C 314 bp YLL009C COX17 1-210 cysteine-rich cytoplasmic protein #9 YLR038C 300 bp YLR038C COX12 1-252 subunit VIb of cytochrome c oxidase #10 YLR395C 300 bp YLR395C COX8 1-237 Cytochrome-c oxidase chain VIII #11 YML129C 381 bp YML129C COX14 1-213 mitochondrial membrane protein #12 YMR256C 501 bp YMR256C COX7 1-183 subunit VII of cytochrome c oxidase #13 YNL052W 313 bp YNL052W COX5A 1-462 Cytochrome-c oxidase chain Va #14 YPL172C 427 bp YPL172C COX10 1-1389 Putative farnesyl transferase required for heme A synthesis #15 YPL132W 487 bp YPL132W COX11 1-903 Putative heme A biosynthetic enzyme involved in forming the formyl group at position 8 of the porphyrin ring Motif number 1 AAGCAGGGTTTCTTTTTTGCTCCTTGCAATATAC 2 132 0 TCTTTTTCTT 0.975992 -169 TAATTACTTGACTTATTTGCTCCCACTCTTGGTC 3 127 1 ACTTTTTCTC 0.815595 -474 ATTCTACCATTCTTTTTTTCTACTCCAATCGTTC 3 179 1 TCTTTTTCTT 0.975992 -422 GAAGAACGACTATTATTTGCTAATACAGAGTAAG 3 236 1 TATTTTTCTT 0.712199 -365 TTTCTCTTCCCTTTATTTGCTACTAACCAAGATG 4 51 0 CTTTTTTCTT 0.943626 -550 CTTGAGTGTGTCTTATTTTCTCTTCCCTTTATTT 4 67 0 TCTTTTTCTT 0.975992 -534 TTCAAAATAATCTTATTTCCTGTTTATGCTAATT 4 221 0 TCTTTTTCTT 0.975992 -380 CTGTTAAATATCTTCTTTCCTGGTAGTTCTTCTC 4 298 0 TCTTTTTCTT 0.975992 -303 TCAAATCCAGATTTGTTTTCTCTTAGTTCTTTTC 4 345 0 ATTTTTTCTT 0.912725 -256 TTAAGAAAAAATTTATTTGCAAGTTTAACTCGTT 4 381 1 ATTTTTTCAT 0.790096 -220 TAGTAATGAATTTTTTTTACTTTTTTTTTTTTTT 5 103 1 TTTTTTTCTT 0.964326 -198 ATCCTTGGACCTTTTTTTTCTAATGAAAGTCTTT 5 248 0 CTTTTTTCTT 0.943626 -53 AGGTTACCTCATTTCTTTACATTTCATCCACATT 6 263 1 ATTTTTTCAT 0.790096 -139 CTCACCAATTTCTTTTTTTGATTTTGTATTGTTC 7 135 1 TCTTTTTGAT 0.649484 -241 ATGAAATTCGTCTTTTTTCGTCTTTTGCACGGTA 7 238 0 TCTTTTTGTT 0.83735 -138 TTTTTTGAAAATTTTTTTTCAAATCATTACCCGG 8 133 1 ATTTTTTCAT 0.790096 -182 TACACTAAAATTTTGTTTAGTTGTACTAGAGACA 8 257 0 TTTTTTTGTT 0.773922 -58 ATTATACTGTATTTATGTGCTTGTTCCTATTTGT 9 273 0 ATTTTGTCTT 0.6826 -28 TGCTGTCAGCCTTTATTTTCAATTTTTCTTAGTC 10 155 0 CTTTTTTCAT 0.857643 -146 TCTCCCCAATTTTTCTTTTCATCCGTATATTTTA 11 39 1 TTTTTTTCAC 0.732337 -343 CTGCGTTCTATTTTTTGTTCTCTTCCTCTCACCA 11 352 0 TTTTTGTCTT 0.847534 -30 AAGGGTTACATCTTGTTTCCAAATAGCGTCTATA 12 108 0 TCTTTTTCAT 0.936028 -394 AAGATGTAACCCTTTTTTTCTTTTAGTTTTGAGA 12 128 1 CCTTTTTCTT 0.961793 -374 CTGCCTTTTTTTTTTTTTGCTGACACTATATGTA 12 310 0 TTTTTTTCTC 0.883745 -192 TATTGTTTTGCTTTCTGTACTTGTTGGTTTAGAA 12 471 0 CTTTTGTCTT 0.774883 -31 CTATAGTATCTCTTTTTTTCGATTTCTCCTTTTT 14 394 1 TCTTTTTCGT 0.795346 -34 TTCGATTTCTCCTTTTTTCCTCTTTAG 14 411 1 CCTTTTTCTT 0.961793 -17 TTTTGCTTTTTCTTGTTTTCTGCCATTCCAAAAC 15 191 1 TCTTTTTCTC 0.919563 -297 **** *** ** * Masking position 8 Map Score: 29.3769 Number of sites scoring better than the average of aligned sites = 3239 Number in coding regions = 1419 Number in noncoding regions = 1820 Number of orfs with sites within 600 bp upstream = 1288 Fraction of orfs with sites within 600 bp upstream = 0.206874 Motif number 2 CGATAAAGGAAAGATCAATAATTCAAAAGGCAAGAACT 2 195 0 AATAAATAAA 0.852202 -106 TTACAATAGGAAACTAAATAAACGATAAAGGAAAGATC 2 217 0 AATAAACTAA 0.520295 -84 CATTGGTGGGAAAAAAAATTACCCGAAATTACTATATT 3 367 0 AAAAAACAAA 0.849865 -234 AGTGACGGGATACATTAAATATAACAAACATACACGTT 3 475 1 TATAAAAAAA 0.761362 -126 CAGTTATACAAATAACAAACAATAGAAAA 3 582 1 AAAAAATAAA 0.782607 -19 CGCTTCTTCCAAGTATAAACACAGGAAAGAAAGATATA 4 113 1 AAAAAAAAAA 0.943347 -488 TACTAAAAAAAAAAAAAAGTAAAAAAAATTCATTACTA 5 103 0 AAAAAAAAAA 0.943347 -198 AAAAGTGCAGAACGTTAAATAAATGAAAGCATAAACTC 5 156 0 AATAAAAAAA 0.96386 -145 CATTTTATCCAAGAATAATAACAGAAAATTCCAATCAA 6 42 1 AAAAAAAAAA 0.943347 -360 CGAACAATACAAAATCAAAAAAAGAAATTGGTGAGTGT 7 132 0 AATAAAAAAT 0.770889 -244 TCATTTATAAAATATAAATCAAATGAAATTCGTCTTTT 7 256 0 AATAAAAAAA 0.96386 -120 TACTTGTCTCTAGTACAACTAAACAAAATTTTAGTGTA 8 253 1 TAAAAAAAAA 0.665768 -62 TCTATCTAGAAAATTAAAGGATACAAAACTAATTAACC 10 227 0 AATAAAAAAA 0.96386 -74 CACAGTATGTAACATTATAAAGACAAAATACTTACTTA 11 137 0 AATATAAAAA 0.632382 -245 GAGAGAAAGGAAGGTAAATAACTGAAAAGA 12 3 0 AATAAATAAA 0.852202 -499 ACAAATCTCAAAACTAAAAGAAAAAAAGGGTTACATCT 12 129 0 AATAAAAAAG 0.738771 -373 CAAGTACAGAAAGCAAAACAATAATAAATA 12 482 1 AAAAAAAAAA 0.943347 -20 GCGGCGGCGAAAAGTTAAAAAGAACAATCAATTAAATA 13 207 1 AATAAAAAAT 0.770889 -107 ATATGGCAGGAATATGAAAAATACATAACATCAATGTC 14 24 0 AATAAAATAA 0.761362 -404 AGTTTTTTTTAATTTTAATCAACACAAAATACACATAT 15 31 0 AATAAACAAA 0.900662 -457 GGCAGAAAACAAGAAAAAGCAAAACAAAGAGTACGAAG 15 177 0 AAAAAAAAAA 0.943347 -311 ** * ** * * *** Masking position 11 Map Score: 11.3027 Number of sites scoring better than the average of aligned sites = 4650 Number in coding regions = 1173 Number in noncoding regions = 3477 Number of orfs with sites within 600 bp upstream = 1270 Fraction of orfs with sites within 600 bp upstream = 0.203983 Motif number 3 CTGGCCATATTTTCAACCATTAAACACTACTAATGTAA 3 92 1 TTAATAACAT 0.912598 -509 CCGCCTCTCATTGGTGGGAAAAAAAATTACCCGAAATT 3 375 0 TTTAAAAAAT 0.606658 -226 GTCAAAGCATTAATAAAGATCAACAATTGCTCTTGCTT 6 206 1 TAAATAAAAT 0.851542 -196 ATTTTTCAAATTGTAATAATAAATAAGTGTGCTAAAAT 6 294 0 TTAATAAAAT 0.970631 -108 AACAATTGTATTTGACACATAAACTAATAAATATACAA 6 372 1 TTAATAATAT 0.870971 -30 TAGTTGCATTTTCGATTCATTAAATACTATTCATGTTA 7 46 1 TTAATAATAT 0.870971 -330 CATTTGCATATACAAAAAATTAACAAATCTATCATATA 10 46 0 TAAATAAAAT 0.851542 -255 AGAATAAAATTTGAATAAATAAATAAACGTACTCTTTA 12 172 0 TTAATAAAAC 0.817657 -330 AGTTCTACTATTCATGGGATGAATAAATAATATCATCT 12 423 0 TTTATAAAAT 0.851542 -79 AATGTGACACTTACAATGATGAATAATTACTATGTAGG 13 105 0 TTAATAAAAT 0.970631 -209 CGGCGAAAAGTTAAAAAGAACAATCAATTAAATAAGAA 13 211 1 TTAAAAACAT 0.737364 -103 GATATTTATATTTGATACATCAATAATTATAACTTAAG 14 86 1 TTAATAAAAT 0.970616 -342 GTCAATGGGCTTGCAAGCATAAAAAAGTCATTTTATTA 14 245 0 TTAATAAAAT 0.970631 -183 ATCACGTCTATTGCAGATATCAAGAATTTTCTTCTTTG 14 309 0 TTAATAAAAT 0.970631 -119 TTTGTGTTGATTAAAATTAAAAAAAACTTTATCTCACT 15 41 1 TTAAAAAAAT 0.898854 -447 ** * ** ** ** * Masking position 9 Map Score: 4.92646 Number of sites scoring better than the average of aligned sites = 380 Number in coding regions = 228 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 4 TACTGCAACCTGATTGGCCCGCTACCACGA 1 290 1 TGATTGGCCC 0.992521 -149 CGCGGGGCCCTGATTGGCTCGTATGGAGCG 6 113 0 TGATTGGCTC 0.978185 -289 AAAAGGGACCTAATTGGTCCGGTCAAAGCA 6 185 1 TAATTGGTCC 0.903312 -217 TTCTGAAAATTGATTGGTCAATGTTATGAA 9 93 0 TGATTGGTCA 0.950324 -208 TTCTCTCGTATGATTGGTGCAAACCGTTTG 10 97 0 TGATTGGTGC 0.977643 -204 AGGCAGTACTTGATTGGCTACGCCGCGCAT 12 338 1 TGATTGGCTA 0.911159 -164 TCCTCGTTTGTGATTGGCCCTACGTTTTGC 13 167 1 TGATTGGCCC 0.992521 -147 GTTGATCTTGTGTTTGGTGCATTGCTTGCA 13 278 0 TGTTTGGTGC 0.886832 -36 ********** Masking position 5 Map Score: 4.95108 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 160 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 5 ACCCGGATGTTTAAAAATTGTTGTCGCCTG 3 43 1 TTAAAAATTG 0.810375 -558 ACTGGACGGTAGAAAAATTGGGTTTGCCAG 5 201 0 AGAAAAATTG 0.9764 -100 TATTACAATTTGAAAAATTGTATCACTTCT 6 314 1 TGAAAAATTG 0.955952 -88 TGCACCAGATAGAAAAGTTGCATTAAAATG 9 188 1 AGAAAAGTTG 0.927169 -113 TAGGGGACTAAGAAAAATTGAAAATAAAGG 10 150 1 AGAAAAATTG 0.9764 -151 ACGGATGAAAAGAAAAATTGGGGAGAAAAG 11 35 0 AGAAAAATTG 0.9764 -347 GGTATGAAGAATAAAATTTGAATAAATAAA 12 187 0 ATAAAATTTG 0.748898 -315 AATTCTTATGAGAAAATTTGCGGGAGTTCT 15 84 0 AGAAAATTTG 0.938065 -404 CGAAGGAAAATGAAAAATAGTTGAATATTA 15 152 0 TGAAAAATAG 0.773819 -336 ********** Masking position 5 Map Score: 4.91468 Number of sites scoring better than the average of aligned sites = 619 Number in coding regions = 451 Number in noncoding regions = 168 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 6 TAAAATCATATTACTACAGTTCTACAGTTATAC 3 558 1 TACTCGTTCT 0.913167 -43 CAAGGATAAAATACTTCGCTTCTTCCAAGTATA 4 97 1 AACTCCTTCT 0.822238 -504 TTTAACTCGTTCCCTGCTTTTCTATTTGGCTTG 4 404 1 TCCTCTTTCT 0.981489 -197 AGTTGAGTAAAACCTTCCGTTCTGATATCACAT 5 64 1 ACCTCGTTCT 0.982889 -237 TAATGTTATAACCCTACCTATCTCCTTCAAAAA 8 168 1 ACCTCTATCT 0.94673 -147 TTCAGTTATTTACCTTCCTTTCTCTCACGTGTA 12 15 1 TCCTCTTTCT 0.981489 -487 ATCAACTTATACCCTACATTTCTATAGACGCTA 12 86 1 ACCTCTTTCT 0.978079 -416 ACAAGATGTAACCCTTTTTTTCTTTTAGTTTTG 12 126 1 ACCTTTTTCT 0.778547 -376 GGAGGCGGTCTGCCTGCAGATCTGATAGTCATA 13 37 0 TCCTCGATCT 0.964526 -277 GCAGACCGCCTCCCTACGCTTCTAAATAGAATG 13 57 1 TCCTCCTTCT 0.972736 -257 TACGCTGTTTTTCCTACAGATCCGCTCCTTAGA 15 238 0 TCCTCGATCC 0.836611 -250 * *** * ***** Masking position 5 Map Score: 4.6838 Number of sites scoring better than the average of aligned sites = 633 Number in coding regions = 465 Number in noncoding regions = 168 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 7 TTAGTAGCAAATAAAGGGAAGAGAAAATAAGAC 4 59 1 AAAAGAAGAG 0.782733 -542 ACAGATCGAACGAAACGGAAAAGAACTAAGAGA 4 328 1 CAAAGAAAAG 0.963594 -273 TCGTCTCAAGCCAAATAGAAAAGCAGGGAACGA 4 410 0 CAAAGAAAAG 0.963594 -191 AATACGTTGACTAAAGGAAAGTGACAGGGAATA 4 497 0 CAAAAAAGTG 0.767616 -104 ATGGCAACATCAAAATCGAAATGGGTGAGTATT 4 558 0 CAAAGAAATG 0.888539 -43 TATTTACTAAAAAAAAAAAAAAGTAAAAAAAAT 5 112 0 AAAAAAAAAG 0.928144 -189 GTTTGCCAGCAAAAACAAAAGTGCAGAACGTTA 5 177 0 AAAAAAAGTG 0.569441 -124 TCGAACAATACAAAATCAAAAAAAGAAATTGGT 7 138 0 CAAAAAAAAA 0.738302 -238 CTCCTTCAAAAAAAGATAAAATGACGATATATA 8 189 1 AAAGAAAATG 0.650173 -126 GAAAGATGCACCAGATAGAAAAGTTGCATTAAA 9 182 1 CAGAGAAAAG 0.748032 -119 ACAGAGCAAACTAAACAGAAAAGTTATCCATTT 10 268 1 CAAAGAAAAG 0.963594 -33 AAGCTAATAGCAAAACGAAAAAACACGTTGTCA 11 86 1 CAAAAAAAAA 0.738302 -296 TCTCAAAACTAAAAGAAAAAAAGGGTTACATCT 12 129 0 AAAGAAAAAG 0.860545 -373 AGTGTCAGCAAAAAAAAAAAAAGGCAGTACTTG 12 317 1 AAAAAAAAAG 0.928144 -185 ATATAAGATTCTAAACCAACAAGTACAGAAAGC 12 463 1 CAAAAACAAG 0.783482 -39 AGCGGCGGCGAAAAGTTAAAAAGAACAATCAAT 13 206 1 AAAGAAAAAG 0.860545 -108 TAAACATCATCCAAGCCAAAAAGACTCGATCTT 14 164 1 CAAGAAAAAG 0.939069 -264 TACTATAGGCCTAAAATAAAAAGACCCCGCTAT 14 369 0 CAAAAAAAAG 0.969935 -59 * *** ****** Masking position 9 Map Score: 8.50506 Number of sites scoring better than the average of aligned sites = 3431 Number in coding regions = 1585 Number in noncoding regions = 1846 Number of orfs with sites within 600 bp upstream = 1278 Fraction of orfs with sites within 600 bp upstream = 0.205268 Motif number 8 GGACTCTGCTAAAGACCATAACAAGGGTCTGCAA 1 237 0 AAAGACAAAA 0.857294 -202 TGTGGTATTAAAAGAATCGATGAAAGAGACTCTT 1 335 1 AAAGATCAAA 0.913766 -104 GACAGAAAGATTCCAAGAATCCACGATCG 2 6 1 AAAGATCAAA 0.913766 -295 ATGGTTTCTAAAAGAATATGGTAATCTAAGATCC 2 64 1 AAAGATAGAA 0.756494 -237 AACAATTTTTAAACATCCGGGTAATAAATTGTTC 3 31 0 AAACACCGAA 0.834151 -570 GCGCCATGGGAAAGAACCGACCAAGAGTGGGAGC 3 145 0 AAAGACCAAA 0.914076 -456 ATTTGCTAATACAGAGTAAGCTATCCTGCTGAAT 3 250 1 ACAGATAGAT 0.512311 -351 TGCGGTATTGACACAATATAGTAATTTCGGGTAA 3 353 1 ACACATAAAA 0.817202 -248 TATCGGTCTAAGAGAATCGAAAAATAACCCCCAG 3 422 1 AGAGATCAAA 0.817524 -179 AGAAAATAAGACACACTCAAGGATAAAATACTTC 4 80 1 ACACATCAAT 0.765413 -521 CTCCCTGAAGAAACAGTATACTAACAATACTCAC 4 533 1 AAACATAAAA 0.844938 -68 TAGCGGAGATAAACAGCCGAACAATTGTATTTGA 6 353 1 AAACACCAAA 0.906433 -49 CTGTTGCATTAAACAATAGACCAATTATTTCAAT 7 294 1 AAACATAAAA 0.844938 -82 ATTTTAGTGTACACAATCAGATAACTACACAATC 8 280 1 ACACATCGAA 0.804312 -35 TCAGATAACTACACAATCAATTATACCCA 8 296 1 ACACATCAAT 0.765413 -19 AAAACAACACACAATTGGTTCAAAA 9 2 1 AAACACAAAT 0.692751 -299 AAAGCACTCGAGAGATTCAAATAAATCTATATGA 9 34 1 AGAGATCAAA 0.817524 -267 AGATAGAGCCACAGAGCAAACTAAACAGAAAAGT 10 258 1 ACAGACAAAA 0.831328 -43 GGTGAGAGGAAGAGAACAAAAAATAGAACGCAGA 11 353 1 AGAGACAAAT 0.511444 -29 GCATATAATCAAACAATAAAGCAATTGTAAGCGT 12 271 0 AAACATAAAA 0.844938 -231 CCTAAAATAAAAAGACCCCGCTATGAGGAATATT 14 359 0 AAAGACCGAT 0.694784 -69 ***** ** * ** Masking position 5 Map Score: 5.26858 Number of sites scoring better than the average of aligned sites = 2302 Number in coding regions = 1601 Number in noncoding regions = 701 Number of orfs with sites within 600 bp upstream = 540 Fraction of orfs with sites within 600 bp upstream = 0.0867331 Motif number 9 TAGCTCATAAAAGGAATGATTCAAGCTCTT 1 171 1 AAGGAATGAT 0.717955 -268 ATAAACGATAAAGGAAAGATCAATAATTCA 2 208 0 AAGGAAAGAT 0.959872 -93 TAAACACAGGAAAGAAAGATATACGAAGAT 4 128 1 AAAGAAAGAT 0.945395 -473 ACGTTGACTAAAGGAAAGTGACAGGGAATA 4 497 0 AAGGAAAGTG 0.749761 -104 AGGGAGATTCAAAGAAAGCTGTAAGCGGCG 6 152 0 AAAGAAAGCT 0.869194 -250 TATCTCCTTCAAAAAAAGATAAAATGACGA 8 186 1 AAAAAAAGAT 0.825268 -129 CTATTTGTGAAAGCAAAGATACTTTATGTA 9 251 0 AAGCAAAGAT 0.959872 -50 ATACTTACTTAAGCAAAGTTATATAGAAGT 11 118 0 AAGCAAAGTT 0.855806 -264 AAGGAAGGAGAAGCAAAGCTCAGAAGTAAG 11 235 0 AAGCAAAGCT 0.901773 -147 TAACTTAAGGAAATAAAGATAGTTTTTGTC 14 115 1 AAATAAAGAT 0.728145 -313 TGCCCTATATAAACAAAGATCGAGTCTTTT 14 182 0 AAACAAAGAT 0.945395 -246 GGAGAAATCGAAAAAAAGAGATACTATAGG 14 393 0 AAAAAAAGAG 0.704518 -35 AGAAAAAGCAAAACAAAGAGTACGAAGGAA 15 174 0 AAACAAAGAG 0.897333 -314 ********** Masking position 5 Map Score: 4.01126 Number of sites scoring better than the average of aligned sites = 936 Number in coding regions = 643 Number in noncoding regions = 293 Number of orfs with sites within 600 bp upstream = 248 Fraction of orfs with sites within 600 bp upstream = 0.039833 Motif number 10 GTTGCAGTAAATGAAGAGATATAGAGGAGGACTC 1 265 0 ATGGATATAG 0.983927 -174 ACCGCTATGAATGTAGTGATATGGTGCGGTATTG 3 329 1 ATGGATATGG 0.986653 -272 TTCGATTTTGATGTTGCCATACAAATAGATAACA 4 571 1 ATGGATACAA 0.842346 -30 ATTGGCTCGTATGGAGCGATACGGCCATCAGTAT 6 97 0 ATGGATACGG 0.980293 -305 AAAAGATAAAATGACGATATATAGCGGCGAATCA 8 199 1 ATGGATATAG 0.983927 -116 TAAAGAATACATGGTGTCATATAGATTTATTTGA 9 50 0 ATGGATATAG 0.983927 -251 GGTCAATGTTATGAAGCTATATGGTAAAGAATAC 9 74 0 ATGGATATGG 0.986653 -227 *** * ****** Masking position 9 Map Score: 2.27116 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 111 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 11 AAGGTGTCTTACAATCCAAAAGAGCTTGAAT 1 189 0 ACAATCAAAA 0.949732 -250 GTTCCAAGTTACAATAGGAAACTAAATAAAC 2 232 0 ACAATGGAAA 0.694459 -69 CAAATAACAAACAATAGAAAA 3 590 1 ACAATGAAAA 0.867693 -11 ATTATAACATACATTTCAAAATAATCTTATT 4 238 0 ACATTCAAAA 0.915081 -363 ACAGAAAATTCCAATCAAAAAGTTGGTGTTA 6 62 1 CCAATAAAAA 0.860412 -340 GCCTTATCGAACAATACAAAATCAAAAAAAG 7 146 0 ACAATCAAAA 0.949732 -230 GCACACAGCTCCAATTCGAAACCCAAGTTAC 8 37 1 CCAATCGAAA 0.932734 -278 CTTCCTCTCACCATTGCCAAACCGCTGTATA 11 334 0 CCATTCCAAA 0.887751 -48 TGTAAGTGTCACATTGCAAAAATCGTCCAAT 13 128 1 ACATTCAAAA 0.915081 -186 AAACGTAGGGCCAATCACAAACGAGGAAAAC 13 163 0 CCAATACAAA 0.681148 -151 TAAACATCATCCAAGCCAAAAAGACTCGATC 14 164 1 CCAAGCAAAA 0.853725 -264 TTGTTTTCTGCCATTCCAAAACATTATTCTC 15 203 1 CCATTCAAAA 0.958018 -285 AACAGCGTAACCATTGGAAAACCCTTTCCCT 15 262 1 CCATTGAAAA 0.887907 -226 TAGATACTAACCAATACAAATCAAAGAACAG 15 340 1 CCAATCAAAT 0.797484 -148 ***** ***** Masking position 3 Map Score: 5.2815 Number of sites scoring better than the average of aligned sites = 959 Number in coding regions = 758 Number in noncoding regions = 201 Number of orfs with sites within 600 bp upstream = 172 Fraction of orfs with sites within 600 bp upstream = 0.0276261 Motif number 12 ATCTTCCTTCAAGCAATTGTGAGACAACAG 1 34 0 AAGCAATTGT 0.980983 -405 GCTTACTAAAAAGCTATTGTTTTGCAGTTT 2 162 1 AAGCTATTGT 0.927147 -139 TGATAAGCAAGAGCAATTGTTGATCTTTAT 6 218 0 GAGCAATTGT 0.971998 -184 ATAAACAGCCGAACAATTGTATTTGACACA 6 361 1 GAACAATTGT 0.921441 -41 GTGCTTTTTGAACCAATTGTGTGTTGTTTT 9 11 0 AACCAATTGT 0.936105 -290 ACAGCAGTAGAAACCATTGTGCTGGCTTAG 10 183 1 AAACCATTGT 0.864378 -118 TCAAACAATAAAGCAATTGTAAGCGTCAGC 12 267 0 AAGCAATTGT 0.980983 -235 ********** Masking position 6 Map Score: 1.7972 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 118 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 13 CTTCCTTGTGCGTCTGTTGTCTCACAATTGC 1 21 1 CGTCTGTTGC 0.933726 -418 TCGGATATTTCGTATATTGCAAGGAGCAAAA 2 121 1 CGTATATTGA 0.963765 -180 CGTCTTTTTTCGTCTTTTGCACGGTATTTTC 7 233 0 CGTCTTTTGA 0.967322 -143 TCTTTTCATCCGTATATTTTACCGTAAAATG 11 52 1 CGTATATTTA 0.748122 -330 TTCCAAATAGCGTCTATAGAAATGTAGGGTA 12 95 0 CGTCTATAGA 0.924209 -407 ACGAGGAAAACGTCTATTGGACGATTTTTGC 13 143 0 CGTCTATTGA 0.985517 -171 CATCAGTCCTCGTATTTTGTCTTCTGTTTGC 13 250 1 CGTATTTTGC 0.867589 -64 GCCCGAATCACGTCTATTGCAGATATCAAGA 14 322 0 CGTCTATTGA 0.985517 -106 ********* * Masking position 5 Map Score: 1.19786 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 148 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 14 TCCAAGATCATTGCAGACCCTTGTTATGGTCT 1 227 1 TGCGACCCTT 0.984706 -212 CCGCGCGTTATTTCCGCCGCTTACAGCTTTCT 6 138 1 TTCGCCGCTT 0.975848 -264 ACAGCTAGAATTGCTGACGCTTACAATTGCTT 12 255 1 TGCGACGCTT 0.989396 -247 TTTTAACTTTTCGCCGCCGCTTGTATCGGCGC 13 195 0 TGCGCCGCTT 0.993763 -119 ACTTAAGCGTTCGCTGCCCCTTTAGACTCTTC 15 372 0 TGCGCCCCTT 0.993099 -116 * ** ******* Masking position 11 Map Score: 0.632599 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 19 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 15 CCTACATCTCATGTATTTTTCAATAAGAGG 4 269 0 ATGTATTTTT 0.943333 -332 CCTTTAGTCAACGTATTCTTCTCCCTGAAG 4 513 1 ACGTATTCTT 0.959692 -88 CTTGGATAAAATGTATACTTATACTAGTCT 6 25 0 ATGTATACTT 0.872162 -377 ATATGACACCATGTATTCTTTACCATATAG 9 62 1 ATGTATTCTT 0.976553 -239 AAGATACTTTATGTATTCTTACTAAAATAT 9 236 0 ATGTATTCTT 0.976553 -65 TGTCAACGTAATGTACTTTTCTCCCCAATT 11 20 1 ATGTACTTTT 0.90411 -362 AAATAAATAAACGTACTCTTTACGAGTACA 12 164 0 ACGTACTCTT 0.931765 -338 CATTGATGTTATGTATTTTTCATATTCCTG 14 26 1 ATGTATTTTT 0.943333 -402 ********** Masking position 5 Map Score: 3.93508 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 138 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714