AlignACE version 2.2 July 7, 1998 AlignACE -jRIB.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 YBL033C 490 bp YBL033C rib1 1-1038 GTP cyclohydrolase II #2 YBR153W 300 bp YBR153W rib7 1-735 Riboflavin biosynthesis protein #3 YBR256C 600 bp YBR256C rib5 1-717 Riboflavin synthase alpha-chain #4 YDR487C 300 bp YDR487C rib3 1-627 3,4-dihydroxy-2-butanone 4-phosphate synthase #5 YOL143C 453 bp YOL143C RIB4 1-510 6,7-dimethyl-8-ribityllumazine synthase (DMRL synthase) #6 YOL066C 300 bp YOL066C RIB2 1-1776 DRAP deaminase Motif number 1 GGACACACAGAAAAAAAACAAAAGGGCTTTC 1 190 1 AAAAAAAAAA 0.977496 -301 CATAGGGCTAAAACAGAAATAGTAGGGTCTA 1 253 1 AAACAGAATA 0.750705 -238 AACTCAAAGGAAAAAGAAAAAGTCTCACCCT 1 309 0 AAAAAGAAAA 0.984417 -182 TCGTAAAAAGAAAAAGAAAAACTCAAAGGAA 1 328 0 AAAAAGAAAA 0.984417 -163 GAAAATCCCGAAACAGAAAAAAGAGGCAAAG 2 153 1 AAACAGAAAA 0.936483 -148 ACATCGATTCAAAAAAAATGAATATTGGCTA 3 146 1 AAAAAAAAGA 0.970169 -455 GCCATAAATGAAAAAAGAGGAAAAAACATGC 3 238 0 AAAAAAGAGA 0.883589 -363 GAAATTACCGAAAAAAAAGAAAAGGACGGAA 3 459 0 AAAAAAAAAA 0.977496 -142 GAGAATTGATAAAAAAAAGCAAGGCTATTAT 4 158 1 AAAAAAAACA 0.881753 -143 TATCTCCAACAAAAAGCAGAAGGCTAAAAAA 4 246 1 AAAAAGCAAA 0.936483 -55 GCAGAAGGCTAAAAAAAAGGAAAGGAAAAGA 4 261 1 AAAAAAAAGA 0.970169 -40 AAGGAAAGGAAAAGAAGAAAAGGCAACGTCG 4 277 1 AAAGAAGAAA 0.702914 -24 TAGCCATATAAAAGAGAACAATGAAATATTG 5 355 1 AAAGAGAAAA 0.936483 -99 AAGAGAAAATAAAAAGAATAAAACCAAAGAT 6 121 0 AAAAAGAAAA 0.984417 -180 AGTAATAATGAAAAAGAATGAAAAAAAAAAA 6 174 1 AAAAAGAAGA 0.979295 -127 AAAAGAATGAAAAAAAAAAAAAAAAAAGAAA 6 185 1 AAAAAAAAAA 0.977496 -116 AAAAAAAAAAAAAAAGAAAAACTAGTCAAAA 6 197 1 AAAAAGAAAA 0.984417 -104 TATTGCCATGAAAAAACAGGAAGAAGAGAGA 6 229 1 AAAAAACAGA 0.883589 -72 AGAACATTAAAAAAAAAACTATCAATATTAG 6 262 1 AAAAAAAATA 0.898702 -39 ******** ** Masking position 5 Map Score: 31.1749 Number of sites scoring better than the average of aligned sites = 10366 Number in coding regions = 1791 Number in noncoding regions = 8575 Number of orfs with sites within 600 bp upstream = 2034 Fraction of orfs with sites within 600 bp upstream = 0.326695 Motif number 2 GCGTCCCCTGTACAACAAAGCATCAACTTA 1 50 0 TACAACAAAG 0.96221 -441 CTATAGTATATATAAAGAAGTTGCTGTGCT 1 407 1 TATAAAGAAG 0.953773 -84 TACATAAAACTACAACAAACCTACAGG 1 474 1 TACAACAAAC 0.696712 -17 TATTCGGTTATATAACACCGCATCACACAC 2 88 1 TATAACACCG 0.927364 -213 TTGATAGTAATACAAAGAAGCTACCAATAG 2 267 0 TACAAAGAAG 0.950728 -34 CCAAATGATATAAAAAGACGGTACTTCCTA 3 538 1 TAAAAAGACG 0.811295 -63 AAGCCCAATTTACAACAACGAGGCGACCAT 4 30 0 TACAACAACG 0.921368 -271 CGAGAATTGATAAAAAAAAGCAAGGCTATT 4 157 1 TAAAAAAAAG 0.853406 -144 AGCAGAAGGCTAAAAAAAAGGAAAGGAAAA 4 260 1 TAAAAAAAAG 0.853406 -41 AAAGTAGCCATATAAAAGAGAACAATGAAA 5 351 1 TATAAAAGAG 0.750242 -103 AAAGGAACAGTATAACGCAGTATAACGCAG 5 413 1 TATAACGCAG 0.978033 -41 TATAACGCAGTATAACGCAGTATAACGCAG 5 423 1 TATAACGCAG 0.978033 -31 TATAACGCAGTATAACGCAGTATAACGCAG 5 433 1 TATAACGCAG 0.978033 -21 TATAACGCAGTATAACGCAGT 5 443 1 TATAACGCAG 0.978033 -11 ********** Masking position 5 Map Score: 13.3288 Number of sites scoring better than the average of aligned sites = 737 Number in coding regions = 481 Number in noncoding regions = 256 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 3 AAAGCATATTGCTCCCCACTCCTATCGCGC 1 78 0 GCTCCCCACT 0.957967 -413 AGAAAAAGTCTCACCCTACACAACTTGTTT 1 296 0 TCACCCTACA 0.964889 -195 GCGCTGGCGCTCACCCCACAAGAGCGTCCG 1 375 0 TCACCCCACA 0.995953 -116 ACTTCTTTAACTACCCCACAAAGCTGCCAG 3 35 1 CTACCCCACA 0.957953 -566 GCGACCATCTGCACACCACACTTGACA 4 8 0 GCACACCACA 0.97902 -293 ATATTTACATTCACCTCACATATATACGCC 4 219 0 TCACCTCACA 0.982544 -82 CAGGTCCGGGTCACACCACTACCCTTACTA 5 115 1 TCACACCACT 0.972289 -339 CTAGTTCCATCCACCTCACTTAAAGTTACC 5 169 0 CCACCTCACT 0.966764 -285 ********** Masking position 8 Map Score: 7.29505 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 180 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 4 TACAAGAACTAAAAATGTTGAATTTGGTGACCTAGGCA 2 21 1 AAAATATTGT 0.795069 -280 ATCTTCTAAAATTGTTGATAGTAATACAAAGAAGC 2 276 0 AAAATAATAT 0.856881 -25 ATTGGCTAGTAAAACTATTCATACTGCTATAAATACAC 3 169 1 AAAATAATGT 0.965736 -432 AAAAAGAGGAAAAAACATGCAGATTGTTTTTGAGCTTT 3 220 0 AAAACAATGT 0.98081 -381 CTACGCGACAAAAATCAATAAAAGAGATTGCTAGCCAT 3 264 0 AAAACAAAGT 0.895667 -337 TATATAAACCAATATCGAAGACAGTGATCTTTTTACAG 3 383 0 AATACAATGT 0.963433 -218 AAAATTTCACAATAGCACGTATATTAATAATAGCCTTG 4 177 0 AATACAATAT 0.881396 -124 GGAACCTCCGAAAACCTCCCAGAGTTTTAATTATACGT 5 238 0 AAAACAATTT 0.931648 -216 CAGGATTTTTAATAGTAAATATAATAGTAAAGAACCTA 6 11 0 AATATAATAT 0.769292 -290 TTTACTATTAAAAATCCTGTAAAGTGATCTGGGCTGTC 6 30 1 AAAACAATGT 0.986538 -271 TAAAAAGAATAAAACCAAAGATAGTGGTACAACTGACG 6 105 0 AAAACAATGT 0.986684 -196 AAAAAAAAGAAAAACTAGTCAAAATTATTGCCATGAAA 6 204 1 AAAATAATTT 0.864922 -97 **** * * * ** * Masking position 11 Map Score: 7.19197 Number of sites scoring better than the average of aligned sites = 1017 Number in coding regions = 745 Number in noncoding regions = 272 Number of orfs with sites within 600 bp upstream = 209 Fraction of orfs with sites within 600 bp upstream = 0.0335689 Motif number 5 GTTGTTTGGCTGAGCGGCCGGACACACAGA 1 171 1 TGAGCGGCCG 0.98266 -320 AAAAAACAAAAGGGCTTTCGTTAAAAGGGA 1 202 1 AGGGCTTTCG 0.934655 -289 TCACCCCACAAGAGCGTCCGACTAATTTCT 1 365 0 AGAGCGTCCG 0.882774 -126 AAGAAGTTGCTGTGCTGGCGTGGACAATAA 1 421 1 TGTGCTGGCG 0.919356 -70 ATCCTTTGCATGAGCTTTCTGTAGAAATTT 3 81 1 TGAGCTTTCT 0.833315 -520 AGATTGTTTTTGAGCTTTTATGTCATAACA 3 208 0 TGAGCTTTTA 0.822753 -393 GGAGAGTACTTGGGCGGCTACTTTAGTTTT 3 420 0 TGGGCGGCTA 0.885064 -181 TGTTGTAAATTGGGCTTTCGATGCTAAGAC 4 43 1 TGGGCTTTCG 0.982945 -258 ATGCTGGAGATGAGCTGCTGAAGCATCCGT 5 35 1 TGAGCTGCTG 0.971347 -419 AGCATCCGTTTGTGCTGTTGGTTTAATATG 5 56 1 TGTGCTGTTG 0.931564 -398 TAAAGTGATCTGGGCTGTCAGGCTAGAAGT 6 49 1 TGGGCTGTCA 0.968549 -252 ********** Masking position 5 Map Score: 4.83212 Number of sites scoring better than the average of aligned sites = 918 Number in coding regions = 731 Number in noncoding regions = 187 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 6 CTTTTGTTTTTTTTCTGTGTGTCCGGCCGCTCAGCC 1 178 0 TTTTCGTGCG 0.979722 -313 TTCTTTTTCTTTTTACGATTTGTCAGAAATTAGTCG 1 341 1 TTTTAGATCG 0.955277 -150 AAGAAGTTTATTCTCCGTGGTTGCAGCTGTG 3 6 0 TTCTCGTTCG 0.979722 -595 GTTTTTGAGCTTTTATGTCATAACAGGTGTATTTAT 3 197 0 TTTTAGTTCG 0.97603 -404 TTTTCCTCTTTTTTCATTTATGGCTAGCAATCTCTT 3 245 1 TTTTCTTTCA 0.88911 -356 CTTTTCTTTTTTTTCGGTAATTTCCATGGAGGAAGG 3 466 1 TTTTCGTTCA 0.97603 -135 CTCTGGGAGGTTTTCGGAGGTTCCCGTAGGTCAATT 5 252 1 TTTTCGATCG 0.990865 -202 AGCGGAGATATTTTCGGAGGTCCCCGTTAATAAGAG 5 314 1 TTTTCGATCG 0.990865 -140 GGCTAGAAGTTTTTCATTTATGTCTGAAACAGATAA 6 69 1 TTTTCTTTCG 0.97603 -232 ***** ** * * * Masking position 4 Map Score: 5.28258 Number of sites scoring better than the average of aligned sites = 360 Number in coding regions = 268 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 7 GTGGCGTACATAAAACTACAACAAACCTAC 1 468 1 TAAAACTACA 0.937155 -23 AAAACTACAACAAACCTACAGG 1 479 1 CAAACCTACA 0.955758 -12 ATCACACACACAAACCCACATGCCTTTCAG 2 109 1 CAAACCCACA 0.958882 -192 TAGTTTTATATAAACCAATATCGAAGACAG 3 397 0 TAAACCAATA 0.879667 -204 TTGGTTTATATAAAACTAAAGTAGCCGCCC 3 409 1 TAAAACTAAA 0.878347 -192 AGAAGCATATTAAACCAACAGCACAAACGG 5 61 0 TAAACCAACA 0.974457 -393 TATGCTTCTCTAAACCAAAAAATTTCAGCC 5 82 1 TAAACCAAAA 0.948642 -372 ATAAAAAGAATAAAACCAAAGATAGTGGTA 6 114 0 TAAAACCAAA 0.886288 -187 ********** Masking position 4 Map Score: 3.04253 Number of sites scoring better than the average of aligned sites = 462 Number in coding regions = 339 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 8 AGCAATATGCTTTTACTTCGTATGCCAAGT 1 95 1 TTTTACTTCG 0.872541 -396 GACTTTTTCTTTTTCCTTTGAGTTTTTCTT 1 316 1 TTTTCCTTTG 0.902036 -175 CCGAATATTCAGTTTCTTCGTAATCTCTAC 2 65 0 AGTTTCTTCG 0.779859 -236 TCTGCTAGATTGTTTCATCGTATCCAAAGC 2 223 0 TGTTTCATCG 0.922932 -78 TAATGCTCAGTTTTCCATCCTTTGCATGAG 3 65 1 TTTTCCATCC 0.959956 -536 TATCCAAAAATTTTACATCGATTCAAAAAA 3 132 1 TTTTACATCG 0.936658 -469 TTTTTCGGTAATTTCCATGGAGGAAGGTTA 3 475 1 ATTTCCATGG 0.895313 -126 CTATTGTGAAATTTTCATTGGCGTATATAT 4 200 1 ATTTTCATTG 0.888514 -101 TGTTGGAGATATTTACATTCACCTCACATA 4 227 0 ATTTACATTC 0.758931 -74 CCTTTTCTTCTTTTCCTTTCCTTTTTTTTA 4 270 0 TTTTCCTTTC 0.853695 -31 CGTGGAAACTAGTTCCATCCACCTCACTTA 5 177 0 AGTTCCATCC 0.885493 -277 TTTTTTTTTTTTTTTCATTCTTTTTCATTA 6 179 0 TTTTTCATTC 0.887688 -122 TTCTTCCTGTTTTTTCATGGCAATAATTTT 6 224 0 TTTTTCATGG 0.893536 -77 ********** Masking position 4 Map Score: 5.11777 Number of sites scoring better than the average of aligned sites = 2690 Number in coding regions = 1908 Number in noncoding regions = 782 Number of orfs with sites within 600 bp upstream = 646 Fraction of orfs with sites within 600 bp upstream = 0.103758 Motif number 9 TGCTGTCTCTAAGTTACCCGATAAGTTGAT 1 29 1 AAGTTACCCG 0.954647 -462 ATCTGGAGCATAAGTACCCGAGCATATATA 1 128 0 TAAGTACCCG 0.922244 -363 TCTGTTTCGGGATTTTCCCGACATCAACTA 2 140 0 GATTTTCCCG 0.901089 -161 AAGGACGGAATTGGTACCCGGAGAGTACTT 3 439 0 TTGGTACCCG 0.970488 -162 AAGGGTAGTGGTGTGACCCGGACCTGATCG 5 111 0 GTGTGACCCG 0.936331 -343 GAGGTTTTCGGAGGTTCCCGTAGGTCAATT 5 258 1 GAGGTTCCCG 0.991825 -196 GATATTTTCGGAGGTCCCCGTTAATAAGAG 5 320 1 GAGGTCCCCG 0.990185 -134 ********** Masking position 7 Map Score: 1.04233 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 151 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 10 GGCTGGTATATATACTAATGCTGTCTC 1 7 1 TATTATACTA 0.853639 -484 GCCAAGTAGTTATATATGCTCGGGTACTTAT 1 118 1 TATTATGCTC 0.973371 -373 TATGCTCGGGTACTTATGCTCCAGATTATAG 1 132 1 TACTATGCTC 0.962998 -359 GCAACTTCTTTATATATACTATAGCGGCGCT 1 400 0 TATTATACTA 0.853639 -91 GTTGTAGTTTTATGTACGCCACTTTTTGTAA 1 459 0 TATTACGCCA 0.946998 -32 GTTGGTACTGTATTTCTGCTAGATTGTTTCA 2 236 0 TATTCTGCTA 0.935513 -65 TTAACATTAATACCTACGCGACAAAAATCAA 3 284 0 TACTACGCGA 0.873619 -317 ATCAGGCAATAACCTATGCTCACCCGCCTCG 4 112 0 AACTATGCTC 0.785502 -189 TCACCTCACATATATACGCCAATGAAAATTT 4 208 0 TATTACGCCA 0.946998 -93 CCTCCGAAAATATCTCCGCTCCCAGAATATG 5 303 0 TATTCCGCTC 0.944531 -151 *** ******* Masking position 5 Map Score: 1.06143 Number of sites scoring better than the average of aligned sites = 488 Number in coding regions = 258 Number in noncoding regions = 230 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 11 ********** No masking Map Score: -2.0013e-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 12 ********** No masking Map Score: -2.0013e-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: -2.0013e-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