AlignACE version 2.2 July 7, 1998 AlignACE -jRPA.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 YDR156W 524 bp YDR156W RPA14 1-414 RNA polymerase I subunit A14 #2 YJL148W 486 bp YJL148W RPA34 1-702 RNA polymerase I subunit, not shared (A34.5) #3 YJR063W 345 bp YJR063W RPA12 1-378 A12.2 subunit of RNA polymerase I #4 YNL248C 300 bp YNL248C RPA49 1-1248 49-kDa alpha subunit of RNA polymerase A #5 YOR340C_YOR341W 804 bp YOR340C RPA43 1-981 DNA-dependent RNA polymerase I subunit A43 YOR341W rpa190 1-4995 RNA polymerase I subunit 190 (alpha) #6 YPR010C 600 bp YPR010C RPA135 1-3612 RNA polymerase I subunit A135 Motif number 1 AAGTAAGCTCGAAATGAAAAATTTTACACC 1 405 0 GAAATGAAAA 0.976073 -120 TTTTTAAACAGAAAAGAAGAATTGATT 2 8 0 GAAAAGAAGA 0.832857 -479 AAAGCTCTAGAAAATGAAAAAAAATTTTCT 2 256 1 AAAATGAAAA 0.936071 -231 TTCTCAGGCTGAAAAGAAAATTTTTTTTCA 2 270 0 GAAAAGAAAA 0.980221 -217 TTTCATGTTTGAGAAAAAAAGTTTCGCAAC 2 334 0 GAGAAAAAAA 0.93757 -153 TGAAATTAAAGAAATGAAAAATTTTATCGA 2 359 1 GAAATGAAAA 0.976073 -128 TTAGGGCTATAAAACAAAAATAGTTAAGTG 3 146 1 AAAACAAAAA 0.776848 -200 TTACGAACGAAAGATGAAAAATATGAAAAA 3 222 1 AAGATGAAAA 0.877494 -124 TGAAAAATATGAAAAAAAAAAAAATCAAAT 3 236 1 GAAAAAAAAA 0.968454 -110 TAAAGAATCCAAGAAGAAAAGAAAGGCTTA 3 299 1 AAGAAGAAAA 0.896924 -47 ATTATCAATTGAAAAGAACAGTATTGCTAA 4 89 0 GAAAAGAACA 0.901674 -212 TTGACTCTTCGCGATGAAAAATGTTTGCGG 4 124 1 GCGATGAAAA 0.843233 -177 TCAGCTCATCGCAATAAAAAATTTTCAGCG 4 161 0 GCAATAAAAA 0.871982 -140 CTGTCGCTTTGAAATGAAAAGATTCCGATG 5 189 0 GAAATGAAAA 0.976073 -616 CACCACTAAGAAAATAAACACGATAGTTAT 5 518 0 AAAATAAACA 0.626646 -287 AAATTTTGGTAAAAAAAAAAAAAAAGAAAA 5 594 1 AAAAAAAAAA 0.916799 -211 AAAAAAAAAAAAAAAGAAAAAATTTTTTTT 5 604 1 AAAAAGAAAA 0.946774 -201 GATGAGATTTGAAATAAAAAAAATTTTTTC 5 619 0 GAAATAAAAA 0.961935 -186 TCGAAGTACGGCAAAAAAAAAGCAGAAAAA 5 761 0 GCAAAAAAAA 0.89218 -44 AGTAACGGAGACAAAAAGATTTGTTTA 6 8 1 GAGACAAAAA 0.825924 -593 AAAAAAAAAAAAAAAAAAAAAAAAAAACAC 6 439 0 AAAAAAAAAA 0.916799 -162 TTTTTCATACGAAAAAAAAAAAAAAAAAAA 6 450 0 GAAAAAAAAA 0.968454 -151 ********** Masking position 4 Map Score: 30.0607 Number of sites scoring better than the average of aligned sites = 5835 Number in coding regions = 2058 Number in noncoding regions = 3777 Number of orfs with sites within 600 bp upstream = 2213 Fraction of orfs with sites within 600 bp upstream = 0.355445 Motif number 2 AGCTCGAAATGAAAAATTTTACACCCGCAA 1 400 0 GAAAAATTTT 0.98819 -125 AGGCTGAAAAGAAAATTTTTTTTCATTTTC 2 265 0 GAAAATTTTT 0.958419 -222 TTCAGCCTGAGAAAGTTTTTTCTTAGGGCA 2 287 1 GAAAGTTTTT 0.915437 -200 TGGGTGTTGCGAAACTTTTTTTCTCAAACA 2 329 1 GAAACTTTTT 0.915437 -158 TTAAAGAAATGAAAAATTTTATCGATGAGC 2 364 1 GAAAAATTTT 0.98819 -123 TCTTCGCGATGAAAAATGTTTGCGGTCACC 4 129 1 GAAAAATGTT 0.944218 -172 CACCCGCGCTGAAAATTTTTTATTGCGATG 4 155 1 GAAAATTTTT 0.958419 -146 TTTTATTGCAGAAAAATTTTTTTCAAACCA 5 147 1 GAAAAATTTT 0.98819 -658 ATTTTATAGTGAAAAATTTTGGTAAAAAAA 5 581 1 GAAAAATTTT 0.98819 -224 AAAAAAAAAAGAAAAAATTTTTTTTATTTC 5 609 1 GAAAAAATTT 0.919499 -196 AGATGCGCTTGAAAAATTTTTCATACGAAA 6 466 0 GAAAAATTTT 0.98819 -135 ********** Masking position 4 Map Score: 20.7908 Number of sites scoring better than the average of aligned sites = 763 Number in coding regions = 282 Number in noncoding regions = 481 Number of orfs with sites within 600 bp upstream = 406 Fraction of orfs with sites within 600 bp upstream = 0.0652104 Motif number 3 TATAAACGTATTCTCTTGAGCCTTCTATCC 1 123 0 TTCTCTTGAG 0.944124 -402 GTCATGAAATTTCTCTTGAGATTATTCAAA 2 41 1 TTCTCTTGAG 0.944124 -446 TGCAATGCCCTTCACTTGACATAAATTTGA 3 260 0 TTCACTTGAC 0.898572 -86 TTGGATTCTTTACACTTGCCATGCAATGCC 3 281 0 TACACTTGCC 0.96896 -65 TAATAGTAAGTATTCTTGCATGAACACTAA 4 209 1 TATTCTTGCA 0.89563 -92 ATCCTTTGTGTATTCTTGACAGAAAATATT 5 220 0 TATTCTTGAC 0.940916 -585 ACACAAAGGATACACTTGCAGCTGGAATAA 5 239 1 TACACTTGCA 0.913397 -566 GATCAGATCGTATCCTTGCCCGCTATCGGA 5 375 1 TATCCTTGCC 0.886547 -430 TTATTGAGATTACTCTTGCGAGTGTTTTTT 6 418 1 TACTCTTGCG 0.983474 -183 TATTTGTCAATATTCTTGAGGAAGACTTGC 6 556 0 TATTCTTGAG 0.940916 -45 ********** Masking position 6 Map Score: 5.82997 Number of sites scoring better than the average of aligned sites = 550 Number in coding regions = 411 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 4 TGATGACGACAGTGGCAAAAGGATAGAAGGCTCAAGA 1 103 1 AGAAAAGATA 0.947708 -422 GAAACCCCTAAGGGGCGAAAGGCGGGTAACATCTAAC 1 346 1 AGGAAAGCGT 0.955397 -179 GCAATGCTGAAGTCGAAAGAGGAGGATTACTCTCATT 2 97 1 AGAAGAGAGT 0.921949 -390 TTTATCGATGAGCATTGAATAGCTCAAGTTATAGGGT 2 381 1 AGGAATGCTA 0.780889 -106 AGCACTTTTTAGCATTGAAATGCTTAAAATGTGTGAA 3 47 1 AGGAAAGCTA 0.971006 -299 GAATCCAAGAAGAAAAGAAAGGCTTAAAGCAATCCAG 3 303 1 AGGAAAGCTA 0.971006 -43 TCTTCATAAAAGCCCTGAGAAGATATA 4 1 0 AGGAGAGATA 0.978936 -300 ATTATATATAAGCAAAAAAACGAGGGAGTGTATAACG 5 43 1 AGAAAAGAGA 0.961597 -762 AAATCATTTTAGCTATAAGAGGAGACATAAGAAACTC 5 435 0 AGAAGAGAGA 0.962286 -370 AACCTTTTTAAGAGATGAGATGAGATTTGAAATAAAA 5 630 0 AGGAGAGAGT 0.967453 -175 GCAAAAAAAAAGCAGAAAAAGGATAAAGTTCACTGTA 5 744 0 AGAAAAGATA 0.947708 -61 GATGACATCGAGTGATGAAATTATTCATAAATCTGCA 6 208 1 AGGAAATATA 0.75025 -393 TGAATAATTAAGAGATGAGATGAGTCTCTAAGATGCG 6 489 0 AGGAGAGAGT 0.967453 -112 ** **** *** * Masking position 8 Map Score: 7.52076 Number of sites scoring better than the average of aligned sites = 1025 Number in coding regions = 701 Number in noncoding regions = 324 Number of orfs with sites within 600 bp upstream = 282 Fraction of orfs with sites within 600 bp upstream = 0.0452939 Motif number 5 TTTCATTTCGAGCTTACTTCAAGATGATGCAT 1 416 1 ACTTACTCAA 0.895246 -109 TATTATCGAAATCTTACCTCAGACGTCTCCAG 1 499 0 ACTTACTCAG 0.987102 -26 CCTACATAAGAACAAACAGCAGTGACTGTAAT 2 142 0 ACAAACGCAG 0.92777 -345 GATTATTATAACCTTACAGAAGGTTGTCCAGT 2 199 1 ACTTACGAAG 0.987102 -288 TCACTATAAAATATTACCGAAGAAAACGGGTA 5 561 0 AATTACGAAG 0.895246 -244 AGAGCCCTTTAACTTACAGAAGTAAATGTACA 6 104 0 ACTTACGAAG 0.987102 -497 CCACTTAATTATCATACCGCAGAAGCGGCCTC 6 345 1 ACATACGCAG 0.98624 -256 TAATTATTCAAACTTACTTCAGCTGTCTCGTA 6 516 1 ACTTACTCAG 0.987102 -85 * ***** **** Masking position 6 Map Score: 4.73704 Number of sites scoring better than the average of aligned sites = 291 Number in coding regions = 206 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 6 GCTTCCACTCATTTCTGTCTCTGGTAATGGCC 1 215 0 ATTCTGTCCT 0.987043 -310 CGACTTCAGCATTGCACTCCTTCCCATTTGAT 2 80 0 ATTCACTCTT 0.963793 -407 AAAGAGGAGGATTACTCTCATTCTTACTACAT 2 112 1 ATTCTCTCTT 0.963793 -375 TTCTTACTACATTACAGTCACTGCTGTTTGTT 2 132 1 ATTCAGTCCT 0.987043 -355 TGCTACCACTATTGCAGTCGTTATCAACCTTT 4 263 1 ATTCAGTCTT 0.984395 -38 GACAGAAAATATTACTGTCGCTTTGAAATGAA 5 201 0 ATTCTGTCCT 0.987043 -604 CTCAATAATAATTTCCGTCATTAGCGATTATA 6 394 0 ATTCCGTCTT 0.973683 -207 *** ***** ** Masking position 1 Map Score: 4.50262 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 148 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 7 GCCGTGGCCCTTCTCACTTTGGTTGGGCTTACG 1 185 0 TTCTCTTTGT 0.985521 -340 TTCCACTCATTTCTGTCTCTGGTAATGGCCGTG 1 212 0 TTCTCTCTGT 0.992937 -313 CGTCTCGAATTTCTTCCTCTGCTAGACGGGCTT 1 253 0 TTCTCTCTGT 0.992937 -272 AACGCCTTACTTCTATCCTCGATAATTTCTAAG 5 475 0 TTCTCCTCGT 0.961964 -330 TTTTCTTTCTGGCTTTGATTATAATCGAA 5 786 0 TTCTCTTTGT 0.985515 -19 AAACAAATCTTTTTGTCTCCGTTACT 6 4 0 TTTTCTCCGT 0.956559 -597 ATGTTTAAGCTTCTTCCTCCGATTAAGTTTTGT 6 74 1 TTCTCTCCGT 0.994144 -527 **** ***** * Masking position 4 Map Score: 5.32731 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 112 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 8 CTTTATGGGCAGAAACAAAATGTATAAATAC 2 229 0 AGAAAAAAAT 0.886619 -258 CTCTAGAAAATGAAAAAAAATTTTCTTTTCA 2 260 1 TGAAAAAAAT 0.974546 -227 TAAACGGGATTAACAAAAAATTGAT 2 472 1 TAACAAAAAT 0.912253 -15 ATTAGGGCTATAAAACAAAAATAGTTAAGTG 3 145 1 TAAAAAAAAA 0.807921 -201 AAATATGAAAAAAAAAAAAATCAAATTTATG 3 240 1 AAAAAAAAAT 0.807921 -106 GCCCTTCACTTGACATAAATTTGATTTTTTT 3 253 0 TGACAAAATT 0.861212 -93 AGTGGAGGTTTACAATAAAATAGAGCCGAAG 5 87 0 TACAAAAAAT 0.866778 -718 AAAATTTTTCTGCAATAAAATACTAATGGCA 5 136 0 TGCAAAAAAT 0.92364 -669 ATGGGTGGTTTGAAAAAAATTTTTCTGCAAT 5 151 0 TGAAAAAATT 0.924766 -654 TGTGTATTCTTGACAGAAAATATTACTGTCG 5 213 0 TGACAAAAAT 0.950807 -592 AAAATTTTGGTAAAAAAAAAAAAAAAGAAAA 5 593 1 TAAAAAAAAA 0.807921 -212 AGATTTGAAATAAAAAAAATTTTTTCTTTTT 5 614 0 TAAAAAAATT 0.868622 -191 ATTTAGCATTTGAAATATAATGAGAAAAGAG 6 132 0 TGAAAATAAT 0.802932 -469 ***** ***** Masking position 5 Map Score: 5.13154 Number of sites scoring better than the average of aligned sites = 2861 Number in coding regions = 1269 Number in noncoding regions = 1592 Number of orfs with sites within 600 bp upstream = 1151 Fraction of orfs with sites within 600 bp upstream = 0.18487 Motif number 9 ATGTATCAAATGGGAAGGAGTGCAATGCTGAAG 2 76 1 TGGAAAGTGC 0.963837 -411 CATATAGGTCTGTGATCGAGTGAGCAGTGAGCA 2 427 1 TGGATAGTGA 0.978678 -60 AACTCTATCGTGACATTCAGTGA 3 1 0 TGCATAGTGA 0.988738 -345 AGCATTTCAATGCTAAAAAGTGCTAGTTTACAG 3 38 0 TGTAAAGTGC 0.907161 -308 TCTTTACACTTGCCATGCAATGCCCTTCACTTG 3 272 0 TGCATAATGC 0.969567 -74 ATTTAGCATTTGAAATATAATGAGAAAAGAGCC 6 130 0 TGAATAATGA 0.793768 -471 AAGACGCTGATGACATCGAGTGATGAAATTATT 6 200 1 TGCATAGTGA 0.988738 -401 CTATTAGAAATGCCATTAAGTGCTTTGAACTCT 6 281 0 TGCATAGTGC 0.992872 -320 ** *** ***** Masking position 5 Map Score: 2.77157 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 112 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 10 ATCCTTTTGCCACTGTCGTCATCATTTGTT 1 97 0 CACTGTCGTC 0.941281 -428 CCGCCACGTCCCGCCTCGTCTCGAATTTCT 1 272 0 CCGCCTCGTC 0.993344 -253 GGCGCCCAGCCCGCCACGTCCCGCCTCGTC 1 282 0 CCGCCACGTC 0.984831 -243 TTTCCACCGCCCCCCTCGTCCTCTACGGTA 1 320 0 CCCCCTCGTC 0.994925 -205 GACACCTAATCACCGACGCCAATTAGCAAT 4 67 1 CACCGACGCC 0.942997 -234 ACCACCCATACACCCTCATCGGAATCTTTT 5 173 1 CACCCTCATC 0.961704 -632 TCGATGTCATCAGCGTCTTCCTTCATTTGA 6 189 0 CAGCGTCTTC 0.935716 -412 ********** Masking position 7 Map Score: 2.45343 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 214 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 11 AATACGTTTATATTTATACAGGGAATCGAA 1 141 1 TATTTATACA 0.813031 -384 CTCTTGAGATTATTCAAACTTGAATGTATC 2 53 1 TATTCAAACT 0.930483 -434 GGTTGTCCAGTATTTATACATTTTGTTTCT 2 220 1 TATTTATACA 0.813031 -267 TTTATGAAGATATTCATGCATAGAATAAGA 4 28 1 TATTCATGCA 0.963399 -273 ATATCATTAGTGTTCATGCAAGAATACTTA 4 215 0 TGTTCATGCA 0.927784 -86 GAATCTTGCTTATTCCAGCTGCAAGTGTAT 5 248 0 TATTCCAGCT 0.860145 -557 TGTTTTTGTATGTTTAAGCTTCTTCCTCCG 6 65 1 TGTTTAAGCT 0.805964 -536 ATCTCTTAATTATTCAAACTTACTTCAGCT 6 510 1 TATTCAAACT 0.930483 -91 TGTCTCGTAATATTCAAGCAAGTCTTCCTC 6 539 1 TATTCAAGCA 0.970021 -62 ********** Masking position 4 Map Score: 1.2348 Number of sites scoring better than the average of aligned sites = 747 Number in coding regions = 536 Number in noncoding regions = 211 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 12 ACACTTGTCAGCGTAAGCCCAACCAAAGTG 1 174 1 GCGTAAGCCC 0.979301 -351 ACAGAAATGAGTGGAAGCGCGTGGAAGCCC 1 229 1 GTGGAAGCGC 0.991851 -296 GTGGAAGCGCGTGGAAGCCCGTCTAGCAGA 1 239 1 GTGGAAGCCC 0.996991 -286 GAGGGGGGCGGTGGAAACCCCTAAGGGGCG 1 333 1 GTGGAAACCC 0.98814 -192 ********** Masking position 5 Map Score: 0.985644 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 23 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 13 GTAGTATTAGCGGTTGAGTTTGGATTGAGT 1 12 1 CGGTTGAGTT 0.967213 -513 GGTTGAGTTTGGATTGAGTTGAGATATTAA 1 23 1 GGATTGAGTT 0.948715 -502 CAATGCTCATCGATAAAATTTTTCATTTCT 2 368 0 CGATAAAATT 0.824835 -119 CTGAATGTCACGATAGAGTTATCGCTGTAA 3 14 1 CGATAGAGTT 0.977698 -332 ATTAGGTGTCCGGTCAAGTTCTTATTCTAT 4 47 0 CGGTCAAGTT 0.934766 -254 AGCAGAAAAAGGATAAAGTTCACTGTATAG 5 741 0 GGATAAAGTT 0.938721 -64 CTTCTTCCTCCGATTAAGTTTTGTACATTT 6 83 1 CGATTAAGTT 0.973193 -518 ********** Masking position 7 Map Score: 0.778112 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 192 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 14 GGTAGTATTAGCGGTTGAGTTTGGAT 1 6 1 TATTAGGGTT 0.95837 -519 AGCGTGTGGTTATTGGGTGTTGCGAAACTTT 2 316 1 TATTGGTGTT 0.95837 -171 TATGACAATGTAGTGGAGGTTTACAATAAAA 5 98 0 TAGTGGGGTT 0.992348 -707 GATGAGGGTGTATGGGTGGTTTGAAAAAAAT 5 162 0 TATGGGGGTT 0.981858 -643 TTTATTTTCTTAGTGGTGGTTCTTTTATTAT 5 530 1 TAGTGGGGTT 0.992348 -275 ****** **** Masking position 2 Map Score: 0.0391763 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 87 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 15 ********** No masking Map Score: -7.93376e-13 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