AlignACE version 2.2 July 7, 1998 AlignACE -jMRS.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 YBR091C 300 bp YBR091C MRS5 1-330 Nuclear protein involved in mitochondrial intron splicing #2 YHR005C-A 300 bp YHR005C-A MRS11 1-282 May act cooperatively with Mrs5p in mitochondrial protein import or other related essential mitochondrial processes #3 YIR021W 600 bp YIR021W mrs1 1-1092 mitochondrial RNA splicing #4 YJL133W 600 bp YJL133W MRS3 1-945 mitochondrial carrier protein #5 YKR052C 600 bp YKR052C MRS4 1-915 mitochondrial carrier protein, highly homologous to Mrs3p #6 YOR334W 300 bp YOR334W MRS2 1-1413 splicing factor #7 YOR370C 494 bp YOR370C MRS6 1-1812 protein of the TCD\/MRS6 family of GDP dissociation inhibitors (Rab escort protein)\; component of Rab geranylgeranyl transferase Motif number 1 CTACTAGTACATAAAAGAAGATCAGAATCG 1 141 0 ATAAAAGAAG 0.886134 -160 GCAGAATGAAAAGAAAAAAGTTAACTAAAA 1 194 1 AAGAAAAAAG 0.947709 -107 AAAATTAAAGAAAAAAAATGTCCGATAGCT 2 152 0 AAAAAAAATG 0.96061 -149 AGATCATGCAAAAAAATAAGACATCATTTA 3 118 0 AAAAAATAAG 0.93276 -483 AATTTCGTCGAAGAAAAATGATCTATGTCA 3 301 1 AAGAAAAATG 0.818599 -300 CACACATTTGAAAAAAAGTGGGCGGAACGT 4 134 0 AAAAAAAGTG 0.826362 -467 AAAAAAAAAGAAAAAAGGAGCAATCGTTCG 4 282 0 AAAAAAGGAG 0.859144 -319 AAAAAAAGCAAAAAAAAAAGAAAAAAGGAG 4 292 0 AAAAAAAAAG 0.989893 -309 CGGTGAGTATAAAAAAAAAGCAAAAAAAAA 4 304 0 AAAAAAAAAG 0.989893 -297 CGATCCCAAGATAAAATAAGGAAGTTGTTG 4 489 0 ATAAAATAAG 0.775482 -112 TTATGTTATAAAAAAAGAAGATATT 4 586 1 AAAAAAGAAG 0.968998 -15 AAAGCGAGAAAAAAAAAATGCTGAATTCCA 5 97 0 AAAAAAAATG 0.96061 -504 AACAACATACAAAAAAAAATCTGTTAGGAG 6 112 0 AAAAAAAAAT 0.812146 -189 AAAAGAAGAAAAAAAAAAAGAGACAAAAGA 6 163 0 AAAAAAAAAG 0.989893 -138 AAAAAAAAAAAAAAAAAAAGAAGAAAAAAA 6 178 0 AAAAAAAAAG 0.989893 -123 TAATGCTGCAAAAAAAAAAAAAAAAAAAAA 6 192 0 AAAAAAAAAA 0.884037 -109 AACTTGAAAAAAAAAAAAAAAAAAAAAAAG 7 89 1 AAAAAAAAAA 0.884037 -406 AAAAAAAAAAAAAAAAAAAGAAAACAGAAC 7 99 1 AAAAAAAAAG 0.989893 -396 AGTGAAGAAGATAAAAAAAGGTTCTATATC 7 130 1 ATAAAAAAAG 0.96061 -365 TTAAACCCTTAAAAAAACAGTAATAAATTA 7 409 0 AAAAAAACAG 0.912173 -86 TATAATACAAATAAAAAAAGGAAGACTAAT 7 457 1 ATAAAAAAAG 0.96061 -38 ********** Masking position 5 Map Score: 37.6202 Number of sites scoring better than the average of aligned sites = 3230 Number in coding regions = 832 Number in noncoding regions = 2398 Number of orfs with sites within 600 bp upstream = 1534 Fraction of orfs with sites within 600 bp upstream = 0.246386 Motif number 2 GTTAACTTTTTTCTTTTCATTCTGCCGCTAA 1 188 0 TTCTTTCATT 0.735596 -113 TTGGAAGCATTTTTTGCATTGATTTCCCAAT 2 97 1 TTTTTGATTG 0.747366 -204 GACATTTTTTTTCTTTAATTTTTTCAGCGAG 2 160 1 TTCTTTATTT 0.921031 -141 AGTAATTGTATTCTTGAATTGGGAGCCTGAA 3 13 1 TTCTTGATTG 0.932466 -588 CGTCATATTATTCTTGTCTCGACATTAGGCC 3 268 1 TTCTTGCTCG 0.960113 -333 CACTTTTTCATTTTTCCCTTTTCCGTTGTTG 3 473 0 TTTTTCCTTT 0.783766 -128 TTTTTCTTTTTTTTTTGCTTTTTTTTTATAC 4 297 1 TTTTTTCTTT 0.887341 -304 TCTTCATCGATTCTTTCCTCTTTCAACAACT 4 466 1 TTCTTTCTCT 0.953124 -135 TTCAGCATTTTTTTTTTCTCGCTTTTGATAG 5 102 1 TTTTTTCTCG 0.852409 -499 TAGCAGGGTGTTCTTGCCTTTCAGTCTTCGC 5 399 0 TTCTTGCTTT 0.970438 -202 AGTTTTTTACTTCTTCACTTTGTACTTCTCA 5 557 0 TTCTTCCTTT 0.944188 -44 TCAAAGAACTTTCTTGTCTTGGAAGGACCAT 6 38 0 TTCTTGCTTG 0.977538 -263 GACAAGAAAGTTCTTTGATTGATCGACCAGC 6 51 1 TTCTTTATTG 0.939255 -250 TTGTATGTTGTTCTTTCCTCTGTGGTGGTCC 6 130 1 TTCTTTCTCT 0.953124 -171 TTTTTTTTTCTTCTTTTTTTTTTTTTTTTTT 6 176 1 TTCTTTTTTT 0.810236 -125 TTGTTCTGTTTTCTTTTTTTTTTTTTTTTTT 7 100 0 TTCTTTTTTT 0.810236 -395 TTTTTTTATCTTCTTCACTTGTTCTGTTTTC 7 118 0 TTCTTCCTTG 0.957316 -377 GTTTCCCGTGTTCTTTTCCCGTCATTAAATA 7 181 1 TTCTTTCCCG 0.847662 -314 ATAAAAATTTTTCTTGTACTGATTGAATTTA 7 285 0 TTCTTGACTG 0.74027 -210 TTAGTCTTCCTTTTTTTATTTGTATTATAGA 7 455 0 TTTTTTATTT 0.714194 -40 ****** **** Masking position 5 Map Score: 18.7546 Number of sites scoring better than the average of aligned sites = 4137 Number in coding regions = 2608 Number in noncoding regions = 1529 Number of orfs with sites within 600 bp upstream = 1122 Fraction of orfs with sites within 600 bp upstream = 0.180212 Motif number 3 TAGCGGCAGAATGAAAAGAAAAAAGTTAACTAAA 1 189 1 AAAAAAAAAA 0.832 -112 AAAAAAGTTAACTAAAAAGTAAGAACAGCAAAGT 1 207 1 AAAAATAAGA 0.924283 -94 CTTTTAACAGATAAACAAGCAAAAGAAGGAACTA 2 261 1 AAACACAAAA 0.780531 -40 TAATAAGGATACAAAACGCCAAAAGAATGCGAAC 3 419 0 AAAACCAAAA 0.961622 -182 CAGACCTAAAACAAAACCCTAAGAAGCACGTGAT 4 204 0 AAAACTAAGA 0.946676 -397 ACTTGATGAAAAAAAACCCTAAAATGTCTCAGAC 4 233 0 AAAACTAAAA 0.898719 -368 GGTGAGTATAAAAAAAAAGCAAAAAAAAAAGAAA 4 299 0 AAAAACAAAA 0.945143 -302 ATTGTAGGGTACGAAACACCAAGAAATGCAATAA 4 406 0 AAAACCAAGA 0.980442 -195 TCGATGAAGAAATGAACGACAAAATTACTTTTGT 4 442 0 AGAACCAAAA 0.837985 -159 ATATATTTACAGCAAACCTTAAGAGGTGTTAACG 4 552 0 AAAACTAAGA 0.946676 -49 TATTTATGTTATAAAAAAAGAAGATATT 4 583 1 AAAAAGAAGA 0.816967 -18 GGATATAACAATGAAAAATCAAGATTTCAGGCAT 5 168 1 AAAAACAAGA 0.971807 -433 CATGGCGAAGACTGAAAGGCAAGAACACCCTGCT 5 395 1 AGAAACAAGA 0.876777 -206 TGAGATTCCAATAAAACCTCCAAATATCTTTATA 5 480 0 AAAACCCAAA 0.726553 -121 CAGAGGAAAGAACAACATACAAAAAAAAATCTGT 6 118 0 AAACACAAAA 0.780531 -183 AAAAAAAAAAAAAAAAAAAAAAGAAGAAAAAAAA 6 177 0 AAAAAAAAGA 0.908326 -124 AAAAAAAAAAAAAAAAAAAAAAGAAAACAGAACA 7 96 1 AAAAAAAAGA 0.908326 -399 ACATTGCGATAATAAACTAAAAGACACTAGGATA 7 348 1 AAAACAAAGA 0.935107 -147 TAAACCCTTAAAAAAACAGTAATAAATTAAACTT 7 404 0 AAAACTAATA 0.583132 -91 * **** ***** Masking position 5 Map Score: 16.6964 Number of sites scoring better than the average of aligned sites = 3158 Number in coding regions = 1595 Number in noncoding regions = 1563 Number of orfs with sites within 600 bp upstream = 1106 Fraction of orfs with sites within 600 bp upstream = 0.177642 Motif number 4 CTTTTCATTCTGCCGCTAATCTACAAACTCGTTAC 1 172 0 TGCCCTACTA 0.983002 -129 AGAAAAAAAATGTCCGATAGCTTCAGAGGGTGATC 2 139 0 TGTCGAACTA 0.981665 -162 CATTGCTGCTTGTCTCACATCTAAACTTCGCCGTT 3 535 0 TGTCCAACTA 0.992183 -66 CCTGAAGTCATGCCCCTCACCTTCATTCGTGGATC 4 50 1 TGCCCTACTA 0.985167 -551 GGTATGGGTGTGTCACACATTTGAAAAAAAGTGGG 4 142 0 TGTCCAATTA 0.942735 -459 AACCCTAAAATGTCTCAGACCTAAAACAAAACCCT 4 218 0 TGTCCAACTA 0.992182 -383 TCTTGACTCATGCCTGAAATCTTGATTTTTCATTG 5 176 0 TGCCGAACTA 0.984773 -425 **** ** * ** * Masking position 9 Map Score: 3.10048 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 59 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 GGAAATGGCATGACACCCCCCCACACACGT 4 108 1 TGACACCCCC 0.997851 -493 TTCAAATGTGTGACACACCCATACCCCATA 4 152 1 TGACACACCC 0.99416 -449 ATCGCTACTTTGACACCCCCGATCGTGTCT 5 329 1 TGACACCCCC 0.997851 -272 ********** Masking position 5 Map Score: 2.11446 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 3 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 CTCTCCTCGTTCCCCTCTCATGTCTTTTAACAGA 2 238 1 TCTCTCATGC 0.916726 -63 AGTATGATAGTTCCTTCTTTTGCTTGTTTATCTG 2 268 0 TCTCTTTTGT 0.966998 -33 CTTGAAAGTTCGCATTCTTTTGGCGTTTTGTATC 3 412 1 CCTCTTTTGC 0.986465 -189 TTTCAACAACTTCCTTATTTTATCTTGGGATCGT 4 486 1 TCTATTTTAC 0.835128 -115 CATTTTTTTTTTCTCGCTTTTGATAGCCAGCCCA 5 107 1 TCGCTTTTGT 0.859367 -494 TGCCGTGGTTCACCCTCTTTTAACCCACAGGAAT 5 297 1 CCTCTTTTAC 0.926465 -304 CGTGTCTCTTTTCGGTATTTTGGCACCCTTTCTT 5 352 1 TCTATTTTGC 0.966998 -249 AAGAACACCCTGCTATCTTTTGCCTACCATTGGC 5 415 1 TCTCTTTTGC 0.994135 -186 ACCATACAATTCCAATCTGATGGCGGGCAATG 6 9 0 TCTCTGATGC 0.916725 -292 TCTGTGGTGGTCCAGTCTTTTGTCTCTTTTTTTT 6 148 1 TCTCTTTTGC 0.994135 -153 * * ******* * Masking position 8 Map Score: 3.39023 Number of sites scoring better than the average of aligned sites = 646 Number in coding regions = 487 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 7 TGTATAAATAAATAATATTGCAAATATAAATA 1 100 1 AATAATTGCA 0.970025 -201 TGAGCTTGATCATAATTCTTCAGGCTCCCAAT 3 30 0 CATAATTTCA 0.970026 -571 AGCGAGTTTTCATAATTTTTCACTTACCAGCA 3 502 0 CATAATTTCA 0.970026 -99 ACCCATACCCCATAATGTTGCACGTGACAGGT 4 168 1 CATAATTGCA 0.989667 -433 ATTGTTCTATCATAATGCTGCAAAAAAAAAAA 6 202 0 CATAATTGCA 0.989667 -99 TTTATCTTTCAATAATGATGGAACGGAATAAA 7 311 0 AATAATTGGA 0.881237 -184 ****** **** Masking position 6 Map Score: 1.29612 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 29 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 8 GGATTTGAACCGATGATCTCCACATTACTA 2 65 0 CGATGATCTC 0.797921 -236 TACGTTCACTGCCAGCTCTCTCGCTGAAAA 2 180 0 GCCAGCTCTC 0.971864 -121 ACGTACAAGAGCAAGCTCTCTAAAGAACTA 2 205 1 GCAAGCTCTC 0.937318 -96 TTATTTTTTTGCATGATCTCCCCAGACCCA 3 129 1 GCATGATCTC 0.968247 -472 TCTCCCCAGACCCAGATGTCATCTGTAAAG 3 145 1 CCCAGATGTC 0.952118 -456 CGAAATTACGGCCTAATGTCGAGACAAGAA 3 278 0 GCCTAATGTC 0.793261 -323 GGAAATTGATCCCTGAAGTCATGCCCCTCA 4 39 1 CCCTGAAGTC 0.924288 -562 CTTGACTCATGCCTGAAATCTTGATTTTTC 5 180 0 GCCTGAAATC 0.844195 -421 TCAGTCTTCGCCATGCTCTCATTCAAGAAA 5 380 0 CCATGCTCTC 0.97062 -221 GGCAAGAACACCCTGCTATCTTTTGCCTAC 5 412 1 CCCTGCTATC 0.954786 -189 ********** Masking position 9 Map Score: 2.18254 Number of sites scoring better than the average of aligned sites = 782 Number in coding regions = 610 Number in noncoding regions = 172 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 9 TTTTCTTTAATTTTTTCAGCGAGAGAGCTGGC 2 168 1 TTTTCAGCGA 0.98331 -133 TGTCTTCCAATTGATTCAGCGAAACCTTTTCT 3 200 1 TTTTCAGCGA 0.983084 -401 CATTAGGCCGTAATTTCGTCGAAGAAAAATGA 3 290 1 TATTCGTCGA 0.91348 -311 GTGAGGGGCATGACTTCAGGGATCAATTTCCC 4 38 0 TGTTCAGGGA 0.889676 -563 GCCCCTCACCTTCATTCGTGGATCTTATCTCC 4 61 1 TTTTCGTGGA 0.96811 -540 TTTTAGGGTTTTTTTTCATCAAGTCTAGATCG 4 243 1 TTTTCATCAA 0.875029 -358 TTGTCGTTCATTTCTTCATCGATTCTTTCCTC 4 454 1 TTTTCATCGA 0.986187 -147 AGAAAGTTCTTTGATTGATCGACCAGCAGCTT 6 55 1 TTTTGATCGA 0.911904 -246 AACGAGAAAATTTTTTCGTGGAACTTGAAAAA 7 68 1 TTTTCGTGGA 0.968114 -427 ** ******** Masking position 6 Map Score: 2.82924 Number of sites scoring better than the average of aligned sites = 700 Number in coding regions = 521 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 10 TGCTCTTGTACGTTCACTGCCAGCTCTCTC 2 188 0 CGTTCACTGC 0.93181 -113 TTACTCTCCTCGTTCCCCTCTCATGTCTTT 2 235 1 CGTTCCCCTC 0.911396 -66 TTATACTCACCGTTTACTGTCATTATGTCT 4 322 1 CGTTTACTGT 0.883555 -279 CTTGGTGTTTCGTACCCTACAATTGACAAA 4 417 1 CGTACCCTAC 0.849006 -184 TAATTAATCACGATTCCCATATTCGTTAAC 4 529 1 CGATTCCCAT 0.800467 -72 TCAGGATGTTCGTACCATGCGTCGCAGGCC 5 232 1 CGTACCATGC 0.719324 -369 GTCAAAGTAGCGATTCCTGTGGGTTAAAAG 5 313 0 CGATTCCTGT 0.92425 -288 ACTACGATTGCGTATACCGTTACTGTTAGC 6 255 0 CGTATACCGT 0.894836 -46 AAGGATTATCCGAACCCCGCCCCGCGGAAT 7 14 0 CGAACCCCGC 0.961 -481 ACAATAGTAGCGTTTCCCGTGTTCTTTTCC 7 170 1 CGTTTCCCGT 0.983126 -325 TTCCCGTGTTCTTTTCCCGTCATTAAATAT 7 183 1 CTTTTCCCGT 0.821129 -312 ********** Masking position 1 Map Score: 1.45704 Number of sites scoring better than the average of aligned sites = 1000 Number in coding regions = 728 Number in noncoding regions = 272 Number of orfs with sites within 600 bp upstream = 235 Fraction of orfs with sites within 600 bp upstream = 0.0377449 Motif number 11 TTGTAGTGAGTAGTATTCCAGTCCCAGTAG 1 46 0 TAGTATTCCA 0.945365 -255 TGTAAATATCTACAATTCCAGCTATTTACG 3 332 1 TACAATTCCA 0.978589 -269 TGTCTTTCGATACTTTTCCACGCTTGAAAG 3 390 1 TACTTTTCCA 0.935251 -211 TTTGTATCCTTATTATTCCAAACTTTGATC 3 438 1 TATTATTCCA 0.954697 -163 AATACCAACCTATACTTCCATTGCTGCTTG 3 558 0 TATACTTCCA 0.904741 -43 GGAAGGACCATACAATTCCAATCTGATGGC 6 19 0 TACAATTCCA 0.978589 -282 ********** Masking position 6 Map Score: 0.657933 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 162 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 12 CAATAAATTGTATAAATAAATAATATTGCAAA 1 92 1 TATAATAATA 0.793677 -209 ATATTGCAAATATAAATAAATACCCATCGATT 1 114 1 TATAATAATA 0.793677 -187 TAGCTGGAATTGTAGATATTTACAATGACATA 3 324 0 TGTAATATTA 0.953535 -277 AGGTTTGCTGTAAATATATTTATGTTATAAAA 4 567 1 TAAAATATTA 0.491536 -34 TCTCGTATGTATGCATTTAGTGACTTATA 5 8 1 TGTAGCATTA 0.83042 -593 TTTAGTGACTTATACATATATATTGTATCTAC 5 26 1 TATAATATTA 0.719776 -575 ACGAACATCCTGAAGGTATATAAAAGAGCTAA 5 213 0 TGAAGTATTA 0.878597 -388 GGAGTGTATATGTAAGTATGTAGGTATACAAG 6 84 0 TGTAGTATTA 0.943483 -217 CAACAACTTTTGAATATATTTAATGACGGGAA 7 196 0 TGAAATATTA 0.784903 -299 TGCCTTCGGATATAAACATTTAAGTTTAATTT 7 383 1 TATAACATTA 0.769446 -112 **** **** ** Masking position 8 Map Score: 0.53347 Number of sites scoring better than the average of aligned sites = 4333 Number in coding regions = 366 Number in noncoding regions = 3967 Number of orfs with sites within 600 bp upstream = 669 Fraction of orfs with sites within 600 bp upstream = 0.107453 Motif number 13 ********** No masking Map Score: -6.00876e-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: -6.00876e-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: -6.00876e-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