AlignACE version 2.2 July 7, 1998 AlignACE -jKIN.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 YAR018C 510 bp YAR018C KIN3 1-1308 protein kinase #2 YCR091W 600 bp YCR091W KIN82 1-2181 Putative serine\/threonine protein kinase most similar to cyclic nucleotide-dependent protein kinase subfamily and the protein kinase C subfamily #3 YDL108W 496 bp YDL108W kin28 1-28, 110-1002 serine-threonine kinase, subunit of transcription factor TFIIK, a subcomplex of TFIIH #4 YDR122W 524 bp YDR122W KIN1 1-3195 Serine\/threonine protein kinase #5 YLR096W 474 bp YLR096W KIN2 1-3444 Serine\/threonine protein kinase #6 YOR233W 586 bp YOR233W KIN4 1-2403 protein kinase Motif number 1 ATCTATATATGCTTTTTTTCTTTTTCTTTTT 1 175 1 GCTTTTTTTT 0.971545 -336 TTTTCTTTTTCTTTTTTTTTTTCAATTGGGG 1 190 1 CTTTTTTTTT 0.865903 -321 TTACAGCCAAGTTTTTTTTTTAAGGTTTCTG 1 337 1 GTTTTTTTTT 0.964409 -174 TAGTTATCAAGCTTTTTTTGTGTGCATTCAA 2 69 1 GCTTTTTTTT 0.971545 -532 AGTGGTTTTGATTTTTTTTTTTCAGTTCTGG 2 141 0 ATTTTTTTTT 0.905625 -460 CATAATAACCCCAGTTTTTTTAGAGAAAGTT 2 487 1 CCAGTTTTTT 0.697848 -114 GGTCAGGTGAGCATTTTTTGTACTGATATTT 3 47 1 GCATTTTTTT 0.974883 -450 TTTTGTACTGATATTTTTTCTCTTTGTTTGC 3 62 1 ATATTTTTTT 0.916029 -435 TGAACCTACAATTTTTTTTGTGTTATGATGT 3 344 1 ATTTTTTTTT 0.905625 -153 GATTTCACTTGTATTTTTTTTCAATGTGTTT 3 424 0 GTATTTTTTT 0.968557 -73 GAGGCCGGGAATATTTTTTTTGATGACTTTT 3 465 0 ATATTTTTTT 0.916029 -32 GGGCTATTACGCATTTTTTTTTTCAACTTCT 4 457 1 GCATTTTTTT 0.974884 -68 GTGTAATGCAGTATATTTTGTAATAAAGTTC 5 334 0 GTATATTTTT 0.832567 -141 ATCTATATGTGCCTTTTTTCTTTCTCTGCCT 6 44 1 GCCTTTTTTT 0.900683 -543 TAACGCATTAGTTGTTTTTTTAGTACATATT 6 418 1 GTTGTTTTTT 0.871234 -169 TTTTTTTAGTACATATTTTTTTAGCAAGTTC 6 432 1 ACATATTTTT 0.689334 -155 ********* * Masking position 6 Map Score: 15.2898 Number of sites scoring better than the average of aligned sites = 1853 Number in coding regions = 576 Number in noncoding regions = 1277 Number of orfs with sites within 600 bp upstream = 930 Fraction of orfs with sites within 600 bp upstream = 0.149374 Motif number 2 TTTCTGATCTCTTTTCCAAACAGATGCGTT 1 104 0 CTTTTCCAAA 0.962072 -407 TTTTTCATTACGTTTCCTAATTAGGTTAAA 1 371 1 CGTTTCCTAA 0.946188 -140 ATAAAAGCGACTTTTCAAAAGAATATCAAA 1 406 1 CTTTTCAAAA 0.954274 -105 AATTTAGAGTAGTTTCCTTATA 2 3 0 AGTTTCCTTA 0.825651 -598 CAATAAAGTACTTTTCATACTACAACAGAC 2 320 1 CTTTTCATAC 0.915451 -281 AATTCTTGTACGTTTCAAACATACTATAAT 2 529 0 CGTTTCAAAC 0.958457 -72 AAAGATTTTCAGTTTCAATAAGACATCAAT 3 239 1 AGTTTCAATA 0.872316 -258 ACTACTAGACAGTTTCCATAGCGGGG 4 7 0 AGTTTCCATA 0.892507 -518 TCGGTCTTTCATTTTCCAACTATTGATTAG 4 373 1 ATTTTCCAAC 0.915929 -152 TCTTCTTTTCCTTTTCCAACCTTTTTAAAT 5 210 0 CTTTTCCAAC 0.958457 -265 CCGAGAAACGCTTTTCAAAAGAAATTTCTA 5 404 1 CTTTTCAAAA 0.954274 -71 ATTTCTTTATATTTTCATTAGTTTACAAAT 6 109 0 ATTTTCATTA 0.762252 -478 AATGACGGCGAGTTTCATTAGGAACGTGAG 6 305 1 AGTTTCATTA 0.795775 -282 GCGTTATTGTCTTTTCAAACCGTATATCTT 6 394 0 CTTTTCAAAC 0.949955 -193 ********** Masking position 5 Map Score: 10.5929 Number of sites scoring better than the average of aligned sites = 1668 Number in coding regions = 1244 Number in noncoding regions = 424 Number of orfs with sites within 600 bp upstream = 359 Fraction of orfs with sites within 600 bp upstream = 0.0576614 Motif number 3 CCAATTGAAAAAAAAAAAGAAAAAGAAAAAAAGC 1 185 0 AAAAAAAAAA 0.912292 -326 AGCTATAGATCAATAAATCTGAAATACGATATCT 1 271 1 CAATAATAAA 0.907563 -240 GCGACTTTTCAAAAGAATATCAAATCATATAACA 1 412 1 AAAAAATAAA 0.936184 -99 AATATCAAATCATATAACATGAAAAGAGCAAGAT 1 427 1 CATAAATAAA 0.872643 -84 CCTTCGTCATCAATGAAACAAAAGAACAAGCCAG 2 111 1 CAATAAAAAG 0.716867 -490 CAGAACTGAAAAAAAAAAATCAAAACCACTAAGA 2 142 1 AAAAAATAAA 0.936184 -459 TTCAACTCTTCAAAGAATATCAAGATAAATATCA 2 208 1 CAAAAATAAG 0.939167 -393 AGGATTACTGCAAACAAGGTTCAACAGTGTTGGT 2 573 1 CAAAAATCAA 0.908311 -28 GTTGTGTCTGCAAACAAAGAGAAAAAATATCAGT 3 68 0 CAAAAAAAAA 0.967841 -429 TTCTATATACCAAAAAATTACAAACTGGCAAGAT 3 267 0 CAAAAAAAAA 0.967841 -230 AAACACATTGAAAAAAAATACAAGTGAAATCACA 3 424 1 AAAAAAAAAG 0.790932 -73 AAGTAAATCTCAAAAAATTTCAAATCACAAAGTG 4 266 0 CAAAAATAAA 0.976983 -259 GTACCTGTTTAAAAGAAGTTGAAAAAAAAAATGC 4 467 0 AAAAAATAAA 0.936184 -58 CTAAACCAGGCAGAGAAAGAAAAAAGGCACATAT 6 48 0 CAGAAAAAAA 0.803279 -539 AAATATAAAGAAATAAATCTCAAAACATGCTTTT 6 125 1 AAATAATAAA 0.77238 -462 TAATGAAAGGCATATAATATACAAGGGTGACAAA 6 187 1 CATAAATCAA 0.61526 -400 TCATTGTTTACAAAAAAATAAAAATGGAATTGAC 6 276 0 CAAAAAAAAA 0.967841 -311 **** ** * *** Masking position 7 Map Score: 13.6187 Number of sites scoring better than the average of aligned sites = 3606 Number in coding regions = 1723 Number in noncoding regions = 1883 Number of orfs with sites within 600 bp upstream = 1248 Fraction of orfs with sites within 600 bp upstream = 0.20045 Motif number 4 TTTAACAAAATGCCACCTTCTAGAGTCGGTT 1 233 0 TGCCACCTCT 0.952221 -278 TAGTAGTGCTTGCCACCACTCCCACAGGATC 4 30 1 TGCCACCCTC 0.969077 -495 ATCAACTTCTTGTCCCCTTTCTTTCCTTCCG 4 154 0 TGTCCCCTTC 0.960539 -371 CATAATTAGTTGTCACCCTTCGCCCCCCTAC 4 338 1 TGTCACCTTC 0.990493 -187 TTCTTAGTCGTGTCACTATTGAATAAATAAA 5 87 1 TGTCACTTTG 0.95352 -388 GGAAGAATTATGTCACTTTTGACGCTCTCGC 5 136 1 TGTCACTTTG 0.95352 -339 AGTCCTGCTTTGCCACCGTTTAAGCAAGGAA 5 257 1 TGCCACCTTT 0.988413 -218 ACTAAAAATTTGTCACCCTTGTATATTATAT 6 198 0 TGTCACCTTG 0.990493 -389 GAGGAAATCCAGCCACCTTTTCACAGGTAAA 6 515 1 AGCCACCTTT 0.930781 -72 ******* *** Masking position 6 Map Score: 5.91537 Number of sites scoring better than the average of aligned sites = 354 Number in coding regions = 289 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 5 TGTATTATTCTCTATATATGTATGTATGCA 1 26 0 TCTATATATG 0.988336 -485 GGTTCACAATTCTATATATAGTGTTAATGT 1 61 0 TCTATATATA 0.915712 -450 AAAAAGCATATCTATATATGCTTTTTTTCT 1 166 1 TCTATATATG 0.988336 -345 AAATTCACCTTCCATATATGTGACTGCCAA 2 28 1 TCCATATATG 0.971132 -573 CCGCTTTGTATCTATATATGATTAGCCAGT 5 25 1 TCTATATATG 0.988336 -450 TACGACTTTATCTATATGTGCCTTTTTTCT 6 35 1 TCTATATGTG 0.971132 -552 ********** Masking position 5 Map Score: 7.09374 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 18 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 TTTCCAAACAGATGCGTTTTCAGTATTGGAAGGTT 1 87 0 GTGCTTTGTA 0.972297 -424 CATATATAGATATGCTTTTTTATCATTACTGGCCT 1 151 0 TTGCTTTTCA 0.907482 -360 ATATATGGAAGGTGAATTTAGAGTAGTTTCCTTAT 2 12 0 GTGATTTGTA 0.965343 -589 AGTTCTGGCTTGTTCTTTTGTTTCATTGATGACGA 2 114 0 TTTCTTTTCA 0.742001 -487 TAGTGGTTTTGATTTTTTTTTTTCAGTTCTGGCTT 2 138 0 GTTTTTTTCA 0.541319 -463 TAAGGTCAGGTGAGCATTTTTTGTACTGATATTTT 3 44 1 TAGCTTTGTA 0.633244 -453 GGTAGTGTGGTATGTTTTTAGCGTATTAACAGCAA 3 104 0 TTGTTTTGTA 0.871947 -393 CAAATTAGAGGGTGATTTTCAATTACAATTGACAA 3 204 0 GTGATTTTTA 0.92689 -293 ATGATGTGAAGCTTCATTTGAAGCATTGTGCAGAG 3 368 1 GTTCTTTGCA 0.901859 -129 TATTTTTTTTGATGACTTTTAAGTAACTGTGATTT 3 450 0 GTGATTTGTA 0.965343 -47 AGCAAAGATGTTTGAATTTTACTAATCAATAGTTG 4 389 0 TTGATTTTAA 0.640349 -136 GTGACATAATTCTTCCTTTCCAGCAACATTAACAT 5 117 0 TTTCTTTGCA 0.863362 -358 CGTCCTTGACTGTGAATTTGTGTCAACGGCGTGCT 5 291 0 TTGATTTTCA 0.886161 -184 TCAGAGTTCCGCTGAATTTCGTGTAATGCAGTATA 5 350 0 GTGATTTGTA 0.965343 -125 TCTCTGCCTGGTTTAGTTTTATTTACTACGTTTAC 6 66 1 GTTATTTTTA 0.788014 -521 TTGTATATTATATGCCTTTCATTAACCCATATAAC 6 176 0 TTGCTTTTAA 0.691689 -411 TCAATTCCATTTTTATTTTTTTGTAAACAATGACG 6 277 1 TTTATTTGTA 0.848843 -310 TAACGCATTAGTTGTTTTTTTAGTACATATTTTTT 6 418 1 GTGTTTTGTA 0.908282 -169 TTGAGCTTACTGTGATTTTCAAGTAAAACACCTTT 6 471 1 TTGATTTGTA 0.950378 -116 * *** *** *** Masking position 8 Map Score: 12.1603 Number of sites scoring better than the average of aligned sites = 2038 Number in coding regions = 1497 Number in noncoding regions = 541 Number of orfs with sites within 600 bp upstream = 400 Fraction of orfs with sites within 600 bp upstream = 0.0642467 Motif number 7 TTTATTGAATGTCCTTGACATGTTTTCCCAGGATCC 2 291 0 GTCTGCTTTT 0.971065 -310 TGATAGCGCCGTCTTCGGCATCCTTTTTCGGAAATA 2 400 1 GTCCGCTTTT 0.995411 -201 ATAAGCTATACTCATCGTCGTTATTTGCAAGCCGGG 4 97 1 CTCCGCTTTT 0.995411 -428 AATACACTTCCTCAACGCCATAATTTCTTGTTAACG 4 195 0 CTCCGCTTTT 0.995411 -330 GTGAATTTGTGTCAACGGCGTGCTCTATTCCTTGCT 5 279 0 GTCCGCTTCT 0.98755 -196 CCTAATGAAACTCGCCGTCATTGTTTACAAAAAAAT 6 291 0 CTCCGCTTTT 0.995411 -296 *** ** * * *** Masking position 11 Map Score: 3.68518 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 64 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 GGCCTCTTTAAATTCAAAAACTTTTCTGATCTCTTT 1 120 0 AATTAATTTC 0.97493 -391 ATGGAAGGTGAATTTAGAGTAGTTTCCTTATA 2 7 0 AATTGATTTC 0.946 -594 AAAGCTTGATAACTAGTAATATTTTCTTGGCAGTCA 2 48 0 AACTTATTTC 0.956238 -553 GCACTCAATGAATTCTTGTACGTTTCAAACATACTA 2 533 0 AATTTGTTTC 0.914688 -68 ACCGCTTCTGAATTCTTACAAATTTCTCTTGGAGGA 3 148 0 AATTTATTTC 0.982739 -349 ATCACCCTCTAATTTGAAAGATTTTCAGTTTCAATA 3 223 1 AATTAATTTC 0.97493 -274 TAACGAAGTAAATCTCAAAAAATTTCAAATCACAAA 4 269 0 AATCAATTTC 0.879857 -256 TGATTAGTAAAATTCAAACATCTTTGCTCCGATTAG 4 396 1 AATTAATTTG 0.81954 -129 GGCACAATAAAACTTTTAGAAATTTCTTTTGAAAAG 5 414 0 AACTTATTTC 0.956238 -61 ATCGCGGCTCAATTGTTAAGTATTTCACT 5 456 1 AATTTATTTC 0.982739 -19 AAGGGTGACAAATTTTTAGTACTTTCGTATACATTT 6 209 1 AATTTATTTC 0.982739 -378 **** ** **** Masking position 2 Map Score: 7.27921 Number of sites scoring better than the average of aligned sites = 502 Number in coding regions = 357 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 9 TGAAGAGTTGAAGAGCCAGCAGGAGTTTTGGAAGGA 2 184 0 AAGGCAAGAT 0.990161 -417 ACCCATGCATGAGTGCGAGGAGCATTAAGTTGGATC 2 260 1 GAGGCAAGAT 0.992341 -341 ATACTACAACAGACGCTAGAAGAACTAGAATGTAAC 2 336 1 AGAGCAAGAT 0.859106 -265 AGAATTCATTGAGTGCCCTAAGGATTACTGCAAACA 2 553 1 GAGGCCAGAT 0.984455 -48 GGAAGGAAAGAAAGGGGACAAGAAGTTGATATTGGT 4 155 1 AAAGGAAGAT 0.857872 -370 ATTCTACGTGAGCAAAAAGTAATCGTAATAAAC 4 502 0 GTGGCAAGAT 0.964155 -23 AGAAGAGCTCAAGTGGACCTAGAAGTCCTGCTTTGC 5 234 1 AAGGGCAGAT 0.937434 -241 ACAGTCAAGGACGGGCCACGAGAACTTTATTACAAA 5 313 1 ACGGCAAGAT 0.968716 -162 GCGGAACTCTGAGCGCGAACAGCATTAGGTACCGAG 5 373 1 GAGGCAAGAT 0.992341 -102 *** ** * ** * * Masking position 11 Map Score: 2.45236 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 177 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 10 CAATAAATCTGAAATACGATATCTGACATGA 1 281 1 GAATACGATA 0.975151 -230 AAAAACATCGGGGAAACGGTAGTAAT 3 6 0 GGAAACGGTA 0.959602 -491 GTGTATTAGCGAGATACGATATCAAGCAGGT 4 224 1 GAATACGATA 0.975151 -301 TTATTATAAGGACATACGGTAACCTAGGCTA 4 302 1 GAATACGGTA 0.991463 -223 TTCTACTGAAGATATACGGTTTGAAAAGACA 6 386 1 GAATACGGTT 0.966276 -201 TATATATTCAGGTATACGGAATGTCCTGATA 6 563 0 GGATACGGAA 0.959602 -24 ** ******** Masking position 6 Map Score: 1.19743 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 19 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 11 CTATATATGCTTTTTTTCTTTTTCTTTTTTTTTT 1 177 1 TTTTTTTTTC 0.825364 -334 AGGTGGCATTTTGTTAAATGTTTCTAGCTATAGA 1 246 1 TTTTATTTTC 0.941688 -265 TTTTTAAGGTTTCTGAATTTTTTCATTACGTTTC 1 353 1 TTTGATTTTC 0.881399 -158 GGAAGGTGAATTTAGAGTAGTTTCCTTATA 2 7 0 TTAGAATTTC 0.609057 -594 AGCTTGATAACTAGTAATATTTTCTTGGCAGTCA 2 48 0 CTGTAATTTC 0.78312 -553 TATACTTTCCTTTTTCCCTCTTTCAGCTATATTG 2 434 1 TTTTCTTTTC 0.836118 -167 CGCTTCTGAATTCTTACAAATTTCTCTTGGAGGA 3 148 0 TTTTAATTTC 0.971749 -349 CACCCTCTAATTTGAAAGATTTTCAGTTTCAATA 3 225 1 TTGAAATTTC 0.653498 -272 CTTTTCCAACCTTTTTAAATTTTCGTTGCTAGAC 5 196 0 CTTTTATTTC 0.797424 -279 GCAGTATATTTTGTAATAAAGTTCTCGTGGCCCG 5 324 0 TTTAAAGTTC 0.733131 -151 CACAATAAAACTTTTAGAAATTTCTTTTGAAAAG 5 414 0 CTTTAATTTC 0.930798 -61 CGCGGCTCAATTGTTAAGTATTTCACT 5 458 1 TTTTATTTTC 0.941688 -17 TGAGATTTATTTCTTTATATTTTCATTAGTTTAC 6 113 0 TTTTTATTTC 0.909637 -474 GGGTGACAAATTTTTAGTACTTTCGTATACATTT 6 211 1 TTTTAATTTC 0.971749 -376 GATAATATTTTTCTGCTCACGTTCCTAATGAAAC 6 316 0 TTTGCAGTTC 0.661649 -271 AGTACATATTTTTTTAGCAAGTTCACTGTTTATT 6 439 1 TTTTAAGTTC 0.930798 -148 ** *** * **** Masking position 12 Map Score: 4.72781 Number of sites scoring better than the average of aligned sites = 2625 Number in coding regions = 1701 Number in noncoding regions = 924 Number of orfs with sites within 600 bp upstream = 706 Fraction of orfs with sites within 600 bp upstream = 0.113395 Motif number 12 ********** No masking Map Score: -3.10975e-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 AGAAACATTTAACAAAATGCCACCTTCTAGAG 1 239 0 AACAAAGCCA 0.914388 -272 TAACTATCGGAAGACTGTGCCACTGCAATCAT 1 308 0 AAGACGGCCA 0.991154 -203 AATGAAACAAAAGAACAAGCCAGAACTGAAAA 2 122 1 AAGAAAGCCA 0.961994 -479 GGAGTTTTGGAAGGATGTGACATTCTTAGTGG 2 167 0 AAGGAGGACA 0.935624 -434 AAGGATGCCGAAGACGGCGCTATCATAATTAT 2 393 0 AAGACGGCTA 0.935624 -208 CGGGGAACCCAACGCGGCGCCAATGCGGAAGG 4 129 1 AACGCGGCCA 0.982787 -396 ATTCACAGTCAAGGACGGGCCACGAGAACTTT 5 309 1 AAGGAGGCCA 0.991152 -166 ***** * **** Masking position 2 Map Score: 0.443732 Number of sites scoring better than the average of aligned sites = 320 Number in coding regions = 256 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 14 ********** No masking Map Score: -3.10975e-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: -3.10975e-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