AlignACE version 2.2 July 7, 1998 AlignACE -jCCT.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 YDL143W 300 bp YDL143W CCT4 1-1587 Cytoplasmic chaperonin subunit required for actin cytoskeleton assembly or function #2 YDR188W 600 bp YDR188W CCT6 1-1641 Cytoplasmic chaperonin of the Cct ring complex (previously called TCP1 or TRiC), distantly related to Tcp1p and to Hsp60 #3 YIL142W 300 bp YIL142W CCT2 1-1584 molecular chaperone #4 YJL111W 427 bp YJL111W CCT7 1-1653 Component of Chaperonin Containing T-complex subunit seven #5 YJL014W 300 bp YJL014W CCT3 1-1605 Cytoplasmic chaperonin subunit gamma #6 YJL008C 300 bp YJL008C CCT8 1-1707 Component of Chaperonin Containing T-complex subunit eight #7 YJR064W 341 bp YJR064W CCT5 1-1689 subunit of chaperonin subunit epsilon Motif number 1 TGCACACTTGCCGCACCTCCAATTACAATTCA 1 253 0 CCGCACCTCA 0.989646 -48 GCGCGCACACCCACGCCCCGCAACCGCACACC 2 135 1 CCACGCCCCA 0.995135 -466 CGCCCCGCAACCGCACACCTCAGCTCAAAGTA 2 148 1 CCGCACACCA 0.989646 -453 GCCGCAGAACCCACACCTCTCACTCTATCGAA 2 358 0 CCACACCTCA 0.992606 -243 AAACAGTGATCCACGGCCCGTATCCATTCTGC 2 388 0 CCACGGCCCA 0.971311 -213 TTTACCTTTTCCACACACTGCACACATACACT 2 521 0 CCACACACTA 0.963548 -80 CTCACTGCTTCCACACCCTTAACCTTTACCTT 2 545 0 CCACACCCTA 0.989438 -56 GCATATATAGCCACATCTCAAAAACTTACATA 5 34 1 CCACATCTCA 0.963548 -267 ACCTCATTTGCCACATCCACCAAGACACTATT 7 251 0 CCACATCCAA 0.912751 -91 GCTCTTTATCACGCACACCTCATTTGCCACAT 7 267 0 ACGCACACCA 0.893051 -75 ********* * Masking position 12 Map Score: 9.48177 Number of sites scoring better than the average of aligned sites = 414 Number in coding regions = 240 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 2 CTTGGTGGCGAAACGAAAAAAATTTCAGTTTCC 1 163 0 AAAGAAAAAT 0.983903 -138 TTAACCCAAATAATAAAAAAGCTACGAGACAAG 2 47 1 TAAAAAAAAT 0.926077 -554 GGAATGCAATTAAAGAAAGATATACGGTACACG 2 258 0 TAAGAAAGAT 0.826124 -343 CTAAGAAGTATAAGGAAAAAGGTCCTTAGTAAG 3 129 0 TAAGAAAAAT 0.965128 -172 TATACTTCTTAGAAGAAAAACCTCGTTTCTAAC 3 150 1 AGAGAAAAAT 0.954921 -151 GCCACCGCGAAGAGAAAAAAATTTCAGATCGTT 3 180 0 AGAAAAAAAT 0.905558 -121 CTTACCCGGAAAAAGAAAACTTTCGTGAATAAT 4 236 1 AAAGAAAACT 0.912989 -192 TTGCTATTGAAAAAAAAAAAAATGAATAATTGT 4 300 1 AAAAAAAAAT 0.965116 -128 GCGTCACGTTAAACGAAAAAGTTTAGTATTAGG 5 146 0 AAAGAAAAAT 0.983903 -155 CGCATGGTGCGAAGAAAAAAAATAGCAAATCGC 5 176 1 GAAAAAAAAT 0.931147 -125 TCATTTATAAAAACAAAAAATCTATGTACTGAC 7 88 1 AAAAAAAAAT 0.965116 -254 TTATGCCATTGAATGAAAAATTTTGTTAAGGAA 7 205 1 GAAGAAAAAT 0.967613 -137 *** ****** * Masking position 7 Map Score: 10.3346 Number of sites scoring better than the average of aligned sites = 3231 Number in coding regions = 1054 Number in noncoding regions = 2177 Number of orfs with sites within 600 bp upstream = 1315 Fraction of orfs with sites within 600 bp upstream = 0.211211 Motif number 3 TTATCGGGGCAGGTGGCGTTG 1 1 0 AGGTGGCGTG 0.885999 -300 TGATATAGCTAAGTGGGCATGAAGGTTATGA 1 225 1 AAGTGGGCAG 0.974915 -76 GAGGTGCGGCAAGTGTGCAAGACGGGTAAAG 1 266 1 AAGTGTGCAG 0.960345 -35 TGCGGGGCGTGGGTGTGCGCGCCGTTGCCAT 2 126 0 GGGTGTGCGG 0.957612 -475 CTTTGAGCTGAGGTGTGCGGTTGCGGGGCGT 2 147 0 AGGTGTGCGT 0.965381 -454 ATAGAGTGAGAGGTGTGGGTTCTGCGGCAGA 2 362 1 AGGTGTGGGT 0.965381 -239 ATAACAGTGTATGTGTGCAGTGTGTGGAAAA 2 516 1 ATGTGTGCAT 0.788269 -85 TAAAGGTTAAGGGTGTGGAAGCAGTGAGAAG 2 549 1 GGGTGTGGAG 0.96852 -52 TTTCTCTTCGCGGTGGCGAGTTTAAAAGACA 3 196 1 CGGTGGCGAT 0.866338 -105 AGAGGATGAAAGGTGGCCATTAAATAGGCAA 3 245 1 AGGTGGCCAT 0.971766 -56 ATTAATATTTAAGTGGCGACTTTTTCATCCT 4 270 1 AAGTGGCGAT 0.931864 -158 TCACTTTATTGAGTGGCGATTTGCTATTTTT 5 193 0 GAGTGGCGAT 0.873488 -108 CACATGATGAAAGCGGGGATGATATTAATGT 7 42 0 AAGCGGGGAG 0.85006 -300 GTGGCAAATGAGGTGTGCGTGATAAAGAGCT 7 269 1 AGGTGTGCGG 0.978143 -73 ********* * Masking position 5 Map Score: 8.44116 Number of sites scoring better than the average of aligned sites = 1242 Number in coding regions = 904 Number in noncoding regions = 338 Number of orfs with sites within 600 bp upstream = 239 Fraction of orfs with sites within 600 bp upstream = 0.0383874 Motif number 4 ATTTGGTATTACTATCACTTGCCACGGGGAAACTGA 1 136 1 AATCACGACG 0.901286 -165 ATACGGGCCGTGGATCACTGTTTACGGGAGTTTTGC 2 397 1 TATCACTACG 0.990984 -204 CAGTGGAAGATAAATCATGACGGACGTTGAAGGCTA 3 31 0 TATCATCACG 0.960801 -270 CACTTAAATATTAATCATTATTCACGAAAGTTTTCT 4 249 0 TATCATTACG 0.991563 -179 CTTCGCACCATGCGTCACGTTAAACGAAAAAGTTTA 5 154 0 TGTCACTACG 0.976843 -147 ACTATTGTACTTGATGATTTTCAACGTATGATCACT 5 262 0 TATGATTACG 0.965526 -39 TAATGGTGTTTTTGTCATTATTAACGGTATTCGAAA 6 150 1 TGTCATTACG 0.978312 -151 AAGTGAGAACATCATCATGCTATACTATTTTCTTCA 6 219 0 AATCATTACT 0.786717 -82 TAGTAAGAATAATATGATAATGTACGCTATTATATC 7 121 0 AATGATTACG 0.917735 -221 ATTCTTACTATTTATCATACTCATCGCATCTACTGT 7 147 1 TATCATTTCG 0.937239 -195 TTCAATGGCATAAATCACTTTACACGTTCTCGAGAA 7 182 0 TATCACTACG 0.990984 -160 * ***** * *** Masking position 7 Map Score: 7.10552 Number of sites scoring better than the average of aligned sites = 486 Number in coding regions = 177 Number in noncoding regions = 309 Number of orfs with sites within 600 bp upstream = 361 Fraction of orfs with sites within 600 bp upstream = 0.0579827 Motif number 5 GTTGTTGAACAAGAAAGTATGATAGTTGTTGA 2 7 0 AAGAAAATAT 0.924301 -594 GAAAGACGGAAAGGATTATGTATAACAGTGTATGTG 2 495 1 AAGATTATAC 0.975716 -106 TACTTTTACTAAATAATGTAGATATCATTACTATTA 3 87 1 AAAAATATAC 0.898678 -214 GGTCCTTAGTAAGGATAGATAATAGTAATGATATCT 3 106 0 AAGATAATAT 0.924301 -195 AACCCATTTGAAGAAAAATAAATATCGAGTGCATAT 4 35 1 AAGAATATAC 0.975715 -393 AATGTAAATAAAGTATCGTCAATACCTTGGATGGTT 4 118 1 AAGATTATAC 0.975716 -310 GATGTCTTGGAAGCAATCACCATACCTGCATTATCC 4 201 1 AAGAAAATAC 0.982242 -227 TATTGAAAAAAAAAAAAATGAATAATTGTTATTAAG 4 304 1 AAAAATATAT 0.66193 -124 ATTAGGATGGAAGTATATAATATCACATAAGATTAT 5 116 0 AAGATAATCC 0.90472 -185 TATATCAAAAAAGCATCGATAATATCGAGTGATCAT 5 235 1 AAGATAATAC 0.982242 -66 AAAAAAAGTGAAGAAAATAGTATAGCATGATGATGT 6 211 1 AAGAAAATAC 0.982242 -90 ATATTGCTATAAAAATGGATGATAGCTGTTATTACT 7 310 0 AAAATAATAC 0.924301 -32 *** ** * *** * Masking position 5 Map Score: 9.86083 Number of sites scoring better than the average of aligned sites = 655 Number in coding regions = 446 Number in noncoding regions = 209 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 6 CCACTTAGCTATATCAACCTCTTGAACTGT 1 211 0 ATATCAACCT 0.927434 -90 TCAACAACTATCATACTTTCTTGTTCA 2 8 1 CTATCATACT 0.937822 -593 ACGTTGAAGGCTACCAACCTAAGAGCAAGG 3 14 0 CTACCAACCT 0.93737 -287 TAATGGCCACCTTTCATCCTCTTTTTTATT 3 237 0 CTTTCATCCT 0.982971 -64 AGTGGCGACTTTTTCATCCTTGCTATTGAA 4 281 1 TTTTCATCCT 0.929592 -147 ATATTATATACTTCCATCCTAATACTAAAC 5 129 1 CTTCCATCCT 0.956812 -172 TGATCATTAGATATCAACATGAATTCAA 6 9 0 ATATCAACAT 0.663183 -292 TTGTACATTAATATCATCCCCGCTTTCATC 7 38 1 ATATCATCCC 0.869988 -304 ATCATCCCCGCTTTCATCATGTGAACATCT 7 50 1 CTTTCATCAT 0.898918 -292 TTCTTACTATTTATCATACTCATCGCATCT 7 148 1 TTATCATACT 0.775272 -194 GTAATAACAGCTATCATCCATTTTTATAGC 7 311 1 CTATCATCCA 0.932322 -31 ********** Masking position 6 Map Score: 5.04928 Number of sites scoring better than the average of aligned sites = 1379 Number in coding regions = 1084 Number in noncoding regions = 295 Number of orfs with sites within 600 bp upstream = 236 Fraction of orfs with sites within 600 bp upstream = 0.0379056 Motif number 7 TTTTTTATTATTTGGGTTAATCGCGTTGTTGAAC 2 33 0 TTTGTTATGC 0.966444 -568 TACCGTTCTCGTTGCGCTCGTTGCTCGTATTGCC 2 89 0 GTTGCTGTGC 0.980417 -512 TTACGGGAGTTTTGCTTTGGTGGCAAAATTTTCG 2 418 1 TTTGTTGTGC 0.98661 -183 TTCGCTCGGTGATGTGTTAGTAGTTGTTATTCTG 2 448 1 GATGTTGTGT 0.929184 -153 CTTCAAATGGGTTGACTTGATTGCAATGCAATGC 4 14 0 GTTGTTATGC 0.98661 -414 TATTACTACAGATGTCTTGGAAGCAATCACCATA 4 191 1 GATGTTGAGC 0.954662 -237 GGTTAATTGATGATTTTATTGCCCTTGAGGTT 6 279 0 GATGTTATGC 0.978691 -22 CTGTTATTACTTTGAGTTTGTAGCTCTTTATCAC 7 287 0 TTTGTTGTGC 0.98661 -55 **** ** ** ** Masking position 8 Map Score: 3.4986 Number of sites scoring better than the average of aligned sites = 499 Number in coding regions = 441 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 8 TAGACATTTTCGACATTAGCTTATGCCAACTTGTATCC 1 41 1 CGAAAGAGCA 0.989137 -260 TTTTTCGTTTCGCCACCAAGAAAGGCTAATTGAATACA 1 176 1 CGCAAAAGCA 0.934098 -125 GGCAAGTGTGCAAGACGGGTAAAGGAGAGTATAGAACG 1 273 1 CAAAGGAGAA 0.957682 -28 AGCTACGAGACAAGAACAGACGAGGCAATACGAGCAAC 2 66 1 CAAAAGAGCA 0.993191 -535 ATATACGGTACACGAAAGGGAGAAGCGACGGCGTTAAC 2 234 0 CACAGGAGCA 0.982824 -367 AAACGATAATCACAACAAGGGAATGCAATTAAAGAAAG 2 272 0 CACAAGAGCA 0.989173 -329 CCACTGATTCCAACGTCAGTAGATGCTACTTTTACTAA 3 61 1 CAAGAGAGCA 0.964875 -240 GTTTAAAAGACAAGAGCAGAGCAATAAAAAAGAGGATG 3 215 1 CAAAAGATAA 0.740058 -86 TCATCAAGTACAATAGTGATATAAGCCACA 5 281 1 CAAAGAAGCA 0.957682 -20 CCGCTAGTGGCAAAAAAAAGTGAAGAAAATAGTATAGC 6 199 1 CAAAAAAGAA 0.8995 -102 TACACGTTCTCGAGAACAGTAGATGCGATGAGTATGAT 7 160 0 CGAAAGAGCA 0.989173 -182 *** * ** * ** * Masking position 13 Map Score: 7.20446 Number of sites scoring better than the average of aligned sites = 711 Number in coding regions = 533 Number in noncoding regions = 178 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 9 CAGGGTCCCCAAAATGAAAGCTCACTGCAATGGG 2 310 0 AAATGAAGCA 0.87576 -291 CTTTGGTGGCAAAATTTTCGCTCGGTGATGTGTT 2 432 1 AAATTTCGCG 0.972728 -169 CGAAGAGAAAAAAATTTCAGATCGTTAGAAACGA 3 172 0 AAATTTAGCG 0.909617 -129 CATCTGTAGTAATATGACAGGGCAACATCTACAG 4 171 0 AAATGAAGCA 0.87576 -257 GGTACTACTTAATATTTGCGGCTAATTCTCTGTA 4 376 0 AAATTTCGTA 0.959026 -52 CCTAATACTAAACTTTTTCGTTTAACGTGACGCA 5 146 1 AATTTTCGTA 0.767081 -155 TTAATAATACAAAATGTTCGGACAAGTGATCATT 6 31 0 AAATGTCGCA 0.988995 -270 TAGATAATTAAAGAGTTGCGAGCACATTTACTAT 6 87 1 AAAGTTCGCA 0.945354 -214 GGAGGTGATGAACATTTTCGAATACCGTTAATAA 6 167 0 AAATTTCGTA 0.959025 -134 TACAAATTGTAATATGTGCGAACACAACCCAA 7 9 0 AAATGTCGCA 0.988995 -333 ** **** ** ** Masking position 2 Map Score: 2.02101 Number of sites scoring better than the average of aligned sites = 820 Number in coding regions = 560 Number in noncoding regions = 260 Number of orfs with sites within 600 bp upstream = 202 Fraction of orfs with sites within 600 bp upstream = 0.0324446 Motif number 10 CTACAGTCCCGGTGCCAGGATACAAGTTGG 1 66 0 GGTGCCAGGA 0.950102 -235 TATATATATCTGAGCGAGCAGCTATTCACA 4 70 0 TGAGCGAGCA 0.927854 -358 TGTGGCTATATATGCGAAGAACTATGCAAT 5 19 0 TATGCGAAGA 0.942386 -282 CGTGACGCATGGTGCGAAGAAAAAAAATAG 5 171 1 GGTGCGAAGA 0.989532 -130 AATGATCACTTGTCCGAACATTTTGTATTA 6 31 1 TGTCCGAACA 0.860752 -270 TAATTAAAGAGTTGCGAGCACATTTACTAT 6 91 1 GTTGCGAGCA 0.946798 -210 AATTGTAATATGTGCGAACACAACCCAA 7 9 0 TGTGCGAACA 0.931596 -333 GAGAACAGTAGATGCGATGAGTATGATAAA 7 157 0 GATGCGATGA 0.887629 -185 ********** Masking position 7 Map Score: 1.33946 Number of sites scoring better than the average of aligned sites = 382 Number in coding regions = 283 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 11 ACTCTCCTTTACCCGTCTTGCACACTTGCC 1 273 0 ACCCGTCTTG 0.92779 -28 TATTGCCTCGTCTGTTCTTGTCTCGTAGCT 2 66 0 TCTGTTCTTG 0.977065 -535 TGCCATGCTTACCGTTCTCGTTGCGCTCGT 2 102 0 ACCGTTCTCG 0.97615 -499 TTAATTGCATTCCCTTGTTGTGATTATCGT 2 278 1 TCCCTTGTTG 0.873595 -323 GAAATTTTTTTCTCTTCGCGGTGGCGAGTT 3 188 1 TCTCTTCGCG 0.917293 -113 TTTTTATTGCTCTGCTCTTGTCTTTTAAAC 3 215 0 TCTGCTCTTG 0.92912 -86 TGTACGACTGACTCTTCTTGCCTATTTAAT 3 263 0 ACTCTTCTTG 0.977065 -38 CATCGCATCTACTGTTCTCGAGAACGTGTA 7 168 1 ACTGTTCTCG 0.976612 -174 ********** Masking position 6 Map Score: 1.24346 Number of sites scoring better than the average of aligned sites = 585 Number in coding regions = 460 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 12 ATTATCGTTTCCCATTGCAGTGAGCTTTCA 2 300 1 CCCATTGCAG 0.950053 -301 ATGAAAGGTGGCCATTAAATAGGCAAGAAG 3 250 1 GCCATTAAAT 0.91488 -51 TAGGCATTGCATTGCAATCAAG 4 3 1 GGCATTGCAT 0.950586 -425 TTTCATCCTTGCTATTGAAAAAAAAAAAAA 4 292 1 GCTATTGAAA 0.923753 -136 CTTCGCCCATTGCATAGTTCTTCGC 5 6 1 CCCATTGCAT 0.976865 -295 TATAAAATAAGCTATTGAAATAGTAAATGT 6 110 0 GCTATTGAAA 0.923753 -191 AGTGATTTATGCCATTGAATGAAAAATTTT 7 199 1 GCCATTGAAT 0.988076 -143 ********** Masking position 4 Map Score: 0.282307 Number of sites scoring better than the average of aligned sites = 665 Number in coding regions = 559 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 13 ********** No masking Map Score: -7.01005e-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 Motif number 14 ********** No masking Map Score: -7.01005e-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 Motif number 15 ********** No masking Map Score: -7.01005e-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