AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i248_cell_division_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -x5 Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 yloU 276 similar to alkaline-shock protein #2 yloW 138 similar to phosphoglycerate dehydrogenase #3 ylpA 25 similar to L-serine dehydratase #4 ylpC 108 ylpC #5 acpA 83 acyl carrier protein #6 rncS 139 ribonuclease III #7 smc 100 chromosome segregation SMC protein homolg #8 ftsE 233 cell-division ATP-binding protein #9 cccB 48 cytochrome c551 #10 yvjA 165 similar to hypothetical proteins #11 prfB 69 peptide chain release factor 2 #12 secA 167 translocase binding subunit (ATPase) #13 yvyD 300 alternate gene name: yviI; similar to ribosomal protein S30AE family Motif number 1 ACTAGTTCCTCCTTCGAATGCATAG 1 262 0 GTCCTCCTTC 0.95287 -15 GCTATTCCTCCTTATGAACCAGAG 2 125 0 ATCCTCCTTA 0.987287 -14 AACTGGCTCCTCCTGACCCTTTTCG 3 10 0 GTCCTCCTGA 0.991786 -16 TGATGCTAAAAGTCCCGCCGAAACGCGGGGC 6 13 1 ATCCCGCCGA 0.919001 -127 AATCCCCCTTATGACTCAGGG 7 1 1 ATCCCCCTTA 0.987033 -100 TACATACTGAAATCCCCCTGAGTCATAAGGG 7 16 0 ATCCCCCTGA 0.991786 -85 AGCGATCCTCCTTATGTAATAAGT 7 87 0 GTCCTCCTTA 0.987033 -14 ACCCTTTACAATTCCTGCTGAAACATAAATC 13 233 0 ATCCTGCTGA 0.977569 -68 * ********* Masking position 3 Map Score: 11.1269 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 38 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 2 TACTTTTTAACATTCATATAATCTTAGATGCTTTCGA 1 41 1 CATTCTTTAG 0.713759 -236 GCTATTCCTCCTTATGAACCAGAGCTTATTAGC 2 116 0 CCTCCTTAGA 0.945444 -23 AATCCCCCTTATGACTCAGGGGGATTTCAG 7 4 1 CCCCCTTAGG 0.985131 -97 AGCGATCCTCCTTATGTAATAAGTATTTCAATT 7 78 0 CCTCCTTAAG 0.989398 -23 AGTTTCTTTTCATTCATATTGTCAAGGCATAAAAACA 8 44 0 CATTCTTAGG 0.973889 -190 ATTTATGACCCATTCATTTGTAAAAAGATGAAAAATC 8 141 0 CATTCTTAAG 0.951514 -93 TAAAAAAACACACCCGTATGCATCAGGTGTGTTTTTC 10 14 0 CACCCTTAGG 0.980684 -152 CATATATCCTCCGTTTCTTCCAATGCTCTCCGAT 10 142 0 CCTCCTTAAT 0.941641 -24 ATTATTTATACATGCCTCTAAAATAGGCGTGTGATGA 12 125 1 CATGCTTAGG 0.956258 -43 GAATAGACAGCATCCATTTTCTATAATGAATCAGAAA 13 52 0 CATCCTTAAT 0.923217 -249 CAAAGAACGCCTCCCTTTTATTAAGGATATGTATCT 13 275 0 CCTCCTTAGG 0.972253 -26 ***** * * *** Masking position 9 Map Score: 11.4406 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 213 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 3 GAATGTTAAAAAGTAGATGTTTTGTGCAAGTG 1 24 0 AAGTGTGTTT 0.844027 -253 AGCACTCGGCAAGGATGTTTTTATC 8 4 0 AAGGTTTTTT 0.888097 -230 GAGTGCTGGCAAGGATGTTTTTATGCCTTGAC 8 29 1 AAGGTTTTTT 0.888097 -205 CGTATGCATCAGGTGTGTTTTTCAGC 10 5 0 AGGTTTTTTT 0.935033 -161 CCTGATGCATACGGGTGTGTTTTTTTATTTCT 10 24 1 ACGGTTGTTT 0.926854 -142 TGTCCGCGGAAGGTTTTTGTTTTTCTTATTTG 12 31 1 AGGTTTGTTT 0.980773 -137 GGCGTGTGTGAGGTATTTGTTTCGTTCAATCA 13 120 1 AGGTTTGTTT 0.980772 -181 GGCGGTTCGGAGGTATATGTATATGCTGATTG 13 146 0 AGGTTTGTAT 0.934121 -155 TTTTCACAAAAGATTTATGTTTCAGCAGGAAT 13 222 1 AGATTTGTTT 0.81673 -79 CCCTTTTATTAAGGATATGTATCTATTTCTCT 13 267 0 AAGGTTGTAT 0.886603 -34 **** * ***** Masking position 8 Map Score: 8.10942 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 189 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 4 ACGTTTGCAACTATTGTTTCATCATCTTTCAA 1 113 1 CTTTTTTCAT 0.896526 -164 CTAGTTCCTCCTTCGAATGCATAGAGTTACAG 1 254 0 CTCGATGCAT 0.933059 -23 CAGCCAGAAACAATCGTTGCATTCCAATCTAT 4 32 1 CATCTTGCAT 0.656871 -77 ATAAGTATTTCAATTCTATCATAAACATTGGT 7 61 0 CATTTATCAT 0.705979 -40 ATTACAGTTTCTTTTCATTCATATTGTCAAGG 8 54 0 CTTTATTCAT 0.882062 -180 CGGTCATACTCTTCGAATGCATTCGACAATTT 8 174 0 CTCGATGCAT 0.933059 -60 ATCACCTAATCTTTTATATCATTTTATCTATC 8 209 0 CTTTTATCAT 0.882061 -25 CTGAAAAACACACCTGATGCATACGGGTGTGT 10 12 1 CACTATGCAT 0.877222 -154 GATTTCACTGCTGCTTTAGCATATTACCACTG 10 65 1 CTCTTAGCAT 0.95091 -101 TTCCAATGCTCTCCGATAGCATTTTAATCCTT 10 127 0 CTCGTAGCAT 0.933054 -39 TTATAACGCTCCTCTATCATCACACGCCTA 12 148 0 CTCTTATCAT 0.932906 -20 AAAATGGATGCTGTCTATTCATCAATGTATGG 13 69 1 CTTCATTCAT 0.7628 -232 TTTACAATTCCTGCTGAAACATAAATCTTTTG 13 228 0 CTCTAAACAT 0.71349 -73 ** ** ****** Masking position 11 Map Score: 9.06518 Number of sites scoring better than the average of aligned sites = 571 Number in coding regions = 502 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 5 ATTCTTATGTCTGCTTTTAAGTGCGGCAGCGCTG 2 30 1 CTGCTTGTGC 0.870798 -109 TGGCAAGCGGGCGCGTTACAGCGCTGCCGCACTT 2 48 0 GCGCGTGCGC 0.518702 -91 TTATGAACCAGAGCTTATTAGCGCTTTGCTTCTA 2 104 0 GAGCTTGCGC 0.797593 -35 GGCTAAAGCCCCGCGTTTCGGCGGGACTTTTAGC 6 17 0 CCGCGTGCGG 0.625403 -123 TTACAGCATGCCGCTTTTACGCGCGCTGTATCCG 6 68 1 CCGCTTGCGC 0.504764 -72 ATAGGCACATCAGGTTCACCGCGCTTCTCTGACT 6 106 0 CAGGTTGCGC 0.959088 -34 ACTGACCGCGGCGCCTGCAGGCGCCTGCGGATCT 11 28 1 GCGCCTGCGC 0.49997 -42 ****** **** Masking position 6 Map Score: 4.97503 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 111 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 AATTCACCTCCCCTCAAGTATTATAGTGGAT 5 60 0 CCTCAAGTAT 0.771811 -24 TTGCCAGCACTCGGCAAGGATGTTTTTATC 8 10 0 TGGCAAGGAT 0.942148 -224 TTGCCGAGTGCTGGCAAGGATGTTTTTATGC 8 24 1 CGGCAAGGAT 0.992098 -210 TACATCTAATCAGGGAAGGATTAAAATGCTA 10 112 1 CGGGAAGGAT 0.989647 -54 TTCGCCCCGGCAAGTTTACTGACCGCG 11 7 1 CGGCAAGTTT 0.948339 -63 CCGCGGACATCACGGAAGGCTTCTCTTCA 12 9 0 CCGGAAGGCT 0.9704 -159 CCGTGATGTCCGCGGAAGGTTTTTGTTTTTC 12 25 1 CCGGAAGGTT 0.975003 -143 * ********* Masking position 6 Map Score: 4.03816 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 118 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 GTAACTCTATGCATTCGAAGGAGGAACTAG 1 256 1 GCATTCGAAG 0.993888 -21 AACAATCGTTGCATTCCAATCTATGAAATT 4 40 1 GCATTCCAAT 0.938531 -69 ATTGTCGAATGCATTCGAAGAGTATGACCG 8 176 1 GCATTCGAAG 0.993888 -58 CTATCGGAGAGCATTGGAAGAAACGGAGGA 10 140 1 GCATTGGAAG 0.983783 -26 ********** Masking position 5 Map Score: 2.99689 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 4 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 8 TCTTGCGGAAACAGCAGCGCTATAGTATAT 1 161 1 ACAGCAGCGC 0.982063 -116 GCTTTTAAGTGCGGCAGCGCTGTAACGCGC 2 42 1 GCGGCAGCGC 0.923186 -97 TTAGTCTAGAAGCAAAGCGCTAATAAGCTC 2 98 1 AGCAAAGCGC 0.872284 -41 CGGTTTAGTCAGAGAAGCGCGGTGAACCTG 6 100 1 AGAGAAGCGC 0.986626 -40 AAGTTTACTGACCGCGGCGCCTGCAGGCGC 11 22 1 ACCGCGGCGC 0.96252 -48 TGAAGAGAAGCCTTCCGTGATGT 12 4 1 AGAGAAGCCT 0.826774 -164 GTGTGATGATAGAGGAGCGTTATAA 12 153 1 AGAGGAGCGT 0.928524 -15 CCTTAATAAAAGGGAGGCGTTCTTTG 13 285 1 AGGGAGGCGT 0.931132 -16 ********** Masking position 7 Map Score: 1.96001 Number of sites scoring better than the average of aligned sites = 570 Number in coding regions = 500 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 9 CGCTTGCCATTTTATATCTGATCAATTAGTCT 2 73 1 TTTATTCTAT 0.939584 -66 TACACTTCATTATACGTCAAATTTAGACATAA 8 90 0 TATACTCAAT 0.858884 -144 GGTGTGTTTTTTTATTTCTTATATCCTTGATT 10 37 1 TTTATTCTAT 0.939591 -129 TTGGGTGTTATTTACATCTAATCAGGGAAGGA 10 100 1 TTTACTCTAT 0.978586 -66 CTAGTCCATGTATACCTCTCATTATCATATCA 12 90 0 TATACTCTAT 0.961045 -78 CTTTTCCCTCTCATGAGTTCTGTG 13 3 1 TTTCCTCTAT 0.943918 -298 ***** *** ** Masking position 7 Map Score: 1.26289 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 37 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 10 TATAATCTTAGATGCTTTCGATATGGATACTT 1 57 1 GATCTTTCAT 0.980445 -220 TTTCGATATGGATACTTTAAATAATTTACCAC 1 72 1 GATCTTTAAT 0.944264 -205 TACTATTACAGTTTCTTTTCATTCATATTGTC 8 58 0 GTTCTTTTAT 0.925982 -176 TATATCCTCCGTTTCTTCCAATGCTCTCCGAT 10 142 0 GTTCTTCCAT 0.95258 -24 ATCAGAAAATGTTCCTTTAAATACTCACAGAA 13 28 0 GTTCTTTAAT 0.956635 -273 ATAGAAAATGGATGCTGTCTATTCATCAATGT 13 65 1 GATCTGTCAT 0.939126 -236 TGAGGTATTTGTTTCGTTCAATCAGCATATAC 13 128 1 GTTCGTTCAT 0.95258 -173 *** ***** ** Masking position 11 Map Score: 2.493 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 109 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 11 ********** No masking Map Score: -3.45791e-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 TTTAAAAAACTAGAGAAACTACGATGAAATTTTCGAGAA 5 16 0 TAGAACAGAA 0.835915 -68 TCTAGTTTTTTAAAAACGAATCCACTATAATACTTGAGG 5 41 1 TAAAACATAA 0.971479 -43 CGGCATGCTGTAATAACTGCACGAATAAAGGGCTAAAGC 6 42 0 TAATACATAA 0.905097 -98 AATTCTATCATAAACATTGGTCAAATAAGACGGCATACA 7 43 0 TAAAACATAG 0.936517 -58 ACGTCAAATTTAGACATAATACTATTACAGTTTCTTTTC 8 70 0 TAGAACATAA 0.960672 -164 TGATTAGATGTAAATAACACCCAAATACAGTGGTAATAT 10 85 0 TAAAACATAA 0.971678 -81 TTGTTATTTCCAAAGAATTTGCAAATAAGAAAAACAAAA 12 45 0 CAAAACATAG 0.913071 -123 GAGGCATGTATAAATAATTTACTAGTCCATGTATACCTC 12 104 0 TAAAACATCA 0.877374 -64 TATAATGAATCAGAAAATGTTCCTTTAAATACTCACAGA 13 29 0 CAGAACTTAA 0.709912 -272 TCCGAACCGCCAATAACAGAGCAAATACAAACAAAATTC 13 167 1 CAATACATAA 0.871637 -134 **** * * * ** * Masking position 6 Map Score: 1.07169 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 45 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 13 AAGATGATGAAACAATAGTTGCAAACGTTTT 1 110 0 AACAATAGTG 0.961221 -167 AAGACCAGGCAATAATCGCTGGCCGTACCTC 1 194 0 AATAATCGTG 0.916485 -83 AACCATATAGTAGAATAGCTGTAACTCTATG 1 236 1 TAGAATAGTG 0.907795 -41 AAGCAGACATAAGAATAGAAGGGCAAATTGC 2 15 0 AAGAATAGAG 0.953769 -124 TTCAGCCAGAAACAATCGTTGCATTCCAATC 4 30 1 AACAATCGTG 0.967672 -79 AATGATATAAAAGATTAGGTGATTTC 8 218 1 AAGATTAGTG 0.907794 -16 AGAGCATTGGAAGAAACGGAGGATATATG 10 147 1 AAGAAACGAG 0.837982 -19 ******** ** Masking position 4 Map Score: 0.859356 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 165 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 14 ACATAAGAATAGAAGGGCAAATTGCCCTT 2 10 0 AGAAGGGCAA 0.93537 -129 GATCAGATATAAAATGGCAAGCGGGCGCGT 2 66 0 AAAATGGCAA 0.859173 -73 CGAAAAGGGTCAGGAGGAGCCA 3 3 1 AAAAGGGTCA 0.930915 -23 ACTGCACGAATAAAGGGCTAAAGCCCCGCG 6 36 0 TAAAGGGCTA 0.916434 -104 AGTGTATTGAAAAAGGGAACTTTCAGATTT 8 116 1 AAAAGGGAAC 0.88847 -118 TAATTGATTAAAAAGGGTTCCATACATTGA 13 90 0 AAAAGGGTTC 0.915168 -211 GCAGGAATTGTAAAGGGTAAAAGAGAAATA 13 246 1 TAAAGGGTAA 0.928636 -55 ********** Masking position 4 Map Score: 0.163939 Number of sites scoring better than the average of aligned sites = 384 Number in coding regions = 312 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 15 ********** No masking Map Score: -3.45791e-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