AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icoldbox_ecoli_bsub_300.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 cspB 300 cold shock protein; may affect transcription #2 deaD 128 inducible ATP-independent RNA helicase #3 yhbM 108 putative control proteins #4 pnp 177 polynucleotide phosphorylase; cytidylate kinase activity #5 rpsO 148 30S ribosomal subunit protein S15 #6 rbfA 163 ribosome-binding factor A #7 infB 24 protein chain initiation factor IF-2 #8 nusA 27 transcription pausing; L factor #9 yhbC 300 orf, hypothetical protein #10 yiaG 300 orf, hypothetical protein #11 cspA 280 cold shock protein 7.4, transcriptional activator of hns #12 ydbR 300 similar to ATP-dependent RNA helicase #13 ydeA 300 similar to glyceraldehyde 3-phosphate dehydrogenase (glycolysis) #14 cspC 262 cold-shock protein #15 deaD 81 ATP-dependent RNA helicase #16 yxiM 182 similar to hypothetical proteins from B. subtilis #17 yxiL 108 yxiL #18 yxiJ 27 yxiJ #19 yxzG 69 yxzG #20 yxiH 122 yxiH #21 yxiG 50 yxiG #22 yxiF 300 yxiF Motif number 1 CGAGTTTCAGAAAAGGGGGCCTGAGTGGCC 4 17 1 AAAAGGGGGC 0.993231 -161 GTCAGCTTGAAAAAAGGGGCCACTCAGGCC 4 34 0 AAAAAGGGGC 0.995435 -144 AATTAATTTTAAAAAGGGGCTAACAGCCCC 6 122 1 AAAAAGGGGC 0.995435 -42 TCTCCTGACAAAAAAGGGGCTGTTAGCCCC 6 137 0 AAAAAGGGGC 0.995435 -27 AAACCCCGATAAATCGGGGCTTTATATAAC 9 225 0 AAATCGGGGC 0.926298 -76 CAAGACATAAAAAAAGGGCCTAAAGCCCAG 9 278 0 AAAAAGGGCC 0.969402 -23 GATTTTCCCGAATAGGGGGCTTTGCGATTG 14 23 1 AATAGGGGGC 0.958557 -240 GTTATTGTTTAAAAAGAGGCAGGGG 21 36 1 AAAAAGAGGC 0.955309 -15 AAAATGGGGCATTTATTGAT 22 1 1 AAAATGGGGC 0.981749 -300 ********** Masking position 2 Map Score: 19.0699 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 27 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 2 GAACAACAACGCCCTCACCCGTTAAGGTGAT 2 49 0 GCCCCACCCG 0.954702 -80 GTTGCCATTTGCCCTCCGCTGCGGCGGGGGG 3 12 1 GCCCCCGCTG 0.991151 -97 CCGGTTAAAAGCCCCCCGCCGCAGCGGAGGG 3 23 0 GCCCCCGCCG 0.989264 -86 TTCCCACTCCCGAAGACCACGG 3 97 0 TCCCCTCCCG 0.979326 -12 TCGGTTCAAATCCGGCCCCCGCAACCACTTT 9 84 1 TCCGCCCCCG 0.968921 -217 ATATATCTCTTACCACTCCTGTTTTGTAAAG 10 110 0 TACCCTCCTG 0.778031 -191 TGCCCTGACTTCACCCCGCTGTGTCTGCTTT 10 214 1 TCACCCGCTG 0.959826 -87 ACTCCTCAAATCACACTGCGGGATCGTGAAT 10 275 0 TCACCTGCGG 0.865201 -26 TGTATATCTGGCCGGCTGCGGCTATGATACA 12 44 1 GCCGCTGCGG 0.925222 -257 TCTCGAATATGCCGGCTGCTGCTCCATCCGC 12 158 0 GCCGCTGCTG 0.966415 -143 GGAGTGTTCATCACATCCCTGTAATCTTTGA 13 151 0 TCACTCCCTG 0.735093 -150 CCTCTTTATCGCACTCACCTGACCCCAAATT 13 180 1 GCACCACCTG 0.869134 -121 TGCAGTTATTTCCGATTCCTGATATAATAAA 14 127 1 TCCGTTCCTG 0.73333 -136 GAGCCGCATTCCCTCCGCTGTCAATTTCTC 22 281 0 TCCCCCGCTG 0.989266 -20 **** ****** Masking position 9 Map Score: 17.3899 Number of sites scoring better than the average of aligned sites = 1016 Number in coding regions = 955 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 3 CTGCGGCGGGGGGCTTTTAACCGGGCAGGA 3 30 1 GGGCTTTTAA 0.957926 -79 TATATACTTTGGAGTTTTAAA 5 138 1 GGAGTTTTAA 0.778955 -11 TCAGGTGGAAGGGCTGTTCACGTTGACCTG 6 92 0 GGGCTGTTCA 0.981073 -72 GACAAAAAAGGGGCTGTTAGCCCCTTTTTA 6 131 0 GGGCTGTTAG 0.840811 -33 CGCGGGCTTTTCACCTCATCCAG 8 15 0 GGGCTTTTCA 0.986031 -13 CCTTCGTAGTGGGATTTGAAAAAATCCTTC 9 155 1 GGGATTTGAA 0.742938 -146 TGTGATTTGAGGAGTTTTCA 10 291 1 GGAGTTTTCA 0.916147 -10 AAGCGTTAAAGGAATGTGCACTACGAGGGG 11 199 0 GGAATGTGCA 0.723344 -82 ATATTCGTCCGGACTTTTCATCGTGACCCG 12 104 1 GGACTTTTCA 0.965577 -197 AAAGTAATTCGGGCTTTGTATACGGATGGA 12 247 1 GGGCTTTGTA 0.835566 -54 GCGATAAAGAGGAGTGTTCATCACATCCCT 13 162 0 GGAGTGTTCA 0.889168 -139 CCCGAATAGGGGGCTTTGCGATTGAGTTGA 14 29 1 GGGCTTTGCG 0.942448 -234 CTCACCCAGTGGGCTTTTCACAAAACGCTG 22 135 0 GGGCTTTTCA 0.986031 -166 ********** Masking position 5 Map Score: 14.8974 Number of sites scoring better than the average of aligned sites = 329 Number in coding regions = 286 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 4 GTTTTTTGATGGGGTTGAAGATGGCTGGAT 1 71 1 GGGGTTGAAG 0.909692 -230 ATGATTGCGTCGGTTTGAAGAACAGACGAT 1 142 1 CGGTTTGAAG 0.974601 -159 AAAAAGATTACGGGCTGATGTGTACGTCAG 2 11 0 CGGGCTGATG 0.931695 -118 GTTTCAGGCGCGGGGTGGAGCAGCCTGGTA 9 26 1 CGGGGTGGAG 0.981882 -275 ACCGCAACTGCGGTCTGGAGCACTTTCCAG 9 184 0 CGGTCTGGAG 0.95911 -117 GCAGACACAGCGGGGTGAAGTCAGGGCATG 10 212 0 CGGGGTGAAG 0.989659 -89 TGCACATCAACGGTTTGACGTACAGACCAT 11 123 1 CGGTTTGACG 0.921916 -158 TATTTTTGTTCGGTGTAAAGGATAGTATGA 14 165 1 CGGTGTAAAG 0.870763 -98 ********** Masking position 6 Map Score: 6.03918 Number of sites scoring better than the average of aligned sites = 256 Number in coding regions = 223 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 5 AAAAACTATAGCTTTCTTCAGGAACGTGTGTATA 1 43 0 GCTTTCCAAA 0.927802 -258 TTAACTTGAGCCTTTCGGCATAAATGGTTTGCAT 1 267 0 CCTTTCCAAA 0.966628 -34 CTAATGAGAGGCTTTACCCACATAGAGCTGGGTT 4 132 1 GCTTTACATA 0.633491 -46 ACGTGAACAGCCCTTCCACCTGAAATTAATTTTA 6 99 1 CCCTTCCCAA 0.934013 -65 TAAGGCAAGTCCCTTCAAGAGTTATCGTTGATAC 11 166 1 CCCTTCGATA 0.857205 -115 ATAAAACTGCCCTTTAGACAAGAAGGACAGGATC 12 275 0 CCTTTACAAA 0.850825 -26 TCCGTACCTGCCCTTCCCCAACAATTTGGGGTCA 13 199 0 CCCTTCCAAA 0.98548 -102 AAACACATATGCCTTGGTCAATTAGAGTATAATG 15 28 1 GCCTTGCATA 0.772946 -54 TTGATCCTCTCCCTTCCGCAATAATC 18 3 0 CCCTTCCAAA 0.98548 -25 CATGATAAATCCCTTCATCACATAAACCGACCCA 19 23 0 CCCTTCCATA 0.978885 -47 ****** ** ** Masking position 5 Map Score: 5.07633 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 170 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 6 ACTTTTATCCACTTTATTGCTGTTTACG 11 5 1 TTTCCTTATT 0.934542 -276 CAACAATTATTTTTCATATTTATGATTAATCGGT 11 64 0 TTTCATTATG 0.834558 -217 TGACCCGAAGTTCTCCGCTGGATTCTTGGGAGCG 12 127 1 TTTCCTGATT 0.888661 -174 GCCGATCTGCTTCTCATCTTATTGAAAAACAAAT 12 190 1 TTTCCTTTTG 0.943179 -111 TGATGAAATATTATCGTATGAATGTTGCAAGAGG 13 108 1 TTTCATGATG 0.738225 -193 CAAATCATCTTTCTTTGCTTTATTAGGAAATTCA 14 56 0 TTTTCTTATT 0.821586 -207 GAAGATTGACTTTTCGTCTTGATGATACTTTGGG 14 193 1 TTTCCTTATG 0.958073 -70 GTCACACTGATTTTCCCCTTCTTGAGACTCTCCC 16 54 1 TTTCCTTTTG 0.943179 -129 CTCAACGCAATTTTTTTCTTAATTCAGTCATCAT 16 101 1 TTTTCTTATT 0.821586 -82 TTTGTTTTCTGCTTGGTGGCAAGGC 21 2 1 TTTTCTGTTG 0.749567 -49 CAATTCTATATTTTTAGATTCTTTTGTCATACAA 22 68 0 TTTTATTTTT 0.424766 -233 CGCTGTCAATTTCTCAACTTCTTTTAAATTGATT 22 262 0 TTTCCTTTTT 0.912056 -39 ** ** *** *** Masking position 9 Map Score: 5.72469 Number of sites scoring better than the average of aligned sites = 273 Number in coding regions = 228 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 7 CGGCAGTATTCTACTCGTAGCGACCTGTTATC 5 26 0 CTACGTAGCG 0.913774 -123 AATACTGCCGCTTAACGTCGCGTAAATTGTTT 5 48 1 CTTAGTCGCG 0.871576 -101 TTGTTTAACACTTTGCGTAACGTACACTGGGA 5 74 1 CTTTGTAACG 0.960562 -75 CGTTAGGTGGCTATAAGTCACGCTAAATGACA 10 156 1 CTATGTCACG 0.960907 -145 CAGCGGAGAACTTCGGGTCACGATGAAAAGTC 12 115 0 CTTCGTCACG 0.979432 -186 TCCCTGTAATCTTTGAGTAACGTTTCCTCTTG 13 135 0 CTTTGTAACG 0.961314 -166 ATCAGTGTGACTTCTTGTCACACTTGATCACA 16 33 0 CTTCGTCACA 0.841714 -150 CATTTATTAGCTATTAGTAACGGACAACCTAG 20 59 0 CTATGTAACG 0.939383 -64 **** ****** Masking position 8 Map Score: 3.95441 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 72 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 ATGTGGGTAAAGCCTCTCATTAGCCGCGCGA 4 124 0 AGCCTTCATT 0.937762 -54 AGAGATCGGCGTCCTTTCATTCTATATACTT 5 116 1 GTCCTTCATT 0.902277 -33 GATTCGATTCAGCCTGTCATTTAGCGTGACT 10 171 0 AGCCTTCATT 0.937762 -130 TTGGAAAACGGTCCTGTCATCAGGACCGTAA 11 34 0 GTCCTTCATC 0.852569 -247 ATACGGATGGATCCTGTCCTTCTTGTCTAAA 12 266 1 ATCCTTCCTT 0.969956 -35 GTCAATCTTCATACTATCCTTTACACCGAAC 14 172 0 ATACTTCCTT 0.888851 -91 CACACAGTATATACTATCCTTGCCCAAAGTA 14 218 0 ATACTTCCTT 0.888851 -45 CCCCTTCTTGAGACTCTCCCCTCATTTTTAT 16 68 1 AGACTTCCCC 0.546277 -115 GTTGATCCTCTCCCTTCCGCAATAA 18 13 0 ATCCTTCCCT 0.92532 -15 ATCATGATAAATCCCTTCATCACATAAACCG 19 28 0 ATCCCTCATC 0.739413 -42 GTTTATTCTTATCATTTCATTTCGAACCTAG 20 91 1 ATCATTCATT 0.65464 -32 ***** ***** Masking position 7 Map Score: 3.60526 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 92 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 9 GGGTTGAAGATGGCTGGATGTCTAAAATAA 1 82 1 TGGCTGGATG 0.918991 -219 CAGGCAATCCATGCCGGATGCAGCGTAAAC 6 40 0 ATGCCGGATG 0.980406 -124 CCGGCATGGATTGCCTGATGTGACGCTGGC 6 53 1 TTGCCTGATG 0.777408 -111 TAGTCTGGATGAGGTGAAAAG 8 2 1 AGTCTGGATG 0.806315 -26 ACACTAATGTATGCCGGCCGAAAATTATGT 12 17 1 ATGCCGGCCG 0.960378 -284 TATGTATATCTGGCCGGCTGCGGCTATGAT 12 42 1 TGGCCGGCTG 0.977205 -259 CACGATGAAAAGTCCGGACGAATATGTTCG 12 99 0 AGTCCGGACG 0.8992 -202 CATCTCGAATATGCCGGCTGCTGCTCCATC 12 161 0 ATGCCGGCTG 0.979841 -140 ********** Masking position 4 Map Score: 5.24892 Number of sites scoring better than the average of aligned sites = 773 Number in coding regions = 448 Number in noncoding regions = 325 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 10 AACCGACGCAATCATTAACGCATAGTTGAACA 1 125 0 ATCAAACGCA 0.848081 -176 TGGTTTGCATAACAGAAACGACTTCGTACTTA 1 245 0 AACAAACGAC 0.974955 -56 TGTATTAACGAACAACAACGCCCTCACCCGTT 2 57 0 AACAAACGCC 0.987715 -72 TGCCGGATGCAGCGTAAACGCCTTATCCCGCA 6 27 0 AGCGAACGCC 0.917093 -137 GTTCATGAAAATAATCAACGACTTCAATTGAT 13 58 0 ATAAAACGAC 0.730183 -243 CCTCTTTTTAAACAATAACGCCTTGCCACCAA 21 23 0 AACAAACGCC 0.987714 -28 AACAAATCTAAACATGAACGACAACGAAAACA 22 219 1 AACAAACGAC 0.974954 -82 **** ****** Masking position 7 Map Score: 1.84497 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 243 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 11 GGTTGCCATTTGCCCTCCGCTGCGGCGGG 3 10 1 TTGCCCTCCG 0.787818 -99 GGTTTTTAGGGTTCCATGCGGGATAAGGCG 6 11 1 GTTCCATGCG 0.949441 -153 AGGCGTTTACGCTGCATCCGGCATGGATTG 6 36 1 GCTGCATCCG 0.901761 -128 GCTGTTCCTTCCTGCTACAGTTT 7 12 0 GTTCCTTCCT 0.749692 -13 ACAGGACCGTTTTCCAACCGATTAATCATA 11 48 1 TTTCCAACCG 0.793564 -233 GCCGGCTGCTGCTCCATCCGCTCCCAAGAA 12 149 0 GCTCCATCCG 0.971694 -152 AGAAGGACAGGATCCATCCGTATACAAAGC 12 259 0 GATCCATCCG 0.926391 -42 TTTTGTTGCCTCCTAGTGTGTAAC 14 249 0 GTTGCCTCCT 0.806929 -14 TGCCAAAAAGGTTCCCAGCGTTTTGTGAAA 22 120 1 GTTCCCAGCG 0.870477 -181 GAGCCGCATTCCCTCCGCTGTCAATTT 22 284 0 ATTCCCTCCG 0.909882 -17 ********** Masking position 5 Map Score: 2.31054 Number of sites scoring better than the average of aligned sites = 423 Number in coding regions = 383 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 12 CAGGTGTTATTCACTTATTCCTTCTTTGAG 1 205 1 TCACTTATTC 0.64817 -96 TCTTTGAGTCTCTCCAATTAAGTACGAAGT 1 227 1 TCTCCAATTA 0.665158 -74 AGGACGCCGATCTCTAATTCAGCGATCCCA 5 101 0 TCTCTAATTC 0.859754 -48 ATCTCTTACCACTCCTGTTTTGTAAAGATT 10 107 0 ACTCCTGTTT 0.666216 -194 TAAGCTGTAATCTCCAATTTGTTTCATTTT 13 24 0 TCTCCAATTT 0.889528 -277 AAGCATTAAATCTCCTGTTCATGAAAATAA 13 76 0 TCTCCTGTTC 0.925431 -225 GATGGTAACATCTCTTATTTAATGTTCCAT 22 29 0 TCTCTTATTT 0.922618 -272 GTTACCATCCTCTCTTATTTGTATGACAAA 22 50 1 TCTCTTATTT 0.922618 -251 GATTCATCATTCTCTTGTTTTCGTTGTCGT 22 236 0 TCTCTTGTTT 0.907702 -65 ********** Masking position 8 Map Score: 1.75696 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 77 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 13 GCGTTAATGATTGCGTCGGTTTGAAGAACAG 1 136 1 TTGCGCGGTT 0.982218 -165 TACACCTACTTTGAGCCGGTTCACACTTTTC 2 85 1 TTGAGCGGTT 0.963957 -44 TGATCTTCCGTTGCAGAGGTTCGCGCGGCTA 4 104 1 TTGCAAGGTT 0.956575 -74 GCAGTGTGATTTGAGGAGTTTTCA 10 287 1 TTGAGAGTTT 0.752903 -14 TCGTAACAAATCGAAAAGGTTGGATAATAAA 13 251 1 TCGAAAGGTT 0.739099 -50 CTCCTGTCTCTTGCAGATGTTCTCATTATAC 15 54 0 TTGCAATGTT 0.710974 -28 GCTTCTATTGCGGAGGTTGGGATGTGAT 16 8 1 TTGCGAGGTT 0.982565 -175 AACAACAGCTTTGGGTCGGTTTATGTGATGA 19 12 1 TTGGGCGGTT 0.940077 -58 ***** ***** Masking position 10 Map Score: 1.91296 Number of sites scoring better than the average of aligned sites = 267 Number in coding regions = 246 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 14 CCCGGTTGCTAACAAGGCGTCCTGCCCGGT 3 49 0 AACAAGGCGT 0.955254 -60 TTCCATGCGGGATAAGGCGTTTACGCTGCA 6 22 1 GATAAGGCGT 0.963562 -142 CTAACCTTCTGCGAAGGCGTAAATCTCTGG 10 69 0 GCGAAGGCGT 0.97218 -232 TGCATCACCCGCCAATGCGTGGCTTAATGC 11 96 1 GCCAATGCGT 0.941042 -185 GCCTTTCGGCGATATGGCGTGCTTTACAGA 11 234 0 GATATGGCGT 0.845914 -47 ACTCTAATTGACCAAGGCATATGTGTTTTG 15 26 0 ACCAAGGCAT 0.813232 -56 TCTGCTTGGTGGCAAGGCGTTATTGTTTAA 21 18 1 GGCAAGGCGT 0.97868 -33 ********** Masking position 4 Map Score: 1.35658 Number of sites scoring better than the average of aligned sites = 423 Number in coding regions = 232 Number in noncoding regions = 191 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 15 AAGTGAATAACACCTGAAATGAGAACTGCT 1 191 0 CACCTGAAAT 0.897911 -110 ACAGCCCTTCCACCTGAAATTAATTTTAAA 6 105 1 CACCTGAAAT 0.897911 -59 GATAATATTTCATCAGAAAGCATTAAATCT 13 93 0 CATCAGAAAG 0.969131 -208 ATAATGAGAACATCTGCAAGAGACAGGAGT 15 56 1 CATCTGCAAG 0.919873 -26 TTAATTCAGTCATCATAAAGAAACAATCAC 16 119 1 CATCATAAAG 0.829252 -64 CCTGTATCCTCATCAGAAAGATGCTGTTTC 17 48 0 CATCAGAAAG 0.969131 -61 ********** Masking position 8 Map Score: 0.606346 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 146 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555