AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i143_Cytochrome-ubiquinol_Oxidase__ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 cydA 300 cytochrome d terminal oxidase, polypeptide subunit I #2 hyaA 300 hydrogenase-1 small subunit #3 appC 133 probable third cytochrome oxidase, subunit I #4 HI1076 300 cytochrome D ubiquinol oxidase, subunit I (cydA) Motif number 1 ACTCCTTGCTCATCGCATGAAGACTCCGAGAG 1 278 0 CATCGCTAAG 0.984121 -23 GGTCCATTTTTATCGCTAAAAGATAAATCCAC 2 79 1 TATCGCAAAG 0.9639 -222 CACTGGCGCACGTCGCCAGAAAGTATTGTTAA 2 152 0 CGTCGCAAAA 0.784652 -149 AAGGATGAGCTTTCGTTTTCAGCATCTCACGT 2 187 1 TTTCGTTCAG 0.744834 -114 CAAGGCAAACCATCGCTTCACGTGAGATGCTG 2 206 0 CATCGCTACG 0.968224 -95 GCTACAGGGACGTCGCTTGCCGACCATAAGCG 2 237 1 CGTCGCTCCG 0.983227 -64 GTCCTGCCGGTGTCGCAAGGAGGAGAGACGTG 2 275 1 TGTCGCAGAG 0.92181 -26 AGACGGTAAGTATCGCTTTCAGTCTTATGAAT 3 13 1 TATCGCTCAG 0.987147 -121 GTCTTATGAATATCGCAATCGGCGAATACCTC 3 34 1 TATCGCACGG 0.933036 -100 ATTTTTCTCTCTTCGCCTACAGGAGTGCGC 3 114 1 CTTCGCTCAG 0.981577 -20 ****** * *** Masking position 3 Map Score: 9.62633 Number of sites scoring better than the average of aligned sites = 1308 Number in coding regions = 1207 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 2 TTGTTCTCGATCAAATTGGCTGAAAGGCGG 1 18 1 TCAAATTGGC 0.986144 -283 TAATTTAGCTATAAATTGATCACCGTCGAA 1 48 1 ATAAATTGAT 0.774129 -253 TAATAAAAACTCAAATTGATCCCACGTATA 1 135 0 TCAAATTGAT 0.966573 -166 TTGACTTAGATCAAATTGAC 4 1 0 TCAAATTGAC 0.990672 -300 TTATATTTTATTTAATTGACTTAGATCAAA 4 16 0 TTTAATTGAC 0.91503 -285 TAGAGATAATCCAAATTGGCGGCTATTCTA 4 129 0 CCAAATTGGC 0.963317 -172 TCAGCTAAGTTTAAATTGACTTATCTACAT 4 195 0 TTAAATTGAC 0.980976 -106 ********** Masking position 5 Map Score: 7.94208 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 59 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 3 AAATTGGCTGAAAGGCGGTAATTTAGCTATA 1 30 1 AAAGGGGTAA 0.980947 -271 GAAAGGTTGCAAACATGTTAATAAAAACTCA 1 152 0 AAACAGTTAA 0.799681 -149 TGCACACAAAAACGGCGTAAAGAAAGGTTGC 1 173 0 AACGGGTAAA 0.940709 -128 GACCCTTTCTAACGGGGTTCACTCTCGGAGT 1 257 1 AACGGGTTCA 0.877261 -44 GCCGGTTGCTAAACGAGTAAAAGAGAAGGAA 2 14 0 AAACGGTAAA 0.908144 -287 GCCGGTGTCGCAAGGAGGAGAGACGTGCGAT 2 280 1 CAAGGGGAGA 0.905394 -21 AAAGACGGTAAGTATCGCTTT 3 1 1 AAAGAGGTAA 0.944052 -133 GTTTCAGGATAAAGAGGGAGATCTACCATTA 3 76 1 AAAGAGGAGA 0.930673 -58 TTGTTTATACAAAGGAGTTGAGA 4 288 1 AAAGGGTTGA 0.975123 -13 ***** ***** Masking position 2 Map Score: 5.12474 Number of sites scoring better than the average of aligned sites = 681 Number in coding regions = 598 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 4 GCGATAAAAATGGACCTATTTTTCTTTTGGC 2 64 0 TGGACTATTT 0.901782 -237 ACAAACTGTGTGGATTTATCTTTTAGCGATA 2 89 0 TGGATTATCT 0.972997 -212 TCTACCATTATCGGGTTATTTTTCTCTCTTC 3 97 1 TCGGTTATTT 0.945955 -37 ATACAAAAATAGGGCTTATTTGTTATATTTT 4 37 0 AGGGTTATTT 0.964042 -264 AGCCGCCAATTTGGATTATCTCTATAATAAC 4 135 1 TTGGTTATCT 0.961755 -166 TAAGTTTAAATTGACTTATCTACATAATTAT 4 189 0 TTGATTATCT 0.924103 -112 TTGAGTAATTAGGGATTATTTAAGGCATCGC 4 231 1 AGGGTTATTT 0.964042 -70 **** ****** Masking position 8 Map Score: 3.93353 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 121 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 5 TTTATAGCTAAATTACCGCCTTTCAGCCAA 1 33 0 AATTACCGCC 0.82161 -268 TTGCAACCTTTCTTTACGCCGTTTTTGTGT 1 171 1 TCTTTACGCC 0.960066 -130 GGCTAAACATCCCCACCGCCCGGCCAAAAG 2 42 1 CCCCACCGCC 0.93784 -259 ATCGCACGTCTCTCCTCCTTGCGACACC 2 283 0 TCTCTCCTCC 0.974446 -18 TGAAAGCGATACTTACCGTCTTT 3 4 0 ACTTACCGTC 0.839904 -130 TTATCCTGAAACTCTACGACCAGAGGTATT 3 58 0 ACTCTACGAC 0.891203 -76 GTTATTTTTCTCTCTTCGCCTACAGGAGTG 3 111 1 TCTCTTCGCC 0.957073 -23 ATCCCTAATTACTCAACTCCAATCAGCTAA 4 217 0 ACTCAACTCC 0.967341 -84 TCTCAACTCCTTTGTATAAA 4 291 0 TCTCAACTCC 0.967341 -10 ********** Masking position 7 Map Score: 6.03057 Number of sites scoring better than the average of aligned sites = 1443 Number in coding regions = 1360 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 6 CAGCCAATTTGATCGAGAACAATTTATCT 1 8 0 GAGAGAACAA 0.963715 -293 TGCATTTTTCGACGGTGATCAATTTATAGCTA 1 53 0 GAGTGATCAA 0.990797 -248 ATGGTATGATGAAAGTGTTCAAACAAATTTCT 1 209 1 GAGTGTTCAA 0.963715 -92 TCAGGATAAAGAGGGAGATCTACCATTATCGG 3 79 1 GAGAGATCTA 0.982964 -55 TTATTTAATTGACTTAGATCAAATTGAC 4 7 0 GATAGATCAA 0.943359 -294 TTTATATCAAAAATGTGATCTATATAGCATTT 4 67 1 AAGTGATCTA 0.899259 -234 ** ******** Masking position 2 Map Score: 2.93754 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 134 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 7 AATTTGAGTTTTTATTAACATGTTTGCAAC 1 148 1 TTTATTAACA 0.951047 -153 TTCACTACGCTTTATTAACAATACTTTCTG 2 138 1 TTTATTAACA 0.951047 -163 TTTTTTACTATTTTTTATCCTTATGTTTAG 4 96 1 TTTTTTATCC 0.922473 -205 TAACTGGTGTTTTTTTAACCTTTAAAAATA 4 162 1 TTTTTTAACC 0.967787 -139 ********** Masking position 5 Map Score: 0.712932 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 29 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 TGAAGCAAATTTGCATTTTTCGACGGTGAT 1 66 0 TTGCATTTTT 0.921231 -235 TCCACACAGTTTGTATTGTTTTGTGCAAAA 2 106 1 TTGTATTGTT 0.921229 -195 CGTCGCCAGAAAGTATTGTTAATAAAGCGT 2 144 0 AAGTATTGTT 0.920911 -157 AGCCCTATTTTTGTATTTATATCAAAAATG 4 52 1 TTGTATTTAT 0.681353 -249 GTGATCTATATAGCATTTTTTACTATTTTT 4 81 1 TAGCATTTTT 0.949396 -220 TAGCATTTTTTACTATTTTTTATCCTTATG 4 91 1 TACTATTTTT 0.814405 -210 TTATCTACATAATTATTTTTAAAGGTTAAA 4 175 0 AATTATTTTT 0.764938 -126 TCGCCTTGTTAATCATTGTTGGAACTAATG 4 258 1 AATCATTGTT 0.757441 -43 ********** Masking position 5 Map Score: 1.13699 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 141 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 9 AAACAGGTTTTTGTTGAAGCAAATTTGCAT 1 80 0 TTGTTGAAGC 0.957717 -221 CAATAGAAATTTGTTTGAACACTTTCATCA 1 215 0 TTGTTTGAAC 0.974756 -86 TTGTTAATCATTGTTGGAACTAATGTTGTT 4 263 1 TTGTTGGAAC 0.983533 -38 GGAACTAATGTTGTTTATACAAAGGAGTTG 4 278 1 TTGTTTATAC 0.908084 -23 ********** Masking position 5 Map Score: 0.0205733 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 47 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 10 ********** No masking Map Score: -1.4826e-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 11 ********** No masking Map Score: -1.4826e-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 ********** No masking Map Score: -1.4826e-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