AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iarcA_ecoli_hinf_100.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 lpdA 300 lipoamide dehydrogenase (NADH); component of 2-oxodehydrogenase and pyruvate complexes; L-protein of glycine cleavage complex #2 gltA_sdhC 600 gltA: citrate synthase, sdhC: succinate dehydrogenase, cytochrome b556 #3 cydA 300 cytochrome d terminal oxidase, polypeptide subunit I #4 focA 300 probable formate transporter (formate channel 1) #5 icdA 201 isocitrate dehydrogenase, specific for NADP+ #6 aldA 196 aldehyde dehydrogenase, NAD-linked #7 glcD_glcC 250 glcD: glycolate oxidase subunit D, glcC: transcriptional activator for glc operon #8 lldP 300 L-lactate permease #9 sodA 284 superoxide dismutase, manganese #10 HI0181 300 formate transporter #11 HI1076 300 cytochrome D ubiquinol oxidase, subunit I (cydA) #12 HI1088 248 superoxide dismutase (sodA) #13 HI1218 279 L-lactate permease (lctP) #14 HI1231 113 dihydrolipoamide dehydrogenase (lpdA) Motif number 1 CAAAATTGTTAACAATTTTTAAACAACAAACGGC 1 70 0 AAAATTTAAC 0.470004 -231 GTTAATTGTAATGATTTTGTGAACAGCCTATACT 2 131 0 ATATTTTAAC 0.814123 -470 TCACGATAACAACATTTATTTAATTTTTAATCAT 2 208 1 AAATTTTAAT 0.903436 -393 CGAAAAATGCAAATTTGCTTCAACAAAAACCTGT 3 74 1 AATTTGTAAC 0.645952 -227 GCCCCAATAGAAATTTGTTTGAACACTTTCATCA 3 215 0 AATTTGTAAC 0.645952 -86 AAATATCGGTAATTTGTATTTAATAAATACGATC 4 25 1 AATTGTTAAT 0.597504 -276 ATACGGAGTAAATATTTGATTATCCAAATAAAAA 4 157 0 AAATTTTATC 0.711096 -144 GCTTTAGAGCAATTTTTTGTTAATGATTTGTAAT 5 101 0 AATTTTTAAT 0.80744 -101 ACATCAATTTAACATTGAGTTAACCAAGACAAGG 7 91 1 AAATTGTAAC 0.80279 -160 GCCAATACATAACATTTAGTTAACCATTCATTGT 8 169 1 AAATTTTAAC 0.937899 -132 CATTTTCAATATCATTTAATTAACTATAATGAAC 9 208 1 ATATTTTAAC 0.814123 -77 TAATATGGGAATTTTGTCTTTAATTAAACAAACC 10 115 1 ATTTGTTAAT 0.30095 -186 AAGAAAAGCAAAAATTATTTCAACAAACTTTGAT 10 158 0 AAATTATAAC 0.506071 -143 TAAAAGTATTAAATTTTCATCAACTTTTTCAATG 10 257 1 AATTTTTAAC 0.871282 -44 CTTATTTGTTATATTTTATTTAATTGACTTAGAT 11 20 0 ATTTTTTAAT 0.548747 -281 ACAGTATTCTAATATTTGATGAAATTTTCGCAAC 12 36 1 AAATTTTAAA 0.520074 -213 GATTTAAAACAAAATTTAATAAATTCACTTTTTA 12 111 1 AAATTTTAAT 0.903434 -138 AAAAAGGAAAAACATTTAATGATCTAAATCAATT 12 145 1 AAATTTTATC 0.711097 -104 TTTTTTTGCTATTATTTGCTCAATTTTGGTTATA 12 177 1 ATATTTTAAT 0.730693 -72 GAATATGATAAAGATTTTTAATGCCATATTAA 13 82 0 AAATTTAAT 0.388268 -198 CTATTTTAAGAAAATGTGATCAATATCTCATAAA 13 191 0 AAATGTTAAT 0.768102 -89 GTTAGATTAAAAGATGTGATTATTTTATGGATTT 13 242 0 AAATGTTATT 0.350569 -38 CTGCCCACCAAAGATTTCATTAATCGGTGGGCTT 14 27 0 AAATTTTAAT 0.903435 -87 ** **** * *** Masking position 10 Map Score: 16.4165 Number of sites scoring better than the average of aligned sites = 297 Number in coding regions = 167 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 2 ACTGTTCAGGATAAAACCCGACAAACTATATGTAG 2 165 0 ATAAACAAAA 0.570631 -436 CAGGAAAAGCATATAATGCGTAAAAGTTATGAAGT 2 283 1 ATAAATTAAA 0.780479 -318 TCCTCCGCTAAAACAGTTAATTAAAAGGGAGCATC 4 81 0 AAAAGTTAAA 0.699315 -220 ATCCAAATAAAAATAAATTTTAAAAATTAACAAAT 4 135 0 AAAAAATAAA 0.780479 -166 TATTCACCGAAAACAAACATATAAATCACAGGAGT 6 167 1 AAAAAAAAAA 0.864363 -30 CTTTCATTGCAAAGAAAAGCAAAAATTATTTCAAC 10 168 0 AAAAAAAAAA 0.864363 -133 ATTGACATTGAAAAAGTTGATGAAAATTTAATACT 10 261 0 AAAAGTTAAA 0.699315 -40 AGTCAATTAAATAAAATATAACAAATAAGCCCTAT 11 25 1 ATAAATAAAA 0.864363 -276 CACATTTTTGATATAAATACAAAAATAGGGCTTAT 11 49 0 ATAAAAAAAA 0.833435 -252 ACATAAGGATAAAAAATAGTAAAAAATGCTATATA 11 87 0 AAAAATAAAA 0.890305 -214 TTGATTTAAAACAAAATTTAATAAATTCACTTTTT 12 109 1 ACAAATAAAA 0.628613 -140 AAAATTGAGCAAATAATAGCAAAAAAATTGATTTA 12 169 0 AAAAATAAAA 0.890305 -80 ATAGAAGAATATAGAATATGATAAAGATTTTTA 13 94 0 ATAAATAAAA 0.864363 -186 AACTAAACACAAATAGTAATAAAAATGTAAGAAAT 13 138 1 AAAAGTAAAA 0.806526 -142 TAAGAAATGGAANCAAAATGTTAAATTTTATGAGA 13 165 1 AANAAATAAA 0.780479 -115 TATGCTTTGCATATAAATCCATAAAATAATCACAT 13 228 1 ATAAAAAAAA 0.833435 -52 AACCCATCCTATAAAGACCGTAAAAGTGCGGTCAA 14 62 1 ATAAGATAAA 0.589125 -52 *** *** * *** Masking position 5 Map Score: 9.63735 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 110 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 3 TATGACCGCCGGAGATAAATATATAGAGGT 1 277 1 GGAGATAAAT 0.531932 -24 ATAAGCCAGGCGAGATATGATCTATATCAA 4 221 1 CGAGATATGA 0.765127 -80 AGCGCTCGAAGGAGAGGTGA 5 192 1 GGAGAGGTGA 0.831982 -10 GCGTGTTTTGCGAGTTAAGAACAGAAAAAT 7 39 0 CGAGTTAAGA 0.614557 -212 TCTTGTGGGGGGAGATGTCTGGTAAAGAAA 8 67 0 GGAGATGTCT 0.75863 -234 CGTGTGACAAGGAGATGAGCAACAGACTCA 8 247 1 GGAGATGAGC 0.924348 -54 TCATCTCGTCGGAGATGTGACGCGACGAAA 9 29 0 GGAGATGTGA 0.966493 -256 ACATCTCCGACGAGATGAGTGTAAAAATCG 9 41 1 CGAGATGAGT 0.944738 -244 GGAAAATGCCCGAGATGTGAAGCAAATCAC 9 138 0 CGAGATGTGA 0.936536 -147 CGACAATACTGGAGATGAAT 9 275 1 GGAGATGAAT 0.837347 -10 TTAGCTGATTGGAGTTGAGTAATTAGGGAT 11 217 1 GGAGTTGAGT 0.922363 -84 TTTATACAAAGGAGTTGAGA 11 291 1 GGAGTTGAGA 0.933853 -10 ********** Masking position 3 Map Score: 7.18965 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 180 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 4 ACAAAATTGTTAACAATTTTTAAACAACAAA 1 74 0 TACAATTTTT 0.910908 -227 TGGAAGTATTGACCAATTCATTCGGGACAGT 2 353 1 GACAATTCAT 0.86106 -248 ATTTGATCGAGAACAATTTATCT 3 3 0 GACAATTTAT 0.917256 -298 TTTCGACGGTGATCAATTTATAGCTAAATTA 3 48 0 GACAATTTAT 0.917256 -253 ATATGATCTATATCAATTTCTCATCTATAAT 4 235 1 TACAATTTCT 0.704931 -66 GGATGCTTTAGAGCAATTTTTTGTTAATGAT 5 108 0 GACAATTTTT 0.965311 -94 GCACAGGTAGGACCAATTTTTCTGTTCTTAA 7 24 1 GACAATTTTT 0.965315 -227 CTACCGGTCAGACCATTTTTTTTCCAGCTCT 7 129 0 GACATTTTTT 0.861795 -122 GAATTGGTAGGGCCAATTCTTGTGGGGGGAG 8 83 0 GGCAATTCTT 0.727593 -218 GAATTGGCCCTACCAATTCTTCGCTTATCTG 8 95 1 TACAATTCTT 0.851109 -206 GTGATCTATATAGCATTTTTTACTATTTTTT 11 81 1 TACATTTTTT 0.696128 -220 TAATGATCTAAATCAATTTTTTTGCTATTAT 12 161 1 AACAATTTTT 0.756558 -88 ** ******** Masking position 5 Map Score: 8.76321 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 112 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 5 GAGCTTACATAAGTAAGTGACTGGGGTGAGGGCGT 1 207 1 AGTATGCTGG 0.808375 -94 TCGGATTGCTAAGTACTTGATTCGCCATTTATTCG 2 410 1 AGTATGTTGC 0.976017 -191 AATACGGAGTAAATATTTGATTATCCAAATAAAAA 4 157 0 AATATGTTTC 0.602749 -144 CACTTACGTGATGTGCGTGTTTTGCGAGTTAAGAA 7 48 0 AGTGTGTTGC 0.984825 -203 CACGCACATCACGTAAGTGATTATGTTACATCAAT 7 64 1 AGTATGTTTG 0.885127 -187 TCACGGCATTAAGTGGGTGATTTGCTTCACATCTC 9 122 1 AGTGTGTTGC 0.984825 -163 TACTTTTCGTAAGGGTATGGTTTTGCAGGAAAATG 9 160 0 AGGGTGTTTG 0.719302 -125 GAAAAGTGGATGATTATCTGGGGGAATT 10 4 1 AGTGTGTTTC 0.965151 -297 CTAAAGAGTTATGTGTTTGAGTTGCGAAAATTTCA 12 55 0 AGTGTGGTGC 0.93813 -194 TTCTTAAAATAGGTATATGCTTTGCATATAAATCC 13 213 1 AGTATGTTGC 0.976017 -67 * *** ** ** ** Masking position 8 Map Score: 3.84977 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 96 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 CAAATCGGTTGCCGTTTGTTGTTTAAAAAT 1 60 1 GCCGTTTGTT 0.955674 -241 TACTTGATTCGCCATTTATTCGTCATCAAT 2 423 1 GCCATTTATT 0.696879 -178 CCTGGCTTTACCCGTTTTTTATTTGGCTCG 2 516 0 CCCGTTTTTT 0.858824 -85 CTTTCTTTACGCCGTTTTTGTGTGCATTCA 3 178 1 GCCGTTTTTG 0.824913 -123 GTCAATACTACCCTATTGTTTGCCGTCATG 5 65 0 CCCTATTGTT 0.851939 -137 AAATTGCCCGTTTGTGAACCACTTGT 6 7 1 CCCGTTTGTG 0.896911 -190 TTTTATTTCTGCCTTTTATTCCTTTTACAC 6 61 1 GCCTTTTATT 0.749598 -136 ATGAGGATTGCCCTTTTCTTTACCAGACAT 8 53 1 CCCTTTTCTT 0.769717 -248 AATTGGTAGGGCCAATTCTTGTGGGGGGAG 8 83 0 GCCAATTCTT 0.720921 -218 AAGTGGCACTGCCAATTGTGTTGTGTAGGG 8 209 0 GCCAATTGTG 0.773834 -92 TTGTCGGGCGGCCGATTGTTAATGCCGCGT 9 251 0 GCCGATTGTT 0.939981 -34 AACAAATAAGCCCTATTTTTGTATTTATAT 11 44 1 CCCTATTTTT 0.692229 -257 ********** Masking position 6 Map Score: 5.31784 Number of sites scoring better than the average of aligned sites = 452 Number in coding regions = 372 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 7 CGCAGCGGCGTTAGCTTCACGCCCTCACCCCA 1 228 0 TTGCTCACGC 0.96352 -73 GAAGCAGTGTTTTGCATGACGCGCAGTTATAG 2 29 0 TTGCTGACGC 0.984275 -572 CGTTTTTTATTTGGCTCGCCGCTCTGTGAAAG 2 502 0 TTGCCGCCGC 0.985119 -99 TGTTACTTTATTCGCCTGATGCTCCCTTTTAA 4 64 1 TTGCTGATGC 0.981073 -237 TGCATATGCGTTTGCGTCCTGCGATACGGATG 5 134 0 TTGCTCCTGC 0.971745 -68 GCAGCTGATTTTTGCGCGCTGCTTCTGTGAAC 7 200 0 TTGCCGCTGC 0.982089 -51 CGATTAACCTTTCGCCTGTTGCCGCCGTTGTC 9 77 1 TTGCTGTTGC 0.953519 -208 ** ** ****** Masking position 2 Map Score: 4.9674 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 166 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 8 CCCTATGGATTTCTGGGTGCAGCAAGGTAGCA 1 158 1 TTCTGGGCAG 0.986534 -143 CCCGTCGTCTTTCAGGCCGCAGCGGCGTTAGC 1 245 0 TTCAGGGCAG 0.938289 -56 TCGTTTTCGCATCTGGAAGCAGTGTTTTGCAT 2 44 0 ATCTGGGCAG 0.989626 -557 TGTTCCGGAGACCTGGCGGCAGTATAGGCTGT 2 111 1 ACCTGGGCAG 0.991394 -490 AGAGGGGAAAACCTGGGTACAGAGCTCTGGGC 2 472 0 ACCTGGACAG 0.937276 -129 CGCATATGCAACGTGGTGGCAGACGAGCAAAC 5 156 1 ACGTGGGCAG 0.979843 -46 GGGCCAATTCTTGTGGGGGGAGATGTCTGGTA 8 73 0 TTGTGGGGAG 0.855975 -228 ****** **** Masking position 11 Map Score: 3.22526 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 312 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 9 AGTGTTTTGCATGACGCGCAGTTATAGAAA 2 26 0 ATGACGCGCA 0.941874 -575 GGAAAAGCATATAATGCGTAAAAGTTATGA 2 285 1 ATAATGCGTA 0.815912 -316 GTCTTACGCAATAAGGCGCTAAGGAGACCT 2 578 1 ATAAGGCGCT 0.959599 -23 TTATAGCCTAATAACGCGCATCTTTCATGA 5 40 1 ATAACGCGCA 0.977933 -162 AGATAAGGCGCTCTGGATCAAC 8 3 1 ATAAGGCGCT 0.959599 -298 AATTCTCACTATAATGCGCAAAATTTGGAG 13 35 0 ATAATGCGCA 0.966273 -245 ********** Masking position 4 Map Score: 2.91731 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 90 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 10 CGAATGAATTGGTCAATACTTCCACACTGT 2 347 0 GGTCAATACT 0.771519 -254 GGCTATAATGCGGCAATTCATAATCTCTGA 5 18 0 CGGCAATTCA 0.906628 -184 AATCGTGAAAGGACAATTCTGTGAAGGGCT 6 103 0 GGACAATTCT 0.942079 -94 AACAACCTAAGGGCAATTCTCTGATGAGGA 8 30 1 GGGCAATTCT 0.983505 -271 GTAAAGAAAAGGGCAATCCTCATCAGAGAA 8 46 0 GGGCAATCCT 0.94831 -255 GAATTGGTAGGGCCAATTCTTGTGGGGGGA 8 84 0 GGCCAATTCT 0.931838 -217 ATCGGCCGCCCGACAATACTGGAGATGAAT 9 265 1 CGACAATACT 0.754214 -20 TGATTATCTGGGGGAATTCACGGTATTACG 10 21 1 GGGGAATTCA 0.732451 -280 TCCAAATTGGCGGCTATTCTACTACTAAAC 11 120 0 CGGCTATTCT 0.828879 -181 ********** Masking position 6 Map Score: 3.51332 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 160 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 11 AGTGGTAGACAAGTTTAATAATTCGGATTG 2 388 1 AAGTTTAATA 0.641796 -213 GTAATTATAAGGTTAAATATCGGTAATT 4 9 1 AAGGTTAAAT 0.929424 -292 AATAAAAATAAATTTTAAAAATTAACAAAT 4 135 0 AATTTTAAAA 0.559317 -166 TGGTTAACTCAATGTTAAATTGATGTAACA 7 87 0 AATGTTAAAT 0.828716 -164 CAACAGGCGAAAGGTTAATCGACAGCACGA 9 68 0 AAGGTTAATC 0.714074 -217 TACTAAACATAAGGATAAAAAATAGTAAAA 11 98 0 AAGGATAAAA 0.778086 -203 ATTATTTTTAAAGGTTAAAAAAACACCAGT 11 164 0 AAGGTTAAAA 0.939937 -137 CCAATCAGCTAAGTTTAAATTGACTTATCT 11 199 0 AAGTTTAAAT 0.744053 -102 TGGAGAATGAAAGGATAATTTGTATGGGA 13 10 0 AAGGATAATT 0.604746 -270 TAATCCTGCTAATGTTAATATGGCATTAAA 13 68 1 AATGTTAATA 0.748867 -212 ATGGAANCAAAATGTTAAATTTTATGAGAT 13 171 1 AATGTTAAAT 0.828716 -109 ACCTCGTAAAAACGTTAAAAATATTGACCG 14 90 0 AACGTTAAAA 0.721452 -24 ********** Masking position 7 Map Score: 3.10265 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 114 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 12 TAAAAATTGTTAACAATTTTGTAAAATACC 1 83 1 TAACAATTTT 0.591216 -218 GTAATGTTTGTAACAACTTTGTTGAATGAT 2 253 0 TAACAACTTT 0.681883 -348 TATTAGTGGTAGACAAGTTTAATAATTCGG 2 384 1 AGACAAGTTT 0.802814 -217 TCCTTACAATAAACAGGTTTTTGTTGAAGC 3 90 0 AAACAGGTTT 0.832735 -211 GAGTTTTTATTAACATGTTTGCAACCTTTC 3 153 1 TAACATGTTT 0.615753 -148 GAAAGTGTTCAAACAAATTTCTATTGGGGC 3 219 1 AAACAAATTT 0.810937 -82 GCCCGTTTGCAAACAAGTGGTTCACAAACG 6 19 0 AAACAAGTGG 0.613504 -178 GGCTTCATAAAAACAAGTGTAAAAGGAATA 6 77 0 AAACAAGTGT 0.891438 -120 TACGCGAATAAAACAAGTTTCAAATTAAGT 10 47 1 AAACAAGTTT 0.880434 -254 TTAATACTTTTAACAAGTTTACGACTACAA 10 239 0 TAACAAGTTT 0.925697 -62 CTATTGTTAAAAACAGATTTCGTTGAGGTT 12 217 0 AAACAGATTT 0.649318 -32 ********** Masking position 5 Map Score: 2.31229 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 96 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 13 ********** No masking Map Score: 2.95829e-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 14 ********** No masking Map Score: 2.95829e-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: 2.95829e-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