AlignACE version 2.2 July 7, 1998 alignACE -z/skink1/amcguire/genomes/ecoli.fna -a/home/amcguire/alignace/lib/ORF_ecoli.txt -b/home/amcguire/alignace/lib/bimes_ecoli.txt -k0 -l300 -jargR.reg -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 = 156 Input sequences: #1 carA 300 bp carA 382 1-1149 CDS #2 argF 300 bp argF 334 1-1005 CDS #3 argA 141 bp argA 443 1-1332 CDS #4 argG 300 bp argG 447 1-1344 CDS #5 argR 300 bp argR 156 1-471 CDS #6 argD 85 bp argD 406 1-1221 CDS #7 argE_argC 153 bp argE 383 1-1152 CDS argC 334 1-1005 CDS #8 argI 161 bp argI 334 1-1005 CDS Motif number 1 TCACTTTATTTGCATATTAATTCACAATGATGAC 1 254 0 TGATTTATCA 0.665732 -47 CACCCTCCAGAGAATATTCACTCACTTTATTTGC 1 275 0 AGATTTACCA 0.81229 -26 GGGTTGCAAATGAATAATTACACATATAAAGTGA 2 237 1 TGATATACCA 0.615221 -64 ACATATAAAGTGAATTTTAATTCAATAAGTGGCG 2 258 1 TGATTTATCA 0.665732 -43 TCGAAATTAGTGTATTTTTATTCTGTTTTTTCGC 3 95 0 TGATTTATCT 0.897501 -47 CACACCTCTTTGCATGATTATTCGAAATTAGTGT 3 116 0 TGATATATCG 0.59752 -26 GAAAGTGAACTGGATATTCATTCACATGATTAGC 4 94 0 TGATTTATCA 0.665732 -207 CCGCTCTCACTGAATTTTTATGCAAAATAAATGA 4 234 0 TGATTTATCA 0.665732 -67 TGCATACAGATGAATTTTTATGCAAACAGTCAGC 5 241 0 TGATTTATCA 0.665732 -60 TCACCCGATATGGTGGTTGATACAACATTATTGT 5 274 0 TGTGTTATCA 0.808871 -27 TGCCATTTAGTGATTTTTTATGCATATTTTGTGG 6 19 1 TGTTTTATCA 0.947854 -67 AAATACTGCATGAATATTGATACTATCATGACCA 7 25 0 TGATTTATCT 0.897501 -129 TCAACGTTAGTGTATTTTTATTCATAAATACTGC 7 50 0 TGATTTATCA 0.665732 -104 TCAATTTATATGGATGATTATTCATTTGCAAGTC 8 100 0 TGATATATCA 0.499795 -62 CCATATAAATTGAATTTTAATTCATTGAGGCGTT 8 121 1 TGATTTATCA 0.665732 -41 ** ** ** ** ** Masking position 10 Map Score: 38.5155 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 6 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 2 TCAACTTAATGGCGGGATTTTTTATATTATT 1 149 0 GGCGGATTTT 0.686637 -152 CCGCCATTAAGTTGACTTTTAGCGCCCATAT 1 165 1 GTTGATTTTA 0.646691 -136 ACACATATAAAGTGAATTTTAATTCAATAAG 2 256 1 AGTGATTTTA 0.932662 -45 TTTATGCGAGAGCGACTTTTTTATCAGTAAT 3 47 0 AGCGATTTTT 0.942831 -95 ATTCGAAATTAGTGTATTTTTATTCTGTTTT 3 100 0 AGTGTTTTTT 0.930666 -42 GGAAGAGTTTAGTGTGTTTTTTGTAAAATAA 4 172 0 AGTGTTTTTT 0.930666 -129 TTCCGCTCTCACTGAATTTTTATGCAAAATA 4 239 0 ACTGATTTTT 0.852258 -62 AATTAAGCAGGGTGTTATTTT 4 290 1 GGTGTATTTT 0.779384 -11 CTAATGCATAAGCGACTGTTAATTACGTAAG 5 32 0 AGCGATGTTA 0.721248 -269 GTTATGAAAGAGCGGGATTTTATCAAATTTC 5 189 0 AGCGGATTTT 0.658208 -112 CTTCTTCAGGGCTGACTGTTTGCATAAAAAT 5 231 1 GCTGATGTTT 0.704779 -70 TGTGCATACAGATGAATTTTTATGCAAACAG 5 246 0 GATGATTTTT 0.706434 -55 ATTGCCATTTAGTGATTTTTTATGCATATTT 6 17 1 AGTGATTTTT 0.969797 -69 GCTCAACGTTAGTGTATTTTTATTCATAAAT 7 55 0 AGTGTTTTTT 0.930666 -99 CCTTACGGCTGGTGGGTTTTATTACGCTCAA 7 80 0 GGTGGTTTTA 0.88834 -74 CCAGCCGTAAGGTGAATGTTTTACGTTTAAC 7 99 1 GGTGATGTTT 0.930012 -55 ATCCATATAAATTGAATTTTAATTCATTGAG 8 119 1 ATTGATTTTA 0.616662 -43 ***** ***** Masking position 9 Map Score: 15.6662 Number of sites scoring better than the average of aligned sites = 938 Number in coding regions = 724 Number in noncoding regions = 214 Number of orfs with sites within 600 bp upstream = 220 Fraction of orfs with sites within 600 bp upstream = 0.0353357 Motif number 3 AAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGT 1 14 1 CATTTCCTTT 0.992823 -287 GTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCG 1 48 1 CATGTCCTGC 0.928733 -253 AAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATA 1 159 1 CATTTTCTTT 0.931329 -142 CAAGCCTCGCCATGTTCTCCGCCATTTTAGAAGCAT 2 34 1 CATGTCCATT 0.914235 -267 ATCCACGCCACATTTTGTCAACGTTTATTGCTAATC 4 65 1 CATTTCCTTT 0.992823 -236 AATGAGTTTTCATTTAATCATCTTTTATCGGAGACA 4 203 0 CATTTCCTTT 0.992823 -98 GTCGCTTATGCATTAGCGCAACATTCCAACAGGTGG 5 47 1 CATTGCCTTC 0.963844 -254 TCTTTCATAACATTATTTCAGCCTTCTTCAGGGCTG 5 209 1 CATTTCCTTC 0.991312 -92 ACACCACTGACATTGCCTCCACCTTTGTGACAAAGA 8 53 1 CATTTCCTTT 0.992821 -109 **** ** * *** Masking position 3 Map Score: 12.0595 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 34 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 4 CATGCATGTTTTACAGGCATTAAGCGACAAAAAGATCATCTA 1 99 0 TCCTGGAAAA 0.967128 -202 GGTGGAGGCAAACCCGTCCGTGTGTGAAAATAATCGTATCTG 2 171 0 ACCTGGAAAA 0.984843 -130 ATTCAATAAGTGGCGTTCGCCATGCGAGGATAAA 2 277 1 TCCCGGAGAA 0.975963 -24 CATAAAATTTACACTTGCACCCTGCGAAAAAACAGAATAAAA 3 72 1 ACCCGGAAAA 0.992227 -70 AACACACTAAACTCTTCCTGTCTCCGATAAAAGATGATTAAA 4 185 1 ACCTCGAAAA 0.89377 -116 TTAGCGCAACATTCCAACAGGTGGTGACAATATACCCTACCG 5 59 1 ACCGGGAAAA 0.966965 -242 GTGACAATATACCCTACCGTTCAGCCAAAACAACATCAATTT 5 82 1 ACCTGCAAAA 0.977769 -219 ATTGAGAAACATGCCTGCGTCACGGCATGCAAATTCTGCTTA 5 144 0 ACCCGCAGCA 0.917267 -157 TGTTGACACACCTCTGGTCATGATAGTATCAATAT 7 4 1 TCCCGCAGAA 0.965348 -150 TTTTACGTTTAACCTGGCAACCAGACATAAGAAGGTGAATAG 7 117 1 ACCCGCAAAA 0.98856 -37 * * * * * ** ** * Masking position 17 Map Score: 8.42444 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 139 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 5 GACCATTTGGTCCACTTTTTTCTGCTCGTTT 1 21 1 TCCACTTTTT 0.935933 -280 TGCATATTAATTCACAATGATGACGTAAATC 1 247 0 TTCACAATGT 0.751596 -54 CGCCATGTTCTCCGCCATTTTAGAAGCATAA 2 41 1 TCCGCCATTT 0.820592 -260 AGGCCAATCATTCTCATTTCTGACTCGACCT 2 90 1 TTCTCATTTT 0.798631 -211 CGGGTTTGCCTCCACCTTTGTAAGAAAGAAT 2 197 1 TCCACCTTTT 0.977393 -104 GCAACCCCATTTCACAATTCTTTCTTACAAA 2 213 0 TTCACAATTT 0.919302 -88 GAATATCCAGTTCACTTTCATTTGTTGAATA 4 109 1 TTCACTTTCT 0.868265 -192 TGGTTATAATTTCACATTTGTTTATGCGTAA 6 50 1 TTCACATTTT 0.961771 -36 CGGGGCTATTCACCTTCTTATGTCTGGTT 7 135 0 TTCACCTTCT 0.951233 -19 TGACATTGCCTCCACCTTTGTGACAAAGATT 8 60 1 TCCACCTTTT 0.977393 -102 ********* * Masking position 8 Map Score: 7.60107 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 180 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 6 TCTGGAAAACGCTTGCGCAGCAAGAAGATTG 1 62 0 GCTGCGCAGC 0.928036 -239 TGTAAAACATGCATGAGCCACAAAATAATAT 1 126 1 GCTGAGCCAC 0.975964 -175 AAGTAAGGCAGCAAGCCTCGCCATGTTCTCC 2 23 1 GCAGCCTCGC 0.854477 -278 AAAGGTGGAGGCAAACCCGTCCGTGTGTGAA 2 185 0 GCAACCCGTC 0.863525 -116 TCCTCGCATGGCGAACGCCACTTATTGAATT 2 276 0 GCAACGCCAC 0.987291 -25 TAAATTTTATGCGAGAGCGACTTTTTTATCA 3 52 0 GCAGAGCGAC 0.968494 -90 TTGCGCTAATGCATAAGCGACTGTTAATTAC 5 37 0 GCTAAGCGAC 0.927023 -264 TGAGAAACATGCCTGCGTCACGGCATGCAAA 5 153 0 GCTGCGTCAC 0.960613 -148 CCCTCCTGTGGCTAACGCCTCAATGAATTAA 8 137 0 GCAACGCCTC 0.971262 -25 ** ******** Masking position 2 Map Score: 6.47791 Number of sites scoring better than the average of aligned sites = 2150 Number in coding regions = 2085 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 7 TGGGCGCTAAAAGTCAACTTAATGGCGGGAT 1 162 0 AAGTCACTTA 0.891191 -139 AAATCAATGCAAATCTGCTTACCGACGAATT 1 221 0 AAATCTCTTA 0.775004 -80 AGAGAATATTCACTCACTTTATTTGCATATT 1 270 0 CACTCATTTA 0.842941 -31 ATTGAATTAAAATTCACTTTATATGTGTAAT 2 253 0 AATTCATTTA 0.931263 -48 AAACGGTAAACATTCTTTTTATATTCACGGC 3 16 1 CATTCTTTTA 0.915774 -126 ACGGCATGCAAATTCTGCTTAAAAGTAAATT 5 134 0 AATTCTCTTA 0.943157 -167 AAACGTAAAACATTCACCTTACGGCTGGTGG 7 96 0 CATTCACTTA 0.971647 -58 GGCTCATTCCTCTTAATGTCCTGCC 8 5 1 CATTCCCTTA 0.926093 -157 AATGAATTAAAATTCAATTTATATGGATGAT 8 116 0 AATTCATTTA 0.931263 -46 ****** **** Masking position 4 Map Score: 5.55791 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 64 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 8 ACGTCATCATTGTGAATTAATATGCAAATA 1 252 1 TGTGAATTAA 0.699384 -49 TGAATTAATATGCAAATAAAGTGAGTGAAT 1 264 1 TGCAAATAAA 0.937469 -37 GAAATGGGGTTGCAAATGAATAATTACACA 2 231 1 TGCAAATGAA 0.947608 -70 ACTTGCACCCTGCGAAAAAACAGAATAAAA 3 84 1 TGCGAAAAAA 0.91777 -58 TTGCTAATCATGTGAATGAATATCCAGTTC 4 92 1 TGTGAATGAA 0.737495 -209 GTGTGTTTTTTGTAAAATAATGCGCTTAAG 4 162 0 TGTAAAATAA 0.815297 -139 TGAATTTTTATGCAAAATAAATGAGTTTTC 4 228 0 TGCAAAATAA 0.946865 -73 GCTGACTGTTTGCATAAAAATTCATCTGTA 5 241 1 TGCATAAAAA 0.832015 -60 TTCATCTGTATGCACAATAATGTTGTATCA 5 261 1 TGCACAATAA 0.806333 -40 CCACAAAATATGCATAAAAAATCACTAAAT 6 23 0 TGCATAAAAA 0.832015 -63 GCTTTAGACTTGCAAATGAATAATCATCCA 8 94 1 TGCAAATGAA 0.947608 -68 ********** Masking position 6 Map Score: 10.8204 Number of sites scoring better than the average of aligned sites = 288 Number in coding regions = 222 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 9 CTCGCATGGCGAACGCCACTTATTGAATTA 2 275 0 GAACGCCACT 0.958632 -26 GGCACACCTCTTTGCATGATT 3 131 0 GCACACCTCT 0.977585 -11 TTATAGTGATCCACGCCACATTTTGTCAAC 4 57 1 CCACGCCACA 0.952319 -244 TGTTGACACACCTCTGGTCATGATA 7 6 1 ACACACCTCT 0.965747 -148 TCTTATTGTCACACACCACTGACATTGCCT 8 41 1 ACACACCACT 0.965749 -121 CTCCTGTGGCTAACGCCTCAATGAATTAAA 8 136 0 TAACGCCTCA 0.819917 -26 ********** Masking position 3 Map Score: 1.55705 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 188 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 10 AGTCAACTTAATGGCGGGATTTTTTATATT 1 152 0 ATGGCGGGAT 0.786173 -149 CGGCGGCATTCTGGAGATATGGGCGCTAAA 1 182 0 CTGGAGATAT 0.73575 -119 TGAATATTCTCTGGAGGGTGTT 1 289 1 CTGGAGGGTG 0.913946 -12 CTTTCTGCTTCTGCAGAGAATCGGAGGCAG 2 144 1 CTGCAGAGAA 0.833215 -157 TCTTACAAAGGTGGAGGCAAACCCGTCCGT 2 192 0 GTGGAGGCAA 0.910904 -109 CTGCTGGGATTTGGTGTACC 4 1 1 CTGCTGGGAT 0.945594 -300 GACGTAAAATCTGCAGGCATTATAGTGATC 4 38 1 CTGCAGGCAT 0.961355 -263 CACCTTACGGCTGGTGGGTTTTATTACGCT 7 83 0 CTGGTGGGTT 0.91602 -71 TGTCACAAAGGTGGAGGCAATGTCAGTGGT 8 55 0 GTGGAGGCAA 0.910904 -107 GCGTTAGCCACAGGAGGGATCT 8 150 1 CAGGAGGGAT 0.945864 -12 ********** Masking position 6 Map Score: 3.24447 Number of sites scoring better than the average of aligned sites = 1110 Number in coding regions = 1015 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 11 ATCTTTTTGTCGCTTAATGCCTGTAAAACAT 1 105 1 CGCTTATGCC 0.976809 -196 GAGATATGGGCGCTAAAAGTCAACTTAATGG 1 168 0 CGCTAAAGTC 0.896433 -133 ACACACTAAACTCTTCCTGTCTCCGATAAAA 4 186 1 CTCTTCTGTC 0.975087 -115 GGCTCATTCCTCTTAATGTCCTGCCGATAC 8 10 1 CTCTTATGTC 0.98862 -152 CCTGCCGATACTCTTATTGTCACACACCACT 8 30 1 CTCTTATGTC 0.988621 -132 ****** **** Masking position 4 Map Score: 1.2986 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 7 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 12 AGTGAATTTTAATTCAATAAGTGGCGTTCG 2 266 1 AATTCAATAA 0.829335 -35 ACAGAATAAAAATACACTAATTTCGAATAA 3 103 1 AATACACTAA 0.973217 -39 TTTTACAAAAAACACACTAAACTCTTCCTG 4 175 1 AACACACTAA 0.955186 -126 TATGCATAAAAAATCACTAAATGGCAATCA 6 15 0 AAATCACTAA 0.909391 -71 TATGAATAAAAATACACTAACGTTGAGCGT 7 58 1 AATACACTAA 0.973217 -96 ********** Masking position 6 Map Score: 2.02577 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 11 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 13 GTCCACTTTTTTCTGCTCGTTTTTATTTCA 1 30 1 TTCTGCTCGT 0.938623 -271 TTTTGCCTTCTCCTGCTCTCCCTTAAGCGC 4 141 1 TCCTGCTCTC 0.984222 -160 GAGCCTGGATTTCCGCTCTCACTGAATTTT 4 250 0 TTCCGCTCTC 0.984222 -51 TTTGATAAAATCCCGCTCTTTCATAACATT 5 193 1 TCCCGCTCTT 0.984222 -108 ********** Masking position 7 Map Score: 0.33909 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 32 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 14 GATTTTAAGGATTATGCTTCTAAAATGGCGG 2 52 0 ATTTGCTTCT 0.930459 -249 AATGAGAATGATTGGCCTTCTTTATGATTTT 2 77 0 ATTGCCTTCT 0.982953 -224 ATCCAATGTCTTTCTGCTTCTGCAGAGAATC 2 135 1 TTTTGCTTCT 0.930466 -166 TGTTGAATACTTTTGCCTTCTCCTGCTCTCC 4 131 1 TTTGCCTTCT 0.982959 -170 ATAACATTATTTCAGCCTTCTTCAGGGCTGA 5 215 1 TTCGCCTTCT 0.954729 -86 CGGGGCTATTCACCTTCTTATGTCTGGT 7 136 0 ATTACCTTCT 0.935562 -18 *** ******* Masking position 8 Map Score: 2.55896 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 82 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 15 CTAACCTGTTCTGGAAAACGCTTGCGCAGC 1 72 0 CTGGAAAACG 0.968884 -229 CGCTTAATGCCTGTAAAACATGCATGAGCC 1 115 1 CTGTAAAACA 0.661649 -186 CGACGAATTTCTGGCAAACGGCGGCATTCT 1 200 0 CTGGCAAACG 0.991315 -101 TTATCCTCGCATGGCGAACGCCACTTATTG 2 280 0 ATGGCGAACG 0.933786 -21 AAATCACTAAATGGCAATCAGAAA 6 5 0 ATGGCAATCA 0.821651 -81 TACGTTTAACCTGGCAACCAGACATAAGAA 7 120 1 CTGGCAACCA 0.952847 -34 GATCCCTCCTGTGGCTAACGCCTCAATGAA 8 141 0 GTGGCTAACG 0.888858 -21 ********** Masking position 7 Map Score: 1.60819 Number of sites scoring better than the average of aligned sites = 1332 Number in coding regions = 1273 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401