AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icarP_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 carA 300 carbamoyl-phosphate synthetase, glutamine (small) subunit #2 yitV 120 similar to hypothetical proteins #3 yitW 63 similar to hypothetical proteins #4 yitX 54 yitX #5 yitY 57 similar to L-gulonolactone oxydase #6 yitZ 44 similar to multidrug resistance protein #7 argC 206 N-acetylglutamate gamma-semialdehyde dehydrogenase #8 carA 70 carbamoyl-phosphate transferase-arginine (subunit A) #9 ileS 300 isoleucyl-tRNA synthetase #10 ylyA 77 alternate gene name: ylmK; similar to hypothetical proteins from B. subtilis #11 lsp 102 signal peptidase II #12 pyrR 273 transcriptional attenuator and uracil phosphoribosyltransferase activity (minor) #13 pyrP 171 uracil permease #14 pyrB 145 aspartate carbamoyltransferase Motif number 1 ATTAAGCGACAAAAAGATCATCTAACCTGTTC 1 91 0 AAAAAGTCTC 0.905218 -210 AAAATAATATAAAAAATCCCGCCATTAAGTTG 1 147 1 AAAAAACCGC 0.993334 -154 AACAAAAAAGGACAGCCTGACATGTG 4 5 1 AAAAAGACGC 0.981409 -50 TTCAGCTGTAAAAAAGGACAGCCTCACATGTC 4 29 0 AAAAAGACGC 0.981409 -26 TCAGCCGCATAAAAAAACAGGCTGACCGCG 7 9 0 AAAAAACAGC 0.900702 -198 ATTCCGCTCAAAAAAAATCAGCACGACTCCAG 7 69 0 AAAAAATCGC 0.958258 -138 TCAGAAAATAAAAAAAGCCCTCTCATCCCATA 9 256 0 AAAAAACCTC 0.974766 -45 TGCAAAAGAGCCCGGCGTAAAAGCCG 10 5 1 AAAGAGCCGC 0.985798 -73 CTTGGCACAAAAAAAGCCCGGCTTTTACGCCG 10 23 0 AAAAAGCCGC 0.995836 -55 TTTTATCAATAAAAAGCACTGGAGTAAAGAAA 11 40 0 AAAAAGACGG 0.904616 -63 TTATTTCAGAAAAGAAACCCTCTGTCAACCGT 12 94 0 AAAGAACCTC 0.918119 -180 CATATAGAAGAAAAAACCCCTCCTGCCAGAGC 12 233 0 AAAAAACCTC 0.974766 -41 AAAGAGGCATACAAAGACCTGCCGAATACTTT 13 70 0 ACAAAGCCGC 0.972132 -102 TAAGGCTGAAAAAAAACCCCGGTCTAAGATAG 14 100 0 AAAAAACCGG 0.963991 -46 ****** ** ** Masking position 5 Map Score: 27.7626 Number of sites scoring better than the average of aligned sites = 632 Number in coding regions = 484 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 2 AACACCCTCCAGAGAATATTCA 1 289 0 CACCCTCCAG 0.795728 -12 AATGTGCCCCTCCTTAGGATAACCA 2 106 0 GCCCCTCCTT 0.947721 -15 AACAAGTTCACCCTCTTGGTCTTTGTGA 7 189 0 CACCCTCTTG 0.948956 -18 CTAACAGCCCACCTCTTGATGAATAATT 8 53 0 CCACCTCTTG 0.948955 -18 CGGACTCTCACCATCTCCGGGTCGCTATGA 9 74 0 CCATCTCCGG 0.834901 -227 TCAGAAAAGAAACCCTCTGTCAACCGTTTT 12 91 0 AACCCTCTGT 0.864443 -183 ATCCTTCTCAGCCTCTCTGGACTGTTTTAA 12 148 0 GCCTCTCTGG 0.959597 -126 TTGTCCTAAAACCCCTCTATGCTCTGGCAG 12 213 1 ACCCCTCTAT 0.870307 -61 AGAAGAAAAAACCCCTCCTGCCAGAGCATA 12 230 0 ACCCCTCCTG 0.967552 -44 CCTCTTTGCAACCTCTCTGGATTGCTTAAA 13 22 0 ACCTCTCTGG 0.948581 -150 CCTTTGTTGTGCACCTCTTTGCAACCTCTC 13 35 0 GCACCTCTTT 0.87635 -137 CTGTATAAAAAAACCTCTTTGCTTTTTTAC 13 104 0 AAACCTCTTT 0.587983 -68 ACCCTTCCAAGCCTCTCTGGACTTTCATTA 14 18 0 GCCTCTCTGG 0.959597 -128 GTTCTTTCCCCTCTCTTTTCAACTTAAG 14 128 0 CCCTCTCTTT 0.923033 -18 ********** Masking position 6 Map Score: 17.9326 Number of sites scoring better than the average of aligned sites = 553 Number in coding regions = 438 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 3 TTGGTCCACTTTTTTCTGCTCGTTTTTATTTC 1 27 1 TTTTTCTGCG 0.968272 -274 CCTCACTCCTTTTTTCTACAGTATAACGTAAA 3 38 0 TTTTTCTACT 0.849264 -26 CTCCCTGCTGTTTTTATGACCA 5 1 0 TTTTTATGAA 0.735645 -57 AAGCAATTTCTTTTTCATAGTGCTCTCCCTGC 5 25 0 TTTTTCATAG 0.470253 -33 TCAGCCTGTTTTTTTATGCGGCTGAAATGCGG 7 16 1 TTTTTATGCC 0.766644 -191 CGCATCAACGTTTTTGTGCTGGAGTCGTGCTG 7 51 1 TTTTTGTGCG 0.926191 -156 GTGCTGATTTTTTTTGAGCGGAATTCCCATTG 7 77 1 TTTTTGAGCA 0.800199 -130 ATATTTAATATTTTTATTCATTTATAAATTTT 7 114 0 TTTTTATTCT 0.822032 -93 ATTGAATTAATTTTTATTCATGTTATAATGTT 7 149 1 TTTTTATTCG 0.833629 -58 TAAAAATGAATTTTTATGCCTTTATATCGAAA 8 16 0 TTTTTATGCT 0.94031 -55 TAAAAATTCATTTTTATAATTAATTATTCATC 8 32 1 TTTTTATAAA 0.357837 -39 TTTCAACCGTTTTTTCATCTGAATTTATGAAC 9 16 0 TTTTTCATCA 0.740654 -285 AAGCATACACTTTTTCCTCTTGAGCATCGTAA 9 178 0 TTTTTCCTCG 0.690813 -123 GTATGCTTGCTTTTTCTAAAAGGGTGGTACCG 9 202 1 TTTTTCTAAG 0.578377 -99 TCCACTGCATTTTTTCAGAAAATAAAAAAAGC 9 270 0 TTTTTCAGAA 0.686626 -31 AGCCGGGCTTTTTTTGTGCCAAGAGTGACATC 10 32 1 TTTTTGTGCA 0.900819 -46 TGTCAACCGTTTTTTCTGAGGTTTTCGATTAA 12 72 0 TTTTTCTGAT 0.863559 -202 CAGGAGGGGTTTTTTCTTCTATATGAACTGTG 12 240 1 TTTTTCTTCT 0.891875 -34 TAGATCACCTTTTTAAGCAATCCAGAGAGGT 13 10 1 TTTTTAAGCT 0.874157 -162 TGCCGAATACTTTTTGGGCCTTTGTTGTGCAC 13 51 0 TTTTTGGGCT 0.610817 -121 CCTCTTTGCTTTTTTACGCAAAGAGGCATACA 13 89 0 TTTTTACGCA 0.755358 -83 CAAAGAGGTTTTTTTATACAGTCATTGAGTCA 13 113 1 TTTTTATACT 0.759323 -59 ACCGGGGTTTTTTTTCAGCCTTAAGTTGAAAA 14 109 1 TTTTTCAGCT 0.9254 -37 ********* * Masking position 5 Map Score: 20.5279 Number of sites scoring better than the average of aligned sites = 1611 Number in coding regions = 1319 Number in noncoding regions = 292 Number of orfs with sites within 600 bp upstream = 324 Fraction of orfs with sites within 600 bp upstream = 0.0520398 Motif number 4 ACAGCCTCACATGTCAGGCTGTCCTTTTTTGTT 4 11 0 ATCAGGCGTC 0.851018 -44 CTTTGTGATAATGTCAGCCATTTTAATTTGTTT 6 18 0 ATCAGCCTTT 0.983665 -27 CGCGGTCAGCCTGTTTTTTTATGCG 7 3 1 CTCAGCCGTT 0.964948 -204 GCGGTGCCGCATTTCAGCCGCATAAAAAAACAG 7 21 0 ATCAGCCCAT 0.93844 -186 AACAAGTTCACCCTCTTGGTCTTTGTG 7 190 0 ATCACCCCTT 0.847378 -17 ATGACTGTCCCTTTCAACCGTTTTTTCATCTGA 9 26 0 CTCAACCTTT 0.896656 -275 AGTCATGTTTCCTTCAGGCCTTCATAGCGACCC 9 53 1 CTCAGGCTTC 0.91617 -248 GGAATCATGTAGATCAGCCCTTTAGTTTCCTTG 9 112 1 ATCAGCCTTT 0.983666 -189 GAGTAAAGAAATATCAGGCATATTAACCGGACA 11 18 0 ATCAGGCTAT 0.881402 -85 GTTTTCGATTAATTCTGCCATATCCTCGGGAAG 12 51 0 ATCTGCCTAT 0.712635 -223 AAGAAACCCTCTGTCAACCGTTTTTTCTGAGGT 12 82 0 CTCAACCTTT 0.896656 -192 TCCGTTATCCTTCTCAGCCTCTCTGGACTGTTT 12 151 0 TTCAGCCCTC 0.811166 -123 * ****** *** Masking position 4 Map Score: 8.60272 Number of sites scoring better than the average of aligned sites = 779 Number in coding regions = 722 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 5 CCTGTTCTGGAAAACGCTTGCGCAGCAAGA 1 68 0 AAAACGCTTG 0.927334 -233 GAATTTCTGGCAAACGGCGGCATTCTGGAG 1 196 0 CAAACGGCGG 0.944681 -105 AAAACAAATTAAAATGGCTGACATTATCAC 6 17 1 AAAATGGCTG 0.91261 -28 CCGCATAAAAAAACAGGCTGACCGCG 7 7 0 AAACAGGCTG 0.68531 -200 TTCAGATGAAAAAACGGTTGAAAGGGACAG 9 25 1 AAAACGGTTG 0.965784 -276 GCAAGGAAACTAAAGGGCTGATCTACATGA 9 116 0 TAAAGGGCTG 0.867381 -185 TGCTTTTTCTAAAAGGGTGGTACCGCGAGA 9 209 1 AAAAGGGTGG 0.950449 -92 TTGGCACAAAAAAAGCCCGGCTTTTACGCC 10 24 0 AAAAGCCCGG 0.842095 -54 AACCTCAGAAAAAACGGTTGACAGAGGGTT 12 81 1 AAAACGGTTG 0.965784 -193 AGGCTGAAAAAAAACCCCGGTCTAAGATAG 14 100 0 AAAACCCCGG 0.896656 -46 ********** Masking position 3 Map Score: 6.27049 Number of sites scoring better than the average of aligned sites = 1215 Number in coding regions = 1095 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 6 CTGCTCGTTTTTATTTCATGCAATCTTCTTGCTG 1 42 1 TTATTATCAT 0.800865 -259 AATATTTTTATTCATTTATAAATTTTCTGTTCAA 7 106 0 TTCTTATAAT 0.954205 -101 AATACGTTCATAAATTCAGATGAAAA 9 3 1 TACTTATAAT 0.881065 -298 GCCCTTTAGTTTCCTTGCTGAACTCACAGTAGGT 9 128 1 TTCTTCTAAT 0.960218 -173 TTTCATTCCTCCACTGCATTTTTTC 9 286 0 TTCTTCTCAT 0.981592 -15 TGCCTGATATTTCTTTACTCCAGTGCTTTTTATT 11 31 1 TTCTTCTCAT 0.981592 -72 TCCAGTGCTTTTTATTGATAAAATGCATAATGGA 11 49 1 TTTTTATAAT 0.762471 -54 AGTTTACGGTTACTTTAATCCATTATGCATTTTA 11 67 0 TACTTATCAT 0.942416 -36 AAACGTTCCTCCAGTTTACGGTTAC 11 88 0 AACTTCTCAT 0.687097 -15 GACAGAGGGTTTCTTTTCTGAAATAATAAACGAA 12 100 1 TTCTTCTAAT 0.960218 -174 GCTGAATAGATTCTTTAAAACAGTCCAGAGAGGC 12 134 1 TTCTTAACAT 0.842067 -140 AGCAAAGAGGTTTTTTTATACAGTCATTGAGTCA 13 111 1 TTTTTATCAT 0.876416 -61 *** ** ** ** * Masking position 12 Map Score: 10.8064 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 104 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 7 GCATGAAATAAAAACGAGCAGAAAAAAGTG 1 33 0 AAAACGAGCA 0.914227 -268 TAATGCCTGTAAAACATGCATGAGCCACAA 1 119 1 AAAACATGCA 0.926907 -182 TAAGTAAGGCAAAACAAGCAAAATCTAAGG 2 26 0 AAAACAAGCA 0.982639 -95 TGGTCATAAAAACAGCAGGGAGAGCAC 5 8 1 AAAAACAGCA 0.92456 -50 AGCGCGAATGCAAGCAATTTCTTTTT 5 42 0 AATGCAAGCA 0.655514 -16 GCCGCATAAAAAAACAGGCTGACCGCG 7 8 0 AAAACAGGCT 0.575247 -199 CCGCTCAAAAAAAATCAGCACGACTCCAGC 7 68 0 AAAATCAGCA 0.71786 -139 CCTTTTAGAAAAAGCAAGCATACACTTTTT 9 195 0 AAAGCAAGCA 0.947037 -106 TTCAGAAAATAAAAAAAGCCCTCTCATCCC 9 259 0 AAAAAAAGCC 0.92456 -42 TTATTTTCTGAAAAAATGCAGTGGAGGAAT 9 277 1 AAAAAATGCA 0.887931 -24 CTCTTGGCACAAAAAAAGCCCGGCTTTTAC 10 27 0 AAAAAAAGCC 0.92456 -51 CATTTTATCAATAAAAAGCACTGGAGTAAA 11 44 0 ATAAAAAGCA 0.790055 -59 CCTCTTTGCGTAAAAAAGCAAAGAGGTTTT 13 95 1 TAAAAAAGCA 0.790055 -77 ********** Masking position 9 Map Score: 12.102 Number of sites scoring better than the average of aligned sites = 359 Number in coding regions = 267 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 8 GTTCCCTCACTCCTTTTTTCTAC 3 51 0 TTCCTCCTCC 0.99068 -13 AACATGACTGTCCCTTTCAACCGTTTTTTCAT 9 30 0 TCCCTTAACC 0.740148 -271 ACAGTCATGTTTCCTTCAGGCCTTCATAGCGA 9 51 1 TTCCTCGGCC 0.92847 -250 ATCTACATGATTCCGGCCATCCCGGACTCTCA 9 94 0 TTCCGCATCC 0.933223 -207 TTTCATTCCTCCACTGCATTTT 9 289 0 TTTCTTCTCC 0.929202 -12 AAGATTTTTCCTTTCGTTCTAAAGGATGT 10 59 0 TTCCTTGTTC 0.857598 -19 ATGCCTGATATTTCTTTACTCCAGTGCTTTTT 11 30 1 TTTCTTCTCC 0.929202 -73 CAGTTTACGGTTACTTTAATCCATTATGCATT 11 70 0 TTACTTATCC 0.824331 -33 TATACACGCATCCCGTCTATCCGTTATCCTTC 12 171 0 TCCCTCATCC 0.966459 -103 GCATTGAAGCTTCCTTCTCTTCATAACCCTTC 14 41 0 TTCCTCCTTC 0.948386 -105 **** ** **** Masking position 1 Map Score: 4.00296 Number of sites scoring better than the average of aligned sites = 427 Number in coding regions = 384 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 9 AACAAAAAAGGACAGCCTGACATGTGAGG 4 10 1 GGACAGCCTG 0.992454 -45 CTGTAAAAAAGGACAGCCTCACATGTCAGG 4 26 0 GGACAGCCTC 0.990112 -29 CGCGGTCAGCCTGTTTTTTTATG 7 4 1 GGTCAGCCTG 0.96467 -203 TGAGAGTCCGGGATGGCCGGAATCATGTAG 9 94 1 GGATGGCCGG 0.942009 -207 CATATTAACCGGACAGACACTG 11 3 0 GGACAGACAC 0.93645 -100 GAAGGATAACGGATAGACGGGATGCGTGTA 12 171 1 GGATAGACGG 0.962351 -103 CCCCGGTCTAAGATAGACTCGGGGTATGGT 14 86 0 AGATAGACTC 0.752766 -60 ********** Masking position 6 Map Score: 4.32061 Number of sites scoring better than the average of aligned sites = 286 Number in coding regions = 274 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 ********** No masking Map Score: 3.13593e-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: 3.13593e-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: 3.13593e-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