AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i087_PTS_sugar_Utilization_ecoli_reg_100.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -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 fruB 300 PTS system, fructose-specific IIA/fpr component #2 ptsH 300 PTS system protein HPr #3 ptsI 44 PEP-protein phosphotransferase system enzyme I #4 crr 40 PTS system, glucose-specific IIA component #5 mtlA 300 PTS system, mannitol-specific enzyme IIABC components #6 BIME180 41 BIME #7 mtlD 88 mannitol-1-phosphate dehydrogenase Motif number 1 TGCTGACGCTGCTGAAATGAAATTGCTGAT 1 64 1 GCTGAAATGA 0.974713 -237 TTCCTTGCGTGCTGAAACAGAAGTATTATG 1 175 1 GCTGAAACAG 0.940798 -126 ACAAGATCGCGCTGAAACGTTTCAAGAAAG 1 205 0 GCTGAAACGT 0.988393 -96 TCTCATAGAGGCTGAATCGTTTCAATTCAG 1 266 1 GCTGAATCGT 0.992043 -35 CTCCTCTCTTGCTGAATTGAAACGATTCAG 1 277 0 GCTGAATTGA 0.982588 -24 GTTCCGACAGGCTGAATCAA 2 1 0 GCTGAATCAA 0.97189 -300 TTTGGCTTTTCCTGTAACGATTAATTTCGC 2 62 0 CCTGTAACGA 0.920424 -239 AAAAGCCAAAGCTGAATCGATTTTATGATT 2 82 1 GCTGAATCGA 0.995025 -219 TCGACTTTAGCCTGTATTGTTAGCGCCAGT 2 225 0 CCTGTATTGT 0.748643 -76 GAAATCTGGCACTGAATCGGTTAACTGTCC 5 184 0 ACTGAATCGG 0.937613 -117 ********** Masking position 6 Map Score: 17.21 Number of sites scoring better than the average of aligned sites = 467 Number in coding regions = 410 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 2 AAATCAAAAGCGCCACGAATAGTCAAA 1 6 1 AAACGCCACG 0.969726 -295 ATTTCATTTCAGCAGCGTCAGCAGCCAATCAG 1 55 0 ACACGTCAGC 0.939721 -246 CTATGAGAAAAAAAGCGCCAACCTGGCTTAGG 1 242 0 AAACGCCAAC 0.884221 -59 TAATGACGTACGAAACGTCAGCGGTCAACACC 2 144 1 CAACGTCAGC 0.973632 -157 TCAGCGGTCAACACCCGCCAGCAATGGACTGT 2 161 1 AACCGCCAGC 0.934766 -140 AGGCTAAAGTCGAACCGCCAGGCTAGACTTTA 2 242 1 CAACGCCAGG 0.948606 -59 ATTTTTAGCGAAAATCGCCGCCTTGTTGCTTT 5 61 1 AAACGCCGCC 0.967636 -240 GCGTTTTGTGATGAACGTCACGTCAATTACCT 5 102 1 AGACGTCACG 0.910037 -199 CACATTAACAAAAAACCTCGGGCTTCCAGCCT 5 247 1 AAACCTCGGG 0.828911 -54 TCCAATCCCACCCTCTCCACATGGAGAA 6 7 1 CCACCTCTCC 0.857401 -35 AATTAACCCCACCTTCTCCATGT 6 29 0 ATACCCCACC 0.892296 -13 CTGCCCCTCTCCTCACGGAGAG 7 1 1 CGCCCTCTCC 0.635736 -88 TTCCCTCACCCAAACCCTCTCCGTGAGGAGAG 7 17 0 CAACCTCTCC 0.939998 -72 TGGGTGAGGGAAAAGCCTCACCCCAGCCCTCT 7 37 1 AAACCTCACC 0.979776 -52 * ** ******* Masking position 6 Map Score: 13.5677 Number of sites scoring better than the average of aligned sites = 3140 Number in coding regions = 2932 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 172 Fraction of orfs with sites within 600 bp upstream = 0.0276261 Motif number 3 AAATGCCATTTCACTGTTGCTGATTGGCTGCTG 1 36 1 TCGTTGCTGA 0.967709 -265 TTGCCATTTTTCCTAATTGCTGATGGGAAAATC 1 98 0 TCATTGCTGA 0.951384 -203 TTACGGCTTTCCTTGCGTGCTGAAACAGAAGTA 1 167 1 CCCGTGCTGA 0.987145 -134 AAAAAAAGCGCCAACCTGGCTTAGGGTTAAAGA 1 234 0 CCCTGGCTTA 0.926448 -67 GCTTTTTTTCTCATAGAGGCTGAATCGTTTCAA 1 258 1 TCGAGGCTGA 0.976509 -43 AGTTCTCCTCTCTTGCTGAATTGAAACGA 1 282 0 CCCTTGCTGA 0.989131 -19 AAATACCAGTTCCGACAGGCTGAATCAA 2 6 0 TCCAGGCTGA 0.91013 -295 ATGTTTGCTGTCGCGCAGGCTGGAAGCCCGAGG 5 262 0 TCCAGGCTGG 0.978998 -39 ATGTTTTTACCCGAGAGGGCTGGGGTGAGGCTT 7 49 0 CCAGGGCTGG 0.952671 -40 ** ******** Masking position 11 Map Score: 10.8726 Number of sites scoring better than the average of aligned sites = 861 Number in coding regions = 817 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 4 TCAGCAACAGTGAAATGGCATTTTGACTAT 1 29 0 TGAAATGGCA 0.872482 -272 AGCAATTAGGAAAAATGGCAAAAAATTGTG 1 110 1 AAAAATGGCA 0.980814 -191 GCGTCTGTTAAAAACTGGCGCTAACAATAC 2 212 1 AAAACTGGCG 0.973777 -89 ATCAAAACAAAAATGTGACACTACTCACAT 5 22 1 AAATGTGACA 0.846089 -279 GATTTTCGCTAAAAATGGCATTTAAATGTG 5 47 0 AAAAATGGCA 0.980814 -254 AGATACTGCGAAATCTGGCACTGAATCGGT 5 193 0 AAATCTGGCA 0.976949 -108 GGTTTTTTGTTAATGTGGCGGCAGAGGTAG 5 234 0 TAATGTGGCG 0.925409 -67 ********** Masking position 3 Map Score: 5.09721 Number of sites scoring better than the average of aligned sites = 520 Number in coding regions = 446 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 5 TGCTGATAACGGATTTTCCCATCAGCAATT 1 87 1 GGATTTTCCC 0.978783 -214 GCGCGATCTTGTCTTTAACCCTAAGCCAGG 1 223 1 GTCTTTAACC 0.944217 -78 GTCGGAACTGGTATTTAACCAGACTAATTA 2 23 1 GTATTTAACC 0.933424 -278 ATTCAGCTTTGGCTTTTCCTGTAACGATTA 2 69 0 GGCTTTTCCT 0.927334 -232 TGTATTTCCCCAACTTATAGG 2 290 0 GTATTTCCCC 0.965095 -11 GCTGGGGTGAGGCTTTTCCCTCACCCAAAC 7 34 0 GGCTTTTCCC 0.98236 -55 CTTCATCAATGTTTTTACCCGAGAGGGCTG 7 60 0 GTTTTTACCC 0.948979 -29 AGTATTAACCTTCATCAATGT 7 78 0 GTATTAACCT 0.715564 -11 ********** Masking position 5 Map Score: 8.11215 Number of sites scoring better than the average of aligned sites = 528 Number in coding regions = 478 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 6 ATGAGCAAAAGTTTGATGTGCTGCACAATTTTT 1 130 0 GTTTTGTGCG 0.961006 -171 GCGGCATAATGTTTAATGACGTACGAAACGTCA 2 131 1 GTTTTGACGA 0.950004 -170 CAACTTATAGGTTTAGTGTTGTGGAACTAAAGT 2 268 0 GTTTTGTTGG 0.978277 -33 TTACACAAGCGTTTTGTGATGAACGTCACGTCA 5 94 1 GTTTTGATGA 0.865242 -207 GGGGTAGAGAGGTAATTGACGTGACGTTCATCA 5 110 0 GGTATGACGG 0.945122 -191 CACTGAATCGGTTAACTGTCCAGTCGACGGCCT 5 172 0 GTTATGTCCG 0.945241 -129 CGAGGTTTTTTGTTAATGTGGCGGCAGAGGTAG 5 234 0 TGTTTGTGGG 0.814982 -67 CCCTTCTTATGTTTGCTGTCGCGCAGGCTGGAA 5 270 0 GTTTTGTCGG 0.992553 -31 **** ***** * Masking position 7 Map Score: 1.6643 Number of sites scoring better than the average of aligned sites = 690 Number in coding regions = 627 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 7 TGTTTCAGCACGCAAGGAAAGCCGTAAAGTT 1 163 0 CCAAGGAAAG 0.962047 -138 TGTTTAATGACGTACGAAACGTCAGCGGTCA 2 140 1 CTACGAAACG 0.910374 -161 ACAGACGCGACGCACGAAGAGCGCAATACAG 2 189 0 CCACGAAGAG 0.987034 -112 AAAAATCAGTCACAAGTAAGGTAGGGTT 3 27 1 CCAAGTAAGG 0.936261 -18 TGATTGATATCACACAAAAGGCCGTCGACTG 5 154 1 CCACAAAAGG 0.928312 -147 CGACAGCAAACATAAGAAGGGGTGTTTTT 5 282 1 CTAAGAAGGG 0.940909 -19 TGCCCCTCTCCTCACGGAGAGGGTTTGGGTG 7 12 1 CCACGGAGAG 0.981082 -77 * ********* Masking position 4 Map Score: 2.75736 Number of sites scoring better than the average of aligned sites = 241 Number in coding regions = 214 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 AAACGTTTCAGCGCGATCTTGTCTTTAACCCT 1 213 1 GCGCGACTGT 0.98824 -88 GATTCAGCCTGTCGGAACTGGTATTTAACCAG 2 13 1 GTCGGACTGT 0.988176 -288 AGTAAATTGGGCCGCATCTCGTGGA 4 4 0 GCCGCACTGT 0.991738 -37 GGCAGAGGTAGCCGGACCTTGTAGATACTGCG 5 213 0 GCCGGACTGT 0.997705 -88 CAGGCTGGAAGCCCGAGGTTTTTTGTTAATGT 5 248 0 GCCCGAGTTT 0.942219 -53 ****** ** ** Masking position 6 Map Score: 1.44034 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 223 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 CTGTTGCTGATTGGCTGCTGACGCTGCTGAA 1 49 1 TTGCTGCTGA 0.971565 -252 TGCTCATAACTTTACGGCTTTCCTTGCGTGC 1 156 1 TTACGGCTTT 0.923561 -145 AATTCTTCCTTTAGCGGCATAATGTTTAATG 2 118 1 TTGCGGCATA 0.933057 -183 CTGGCGGGTGTTGACCGCTGACGTTTCGTAC 2 151 0 TTACCGCTGA 0.918968 -150 CTCTTCGTGCGTCGCGTCTGTTAAAAACTGG 2 199 1 GTGCGTCTGT 0.853164 -102 GCCTGTATTGTTAGCGCCAGTTTTTAACAGA 2 215 0 TTGCGCCAGT 0.904536 -86 TGCGGCCCAATTTACTGCTTAGGAGAAGATC 4 20 1 TTACTGCTTA 0.840927 -21 TTTTGTTAATGTGGCGGCAGAGGTAGCCGGA 5 229 0 GTGCGGCAGA 0.978031 -72 ** ******** Masking position 2 Map Score: 1.56881 Number of sites scoring better than the average of aligned sites = 1872 Number in coding regions = 1747 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 10 AGTTTGATGTGCTGCACAATTTTTTGCCAT 1 124 0 GCTGCACAAT 0.984575 -177 TCTTCCTTTAGCGGCATAATGTTTAATGAC 2 121 1 GCGGCATAAT 0.98459 -180 TCCACGAGATGCGGCCCAATTTACTGCTTA 4 11 1 GCGGCCCAAT 0.993218 -30 ********** Masking position 8 Map Score: 0.125443 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 24 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 11 ********** No masking Map Score: -3.5787e-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: -3.5787e-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 13 ********** No masking Map Score: -3.5787e-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