AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i087_PTS_sugar_Utilization_ecoli_reg_300.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 0.977818 -295 ATTTCATTTCAGCAGCGTCAGCAGCCAATCAG 1 55 0 ACACGTCAGC 0.955464 -246 CTATGAGAAAAAAAGCGCCAACCTGGCTTAGG 1 242 0 AAACGCCAAC 0.91312 -59 TAATGACGTACGAAACGTCAGCGGTCAACACC 2 144 1 CAACGTCAGC 0.980691 -157 TCAGCGGTCAACACCCGCCAGCAATGGACTGT 2 161 1 AACCGCCAGC 0.951737 -140 AGGCTAAAGTCGAACCGCCAGGCTAGACTTTA 2 242 1 CAACGCCAGG 0.962113 -59 ATTTTTAGCGAAAATCGCCGCCTTGTTGCTTT 5 61 1 AAACGCCGCC 0.976273 -240 GCGTTTTGTGATGAACGTCACGTCAATTACCT 5 102 1 AGACGTCACG 0.932981 -199 CACATTAACAAAAAACCTCGGGCTTCCAGCCT 5 247 1 AAACCTCGGG 0.86958 -54 TCCAATCCCACCCTCTCCACATGGAGAA 6 7 1 CCACCTCTCC 0.892178 -35 AATTAACCCCACCTTCTCCATGT 6 29 0 ATACCCCACC 0.919364 -13 CTGCCCCTCTCCTCACGGAGAG 7 1 1 CGCCCTCTCC 0.706039 -88 TTCCCTCACCCAAACCCTCTCCGTGAGGAGAG 7 17 0 CAACCTCTCC 0.955673 -72 TGGGTGAGGGAAAAGCCTCACCCCAGCCCTCT 7 37 1 AAACCTCACC 0.985223 -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 0.967505 -265 TTGCCATTTTTCCTAATTGCTGATGGGAAAATC 1 98 0 TCATTGCTGA 0.951076 -203 TTACGGCTTTCCTTGCGTGCTGAAACAGAAGTA 1 167 1 CCCGTGCTGA 0.98706 -134 AAAAAAAGCGCCAACCTGGCTTAGGGTTAAAGA 1 234 0 CCCTGGCTTA 0.926249 -67 GCTTTTTTTCTCATAGAGGCTGAATCGTTTCAA 1 258 1 TCGAGGCTGA 0.976383 -43 AGTTCTCCTCTCTTGCTGAATTGAAACGA 1 282 0 CCCTTGCTGA 0.989062 -19 AAATACCAGTTCCGACAGGCTGAATCAA 2 6 0 TCCAGGCTGA 0.910526 -295 ATGTTTGCTGTCGCGCAGGCTGGAAGCCCGAGG 5 262 0 TCCAGGCTGG 0.978893 -39 ATGTTTTTACCCGAGAGGGCTGGGGTGAGGCTT 7 49 0 CCAGGGCTGG 0.952368 -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 ATAGTCAAAATGCCATTTCACTGTTGCTGA 1 29 1 TGCCATTTCA 0.864477 -272 CACAATTTTTTGCCATTTTTCCTAATTGCT 1 110 0 TGCCATTTTT 0.979449 -191 GTATTGTTAGCGCCAGTTTTTAACAGACGC 2 212 0 CGCCAGTTTT 0.971926 -89 ATGTGAGTAGTGTCACATTTTTGTTTTGAT 5 22 0 TGTCACATTT 0.836735 -279 CACATTTAAATGCCATTTTTAGCGAAAATC 5 47 1 TGCCATTTTT 0.979449 -254 ACCGATTCAGTGCCAGATTTCGCAGTATCT 5 193 1 TGCCAGATTT 0.975316 -108 CTACCTCTGCCGCCACATTAACAAAAAACC 5 234 1 CGCCACATTA 0.920423 -67 ********** Masking position 5 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 TAATTGCTGATGGGAAAATCCGTTATCAGC 1 88 0 TGGGAAAATC 0.765198 -213 CCTGGCTTAGGGTTAAAGACAAGATCGCGC 1 223 0 GGTTAAAGAC 0.973002 -78 TAATTAGTCTGGTTAAATACCAGTTCCGAC 2 23 0 GGTTAAATAC 0.970947 -278 TTTATGATTTGGTTCAATTCTTCCTTTAGC 2 103 1 GGTTCAATTC 0.846954 -198 GCGTCGCGTCTGTTAAAAACTGGCGCTAAC 2 207 1 TGTTAAAAAC 0.884328 -94 TAACAATACAGGCTAAAGTCGAACCGCCAG 2 233 1 GGCTAAAGTC 0.910141 -68 CCTATAAGTTGGGGAAATACA 2 290 1 GGGGAAATAC 0.958084 -11 CAGCCCTCTCGGGTAAAAACATTGATGAAG 7 60 1 GGGTAAAAAC 0.975818 -29 ********** Masking position 6 Map Score: 4.9322 Number of sites scoring better than the average of aligned sites = 551 Number in coding regions = 503 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 6 ATGGCATTTTGACTATTCGTGGCGCTTTTGA 1 14 0 GACATTCGTG 0.920466 -287 ATAACTTTACGGCTTTCCTTGCGTGCTGAAA 1 161 1 GGCTTCCTTG 0.927454 -140 ATTCAGCTTTGGCTTTTCCTGTAACGATTAA 2 68 0 GGCTTTCCTG 0.97999 -233 GTTGACCGCTGACGTTTCGTACGTCATTAAA 2 142 0 GACTTTCGTA 0.734473 -159 GACTGTATTGCGCTCTTCGTGCGTCGCGTCT 2 187 1 CGCCTTCGTG 0.979126 -114 TAAATTGGGCCGCATCTCGTGGA 4 3 0 CGCTCTCGTG 0.972622 -38 TTTTTACACAAGCGTTTTGTGATGAACGTCA 5 91 1 AGCTTTTGTG 0.854746 -210 TCCAGTCGACGGCCTTTTGTGTGATATCAAT 5 156 0 GGCTTTTGTG 0.978434 -145 TACAAGGTCCGGCTACCTCTGCCGCCACATT 5 222 1 GGCACCTCTG 0.607653 -79 CTCACCCAAACCCTCTCCGTGAGGAGAGGGG 7 14 0 CCCCTCCGTG 0.846848 -75 *** ******* Masking position 10 Map Score: 3.89358 Number of sites scoring better than the average of aligned sites = 1298 Number in coding regions = 1198 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 7 GATAACGGATTTTCCCATCAGCAATTAGGA 1 91 1 TTTCCCATCA 0.714854 -210 TTTTTTGCCATTTTTCCTAATTGCTGATGG 1 105 0 TTTTTCCTAA 0.943804 -196 GCACATCAAACTTTTGCTCATAACTTTACG 1 142 1 CTTTTGCTCA 0.943595 -159 GGTTGGCGCTTTTTTTCTCATAGAGGCTGA 1 251 1 TTTTTTCTCA 0.836193 -50 GATCTTCTCCTAAGCAGTAAATT 4 28 0 CTTCTCCTAA 0.919528 -13 AAGGCGGCGATTTTCGCTAAAAATGGCATT 5 55 0 TTTTCGCTAA 0.894854 -246 AGCCCGAGGTTTTTTGTTAATGTGGCGGCA 5 241 0 TTTTTGTTAA 0.535477 -60 CTGCCCCTCTCCTCACGGAGAGGGT 7 6 1 CCTCTCCTCA 0.83988 -83 GGGGTGAGGCTTTTCCCTCACCCAAACCCT 7 31 0 TTTTCCCTCA 0.964561 -58 ********** Masking position 3 Map Score: 2.90977 Number of sites scoring better than the average of aligned sites = 476 Number in coding regions = 356 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 8 GTTGCTGATTGGCTGCTGACGCTGCTGAAA 1 51 1 GGCTGCTGAC 0.854459 -250 GGCGGGTGTTGACCGCTGACGTTTCGTACG 2 150 0 GACCGCTGAC 0.954491 -151 TCACACAAAAGGCCGTCGACTGGACAGTTA 5 163 1 GGCCGTCGAC 0.971798 -138 CCGTCGACTGGACAGTTAACCGATTCAGTG 5 175 1 GACAGTTAAC 0.939663 -126 CAGCCTGCGCGACAGCAAACATAAGAAGGG 5 273 1 GACAGCAAAC 0.925133 -28 ********** Masking position 9 Map Score: 0.696611 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 222 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 ATGGCAAAAAATTGTGCAGCACATCAAACT 1 124 1 ATTGTGCAGC 0.984575 -177 GTCATTAAACATTATGCCGCTAAAGGAAGA 2 121 0 ATTATGCCGC 0.98459 -180 TAAGCAGTAAATTGGGCCGCATCTCGTGGA 4 11 0 ATTGGGCCGC 0.993218 -30 ********** Masking position 1 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 10 ********** 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 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