AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i117_Oligopeptide_Transport_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 oppA 300 oligopeptide transport; periplasmic binding protein #2 oppB 85 oligopeptide transport permease protein #3 rtn 180 orf, hypothetical protein #4 yejA 75 orf, hypothetical protein #5 nikA 110 periplasmic binding protein for nickel #6 dppB 172 dipeptide transport system permease protein 1 #7 dppA 300 dipeptide transport protein #8 HI0853 140 heme-binding lipoprotein (dppA) #9 HI1123 80 oligopeptide ABC transporter, permease protein (oppB) #10 HI1124 295 oligopeptide ABC transporter, periplasmic-binding protein (oppA) #11 HI1187 89 dipeptide ABC transporter, permease protein (dppB) #12 HI1188 300 DNA helicase II (uvrD) Motif number 1 GCGAGTAAGAACCGCATTTGGTACTTTC 1 7 1 AAGCCGCATT 0.817917 -294 AAAAGATAACAATGACCGGACTATAGCCTGGA 3 124 0 AATCCGGACT 0.923717 -57 TTTACTCATCATTAGCCGCAATCCGGCATGCT 4 44 0 ATTCCGCAAT 0.957796 -32 TCGTCATACTTATTTCCGCCATCTATTTTAAT 5 75 1 TATCCGCCAT 0.844004 -36 CTCACAAATCAATTCCCGCCCTTATCGGACAG 6 100 0 AATCCGCCCT 0.975729 -73 CATTTTATGGAGGATCCGCACTGTTACACTGA 7 154 1 AGGCCGCACT 0.9477 -147 TACGACGATTTTTAACCGCACTTAAATACGAG 9 18 0 TTTCCGCACT 0.987457 -63 CGTCGTATTTTTTGACCGCACTTTTCGCCCAT 9 43 1 TTTCCGCACT 0.987456 -38 TGCGGTAAAAATTCACCGCACTCTTCAAAGAA 11 44 0 ATTCCGCACT 0.991392 -46 TGCGGTGAATTTTTACCGCACTTTTATTATCT 11 56 1 TTTCCGCACT 0.987457 -34 *** ******* Masking position 12 Map Score: 12.7744 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 195 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 2 ACCAATAAAGAATCGTCTGGCGGTTGCCCGGAA 1 36 0 AATGTGGCGG 0.976051 -265 TGGCAATACGTGGGGCAGGAGTGTCCTG 2 6 1 ATAGTGGCAG 0.984334 -80 GTTCTGGATCAATAGATGGGCAGTCGGGTGGGC 5 14 0 AATGAGGCAG 0.963434 -97 ACTGATGTTAATTAGTACGGCATCCCCACCTCA 7 181 1 ATTGTGGCAT 0.894192 -120 AAAAAACAAAAAAGGTCAGGCAGCGACAACCCA 7 234 1 AAAGTGGCAG 0.992845 -67 TTTAACCATAAATGGTAGGGCATTCCCTGCCTA 8 108 1 AATGTGGCAT 0.949146 -33 ACCTCAATGTTAGGCAGGGAATGCCCT 8 124 0 CAAGTGGCAG 0.966599 -17 AAAAGTGATGATATGAGAGGCGGGGGATCTAGG 10 123 0 ATAGAGGCGG 0.882494 -173 CGTAGATAATAAAAGTGCGGTAAAAATTCACCG 11 58 0 AAAGTGGTAA 0.72817 -32 TGAGTATATCAAAAGTAGGGTAGAACATTTTAA 12 208 0 AAAGTGGTAG 0.959981 -93 *** ** ***** Masking position 5 Map Score: 8.90353 Number of sites scoring better than the average of aligned sites = 385 Number in coding regions = 348 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 3 TAAAGAGCGTCGCGAAAGAATAATGTGTCTC 1 88 1 CGCGAAGAAT 0.898604 -213 TGGATCAAGACGCGGAAACATCATTTTCTCT 3 97 0 CGCGAAACAT 0.898604 -84 TTGACCCGACCGGGCAAAAAACAAAAAAGGT 7 219 1 CGGGAAAAAA 0.961007 -82 TATTTAAGTGCGGTTAAAAATCGTCGTATTT 9 22 1 CGGTAAAAAT 0.982747 -59 GCGAAAAGTGCGGTCAAAAAATACGACGATT 9 40 0 CGGTAAAAAA 0.967616 -41 TCTAATAAATCGCTAAAAAAATTGCTAAAAG 10 151 0 CGCTAAAAAA 0.960195 -145 TCTATTTATTAGCTCAAAAATTCATTTTTGT 10 233 0 AGCTAAAAAT 0.818452 -63 AGAAATTAATCGGTAAAAAATATAATACTCT 11 17 0 CGGTAAAAAT 0.982747 -73 AATAAAAGTGCGGTAAAAATTCACCGCACTC 11 53 0 CGGTAAAATT 0.899793 -37 **** ****** Masking position 6 Map Score: 7.45008 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 217 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 TCTTTAATTGTTAATTATTCTCATTACCAATAAAGA 1 58 0 TTTATCTCTA 0.965459 -243 ATCACCGACTTTATTTATTCTGGTGATTCAGACGAT 1 154 0 TTTATCTGTA 0.978483 -147 CAATCCGGGATTACACATGCTGGTTAATACCAGTAA 1 250 1 TTCATCTGTA 0.978057 -51 ATGCAATCCCTTGGCTATCCTGACGAGTTAACTGAA 3 23 1 TTTATCTGCA 0.962618 -158 CGGATTTCCTTTTACTCATCATTAGCCGCAA 4 55 0 TTTTTCTCTA 0.833582 -21 ATTTTAAGTATTCGTCATACTGATTACCTGTTCTGG 5 40 0 TTCATCTGTA 0.978057 -71 GTATTGACGTTTTCACATTCTGTTGACAGATTGTAG 7 107 1 TTCATCTGTA 0.978057 -194 CTACCCTACTTTTGATATACTCACAAATCTTATTGT 12 218 1 TTTATCTCCA 0.940574 -83 ** *** *** * * Masking position 16 Map Score: 5.26197 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 54 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 ATGTGTAATCCCGGATTGGGACCCTGCACA 1 238 0 CCGGATTGGG 0.968855 -63 TGAAAGCATGCCGGATTGCGGCTAATGATG 4 40 1 CCGGATTGCG 0.990027 -36 TCCGCCCACCCGACTGCCCATCTATTGA 5 9 1 CCCGACTGCC 0.963905 -102 AATCTGTATACCCGGTGGCGCTGTGCCTCT 6 35 1 CCCGGTGGCG 0.984084 -138 AGTATTGCTGCCGGATGGCGCTGCACGCAG 6 63 0 CCGGATGGCG 0.98543 -110 ACACGCAGTTCCAGGCTGCGGGTCACTATA 6 140 1 CCAGGCTGCG 0.958574 -33 TGGTGTAAATCCCGGTTGGCTGTATTGACG 7 86 1 CCCGGTTGGC 0.970138 -215 TTGTTTTTTGCCCGGTCGGGTCAACGTTAT 7 213 0 CCCGGTCGGG 0.5084 -88 ********** Masking position 4 Map Score: 10.3937 Number of sites scoring better than the average of aligned sites = 508 Number in coding regions = 463 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 6 AATGTGTCTCGACAGGGGAGACACAGTACG 1 109 1 GACAGGGGAG 0.945402 -192 CAATACGTGGGGCAGGAGTGTCCTGCTCCA 2 14 1 GGCAGGAGTG 0.939271 -72 GCCCTTATCGGACAGGGAATGAAGTATTGC 6 85 0 GACAGGGAAT 0.947433 -88 GTCCGATAAGGGCGGGAATTGATTTGTGAG 6 102 1 GGCGGGAATT 0.940403 -71 AACGTTATGAGGTGGGGATGCCGTACTAAT 7 191 0 GGTGGGGATG 0.815447 -110 CTCAATGTTAGGCAGGGAATGCCCTACCAT 8 119 0 GGCAGGGAAT 0.98509 -22 TGATATGAGAGGCGGGGGATCTAGGATGTA 10 118 0 GGCGGGGGAT 0.98449 -178 GTAAAGATTTGTCAGGAAATTATTTGAAGA 10 205 0 GTCAGGAAAT 0.799811 -91 ********** Masking position 5 Map Score: 4.60971 Number of sites scoring better than the average of aligned sites = 741 Number in coding regions = 661 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 TGTTGTCGTAATTTCAGGAAATTAACGGAA 3 159 1 ATTTCAGGAA 0.892708 -22 AAGTATGACGATTTTAAGTATTCGTCATAC 5 56 0 ATTTTAAGTA 0.753396 -55 TCAGGAAATTATTTGAAGAAAAATTGAGTT 10 194 0 ATTTGAAGAA 0.839886 -102 TCAAAAATTCATTTTTGTAAAGATTTGTCA 10 221 0 ATTTTTGTAA 0.794041 -75 ATTAGGCGATATTTTTATAAAAAGTCTTCT 10 261 0 ATTTTTATAA 0.708506 -35 CATCATGGGTATTTTTGGAAAAATGAGAAA 12 49 1 ATTTTTGGAA 0.943996 -252 GAAACCTTGCATTTTAGGAATGAGAGGTAA 12 75 1 ATTTTAGGAA 0.964336 -226 AGGGTAGAACATTTTAAGAATAATATTAAG 12 195 0 ATTTTAAGAA 0.944566 -106 ********** Masking position 1 Map Score: 3.08216 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 46 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 GGGGCAGGAGTGTCCTGCTCCACGGTGTCTGA 2 22 1 TGTTGCTCCA 0.988877 -64 GATGTTTCCGCGTCTTGATCCAGGCTATAGTC 3 106 1 CGTTGATCCA 0.957736 -75 CGACTGCCCATCTATTGATCCAGAACAGGTAA 5 21 1 TCTTGATCCA 0.954332 -90 TTCCGCCATCTATTTTAATCCATTGGGGTTAC 5 88 1 TATTAATCCA 0.923329 -23 CAGAGAAATTTGTGCTACTCCA 7 1 0 TGTTACTCCA 0.977186 -300 TATTCTGCTCCAATTGTGATGT 7 289 0 TATTGCTCCA 0.967797 -12 ATTAATTTGTTATAATCCATAGAATTTTT 8 8 1 TGTTAATCCA 0.972604 -133 *** ******* Masking position 12 Map Score: 4.5061 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 61 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 9 TCGCGAAAGAATAATGTGTCTCGACAGGGGAG 1 97 1 ATATGTGCTC 0.714702 -204 ATGTCGATTCGTACTGTGTCTCCCCTGTCGAG 1 116 0 GTCTGTGCTC 0.94578 -185 ACTTTCTGCTGTCAGGTTACTTTATCGTTACG 1 197 0 GTAGGTTCTT 0.773295 -104 CCCTGCACAGGCTCGGAGACTTTCTGCTGTCA 1 215 0 GCCGGAGCTT 0.944577 -86 ATACCCGGTGGCGCTGTGCCTCTGCGTGCAGC 6 42 1 GCCTGTGCTC 0.965299 -131 AACCCGGATTCTCTATAGTGACC 6 160 0 ACCGGATCTC 0.94578 -13 TAATCTTTGTGTGTGGATTCTCACCGTTGGTG 7 59 1 GTTGGATCTC 0.857088 -242 CAGTGTAACAGTGCGGATCCTCCATAAAATGC 7 153 0 GTCGGATCTC 0.974853 -148 TCGCCTAATGACAAGGAGGCTCAA 10 282 1 ACAGGAGCTC 0.93403 -14 TTCCTAAAATGCAAGGTTTCTCATTTTTCCAA 12 63 0 GCAGGTTCTC 0.969199 -238 ** ***** *** Masking position 11 Map Score: 4.85766 Number of sites scoring better than the average of aligned sites = 441 Number in coding regions = 402 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 10 GATTCCGTTAATTTCCTGAAATTACGACAAC 3 160 0 ATTTCCTAAA 0.840599 -21 CCATAGAATTTTTTTATTTAAAAAAAGGGAAA 8 27 1 TTTTATTAAA 0.835424 -114 CAAAACTCAATTTTTCTTCAAATAATTTCCTG 10 191 1 TTTTCTTAAA 0.94428 -105 TCCTGACAAATCTTTACAAAAATGAATTTTTG 10 218 1 TTTTACAAAA 0.844253 -78 AATAGAAGACTTTTTATAAAAATATCGCCTAA 10 258 1 TTTTATAAAA 0.467581 -38 AGGTTTCTCATTTTTCCAAAAATACCCATGAT 12 50 0 TTTTCCAAAA 0.928157 -251 CGTTTACCTCTCATTCCTAAAATGCAAGGTTT 12 76 0 TATTCCTAAA 0.913578 -225 GGGATTCTCCTATATCCTTAAACTCAACATCA 12 162 0 TTATCCTAAA 0.840596 -139 CCGCTTAATATTATTCTTAAAATGTTCTACCC 12 192 1 TATTCTTAAA 0.843077 -109 * ****** *** Masking position 5 Map Score: 0.780347 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 130 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 11 TGATGAATGAAAACAAAAAAGCACTGCCTA 3 68 0 AAACAAAAAA 0.94381 -113 AAGATTAAAAAAACTTCAAACAGCTATTTG 7 36 0 AAACTTCAAA 0.70461 -265 ACCGGGCAAAAAACAAAAAAGGTCAGGCAG 7 227 1 AAACAAAAAA 0.94381 -74 CAAAGGGTTAAAACAACAAACATCACAATT 7 270 1 AAACAACAAA 0.963519 -31 CCCTTTTTTTAAATAAAAAAATTCTATGGA 8 26 0 AAATAAAAAA 0.685405 -115 CTATCTCCACCAACAAGAAATATCAATAAG 8 70 0 CAACAAGAAA 0.868937 -71 TCCTTAAACTCAACATCAAAACCATATGCT 12 150 0 CAACATCAAA 0.885473 -151 ********** Masking position 3 Map Score: 0.780895 Number of sites scoring better than the average of aligned sites = 169 Number in coding regions = 114 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 12 GCGAGTAAGAACCGCATTTGGTACT 1 5 1 GTAAGAACGC 0.897672 -296 TCGCATTACAGAAGGCACAGGCCAGAAGGTA 2 60 1 GAAGGCACGG 0.942277 -26 CGAGTTAACTGAAAGCACTGCTTAGGCAGTG 3 46 1 GAAAGCACGC 0.992137 -135 ATGAAAACAAAAAAGCACTGCCTAAGCAGTG 3 61 0 AAAAGCACGC 0.97177 -120 AATAAGGGACGTAAGCACACC 4 1 0 GTAAGCACCC 0.966145 -75 TATTCATAGTGAAAGCATGCCGGATTGCGGC 4 31 1 GAAAGCATCC 0.873524 -45 CGCTGCACGCAGAGGCACAGCGCCACCGGGT 6 44 0 AGAGGCACGC 0.912548 -129 ******** ** Masking position 7 Map Score: 1.71136 Number of sites scoring better than the average of aligned sites = 425 Number in coding regions = 389 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 13 CCTGTGCAGGGTCCCAATCCGGGATTACAC 1 236 1 GTCCCAATCC 0.880893 -65 GGGCAGGAGTGTCCTGCTCCACGGTGTCTG 2 23 1 GTCCTGCTCC 0.969343 -63 ATGTTTCCGCGTCTTGATCCAGGCTATAGT 3 107 1 GTCTTGATCC 0.92648 -74 GTGCCTCTGCGTGCAGCGCCATCCGGCAGC 6 57 1 GTGCAGCGCC 0.905084 -116 AGAGAAATTTGTGCTACTCCA 7 2 0 GTGCTACTCC 0.952626 -299 TAATCTTTGTGTGTGGATTCTCACCGTTGG 7 59 1 GTGTGGATTC 0.712069 -242 CTCACCGTTGGTGTAAATCCCGGTTGGCTG 7 78 1 GTGTAAATCC 0.848402 -223 CAGTGTAACAGTGCGGATCCTCCATAAAAT 7 155 0 GTGCGGATCC 0.982656 -146 ********** Masking position 2 Map Score: 1.60888 Number of sites scoring better than the average of aligned sites = 486 Number in coding regions = 463 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 14 ********** No masking Map Score: -5.83823e-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 TTTATTGGTAATGAGAATAATTAACAATTAAA 1 60 1 AAGAATAATT 0.890441 -241 CGTCTGAATCACCAGAATAAATAAAGTCGGTG 1 156 1 AAGAATAAAT 0.810009 -145 GTTTTCATTCATCAGAGAAAATGATGTTTCCG 3 84 1 AAGAGAAAAT 0.912768 -97 AGCTATTTGCAGCAGAGAAATTTGTGCTACTC 7 13 0 AAGAGAAATT 0.952261 -288 CCTTTTTTTAAATAAAAAAATTCTATGGATTA 8 23 0 AAAAAAAATT 0.603006 -118 TTTATTTAAAAAAAGGGAAATTTGCTTATATC 8 39 1 AAGGGAAATT 0.942705 -102 AATTAGCATTAAAAGGGTAATTTATGTAGGAA 10 62 1 AAGGGTAATT 0.896167 -234 AAATATTTACAATAGGAAAAATCAATACATCC 10 93 1 AAGGAAAAAT 0.870196 -203 GGAAATTATTTGAAGAAAAATTGAGTTTTGTG 10 189 0 TAGAAAAATT 0.709511 -107 * ********* Masking position 4 Map Score: 1.08717 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 108 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639