AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i096_Nitrogen_Transport_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 cof 87 orf, hypothetical protein #2 ybaO 65 putative LRP-like transcriptional regulator #3 mdlA 29 ATP-binding component of a transport system #4 glnK 180 nitrogen regulatory protein P-II 2 #5 amtB 29 probable ammonium transporter #6 glnB 60 regulatory protein P-II for glutamine synthetase #7 yfhG 164 putative alpha helix protein #8 yfhK 300 putative 2-component sensor protein Motif number 1 ATCACCATTAACCGTGTCACAGA 1 75 1 ACGTGTCAGA 0.57661 -13 CCGGGCAATTGCCCGGTGCTGGAAGGGATCTCG 2 11 0 GCCGGTGCGA 0.996852 -55 CTATGACAGTGCACAGTGCGTTACATTTTTGCA 4 34 0 GCCAGTGCTA 0.934767 -147 AAATGAAAACGCACTATGACAGTGCACAGTGCG 4 47 0 GCCTATGAGT 0.73822 -134 GGTATTGCAAGCGGTGTGCCAGAAATGAAAAAC 4 111 0 GCGTGTGCGA 0.987177 -70 CGTTCCTGTTGCTGTGTGCCAGAGA 5 3 0 GCGTGTGCGA 0.987177 -27 GTTCGGCCCCGGGCAGTGCTCGAAATCTTCACG 7 49 1 GGCAGTGCGA 0.984257 -116 CGGTTTCTCCGCGCTGTCCATGTCCAGACTGTC 7 98 1 GCCTGTCCGT 0.939176 -67 TTAAAGCCTATCCCAGTGGGCGTAATTGTTGCA 7 131 0 TCCAGTGGGT 0.736055 -34 CGACACAGTGGCTGATTTACATTCA 8 3 1 ACCAGTGGGA 0.966192 -298 GGCTGACATAAGTCGGTGAATGAGCCACTGGTT 8 128 0 AGCGGTGAGA 0.900247 -173 TCGACGTTTCGCCCGATGGTTGATATAGCTACG 8 232 0 GCCGATGGGA 0.946758 -69 TTATGGAATAAGGCGGTGCCTAACTCGACGTTT 8 256 0 AGCGGTGCAA 0.696509 -45 ** ****** ** Masking position 7 Map Score: 11.2837 Number of sites scoring better than the average of aligned sites = 2455 Number in coding regions = 2325 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 2 CGAGATCCCTTCCAGCACCGGGC 2 3 1 AGATCCTTCC 0.89585 -63 AGATCCCCTCCGGTCAGAATT 4 170 0 AGATCCCTCC 0.98514 -11 TTTATTTGTCAGTTCGGCCCCGGGCAGTGCT 7 38 1 AGTTCGCCCC 0.986256 -127 CACGTACGATATGTACGCTCCGGTTTCTCCG 7 78 1 ATGTAGCTCC 0.962856 -87 TGAGGGGTTTATGTCTCCTCCGCTGTTTGAA 8 32 0 ATGTCCCTCC 0.986366 -269 TCACCGACTTATGTCAGCCCCTTCGGGACGT 8 142 1 ATGTCGCCCC 0.987459 -159 CGAAACGTCGAGTTAGGCACCGCCTTATTCC 8 254 1 AGTTAGCACC 0.878378 -47 ***** ***** Masking position 1 Map Score: 5.05274 Number of sites scoring better than the average of aligned sites = 327 Number in coding regions = 307 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 3 CGAGATCCCTTCCAGCACCGGGCAA 2 6 1 TCCCTTCCAG 0.943065 -60 AGATCCCCTCCGGTCAGAATTCG 4 168 0 TCCCCTCCGG 0.998557 -13 ATTTGTCAGTTCGGCCCCGGGCAGTGCTCG 7 41 1 TCGGCCCCGG 0.973614 -124 GTACGATATGTACGCTCCGGTTTCTCCGCG 7 81 1 TACGCTCCGG 0.982444 -84 GGGGTTTATGTCTCCTCCGCTGTTTGAATG 8 30 0 TCTCCTCCGC 0.968159 -271 ACTTATGTCAGCCCCTTCGGGACGTGCTAC 8 148 1 GCCCCTTCGG 0.975093 -153 ********** Masking position 8 Map Score: 4.09375 Number of sites scoring better than the average of aligned sites = 395 Number in coding regions = 359 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 4 TAATATTGTTCCGGGTTTAT 1 1 0 CCGGGTTTAT 0.972514 -87 TCTGTGACACGGTTAATGGTGATTGAG 1 71 0 CACGGTTAAT 0.841354 -17 CCTTCCAGCACCGGGCAATTGCCCGGTTTT 2 18 1 CCGGGCAATT 0.961577 -48 CGGGCAATTGCCCGGTTTTTTTTGCGTTGA 2 29 1 CCCGGTTTTT 0.971687 -37 CCTATCCTATCAGGCTATTTTATTTGTCAG 7 20 1 CAGGCTATTT 0.877901 -145 GAGTTAGGCACCGCCTTATTCCATAACAAA 8 263 1 CCGCCTTATT 0.895737 -38 CATAACAAAGCCGGGTAATTCCCGGCT 8 284 1 CCGGGTAATT 0.987854 -17 ********** Masking position 10 Map Score: 2.92348 Number of sites scoring better than the average of aligned sites = 952 Number in coding regions = 808 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 5 ATTTTTGCACCAACGATGAAATATTGCGCTA 4 12 0 CAAGATGAAA 0.968189 -169 ATCGTTGGTGCAAAAATGTAACGCACTGTGC 4 26 1 CAAAATGTAA 0.953564 -155 AGCGGTGTGCCAGAAATGAAAAACGAGAAAG 4 104 0 CAGAATGAAA 0.986474 -77 CACACAGCAACAGGAACGAAAA 5 18 1 CAGAACGAAA 0.977159 -12 GTAACTGTGCCAATAAAGAAAATAGTTTGGT 8 86 0 CAAAAAGAAA 0.96395 -215 *** ******* Masking position 6 Map Score: 1.54292 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 69 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 6 CTTCCGTATATATCAGGTGATACTCAATCA 1 49 1 TATCAGGTGA 0.95713 -39 ATATCCAGAATCAGGTCAGGACACAACG 3 9 1 AATCAGGTCA 0.96621 -21 GCAGATCAAAAGACAGGCGACCTTTTCAAG 6 34 1 AGACAGGCGA 0.94591 -27 CAGCCTATCCTATCAGGCTATTTTATTTGT 7 17 1 TATCAGGCTA 0.858556 -148 TGTTGCAGACAGTCTGGACATGGACAGCGC 7 108 0 AGTCTGGACA 0.904401 -57 ATAGGCTTTAAGTCTGGTGAAT 7 153 1 AGTCTGGTGA 0.972361 -12 ********** Masking position 10 Map Score: 0.579379 Number of sites scoring better than the average of aligned sites = 602 Number in coding regions = 548 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 7 ********** No masking Map Score: -1.89414e-13 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 8 ********** No masking Map Score: -1.89414e-13 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 9 ********** No masking Map Score: -1.89414e-13 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