AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i011_CTP_synthase_ecoli_hinf_reg_300.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 pyrG 227 CTP synthetase #2 mazG 70 orf, hypothetical protein #3 chpR 77 suppressor of inhibitory function of ChpA, PemI-like, autoregulated #4 relA 47 (p)ppGpp synthetase I (GTP pyrophosphokinase); regulation of RNA synthesis; stringent factor #5 ygcA 56 putative enzyme #6 HI1077 300 CTP synthetase (pyrG) Motif number 1 CAAGCGCTTGTCATTTAAAAAATGACACAA 1 35 0 TCATTTAAAA 0.791843 -193 CATCGTCTTTTCAACCTAACTTCTCAGGTT 1 204 1 TCAACCTAAC 0.959943 -24 ACAGTATATATCAATCTACATTGTAGATAC 3 25 0 TCAATCTACA 0.976916 -53 CGAGACTTTCTCAATTTAACAGTGTGACCT 5 34 0 TCAATTTAAC 0.775569 -23 AATATTTGTCTCAACCAACACATCTCTTGA 6 19 1 TCAACCAACA 0.985321 -282 ACTTAATTTATCATTCAACATTTGTAATGT 6 89 1 TCATTCAACA 0.963477 -212 ACAGACAAAATCAACCAAAAGTGCGGTCAA 6 232 0 TCAACCAAAA 0.976916 -69 TTATAGCTAATCATCCTACAGACAAAATCA 6 249 0 TCATCCTACA 0.976659 -52 ********** Masking position 3 Map Score: 9.13083 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 154 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 2 ATTTAAAAAATGACACAAATGGCGCTTGACCGC 1 20 0 TGCCAAAGGC 0.988666 -208 TAAATGTTTTTGACGCAAATCAAGCGCTTGTCA 1 52 0 TGCCAAACAA 0.807439 -176 CAAAAACATTTACCCCAAAGGGGCTATTTTCTC 1 73 1 TACCAAAGGG 0.985111 -155 AATAGTGCGCTGGCGAAGAGGAGGGATAATGAA 1 118 1 TGCAAGAGAG 0.943854 -110 GACGATGGAATAACCAAGACGGGAAAGCAGTAT 1 178 0 TACAAGAGGG 0.958829 -50 AACCCTTTCCTCAAACCGCTATCATATGT 3 59 0 TTCCAAACGC 0.941544 -19 GGACCAGACCTGCCGAAATCGGCAAATCGCAA 4 10 0 TGCAAATGGC 0.839689 -38 TGACCTTAATTGTCCCATAACGGAACTCC 5 7 0 TGCCATACGG 0.959654 -50 ATTGAGTTCATTGCGCAAATCAGGTAAACTACC 6 166 1 TTCCAAACAG 0.898153 -135 GATAATTAGCTATCAAAGACGGGATGGTAGTTT 6 191 0 TACAAGAGGG 0.958829 -110 ** * **** *** Masking position 7 Map Score: 6.3504 Number of sites scoring better than the average of aligned sites = 875 Number in coding regions = 787 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 3 ACTATTGAAATCAGGAGTGAGAAAATAGCCC 1 93 0 TCAGAGTGAG 0.988723 -135 ACTCCTGATTTCAATAGTGCGCTGGCGAAGA 1 106 1 TCAAAGTGCG 0.98524 -122 GCTGAACCTGAGAAGTTAGGTTGAAAAGA 1 209 0 TGAGAGTTAG 0.870474 -19 TGTGACCAGAATAGAAGTGAGTTAGTAACA 2 10 0 ATAGAGTGAG 0.932231 -61 TGAATTGTCCTGAAAATTGCGGGTCTGTCAG 2 50 0 TGAAATTGCG 0.912882 -21 CTTTCTCAATTTAACAGTGTGACCTTAATTG 5 28 0 TTAAAGTGTG 0.914412 -29 TAAGCCAAAACTAGCATTGAGTTCATTGCGC 6 151 1 CTAGATTGAG 0.895516 -150 ACAAAATCAACCAAAAGTGCGGTCAAAAATC 6 227 0 CCAAAGTGCG 0.978158 -74 **** ****** Masking position 6 Map Score: 4.35278 Number of sites scoring better than the average of aligned sites = 380 Number in coding regions = 333 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 4 CAGTATACCCGAACATGACCTGTGCCACAAAC 1 152 0 GACTGACCTG 0.995024 -76 GGGTCTGTCAGGTGGAAACCTGTGACCAGAAT 2 29 0 GTGAAACCTG 0.949557 -42 TCTCCTTTAGGGACCAGACCTGCCGAAATCGG 4 21 0 GACAGACCTG 0.992885 -27 AGACGGGATGGTAGTTTACCTGATTTGCGCAA 6 176 0 GAGTTACCTG 0.980505 -125 AGGGAACCTAATCTGTATTGGAATA 6 286 0 GACTAATCTG 0.961197 -15 * ** ******* Masking position 8 Map Score: 0.863104 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 144 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 CTTGATTTGCGTCAAAAACATTTACCCCAAAGGG 1 61 1 GAAAACATTA 0.990137 -167 CATGACCTGTGCCACAAACTTTCATTATCCCTCC 1 137 0 GAAAACTTTA 0.96119 -91 TGTGTTGGTTGAGACAAATATTAAAATATG 6 7 0 GAAAATATTA 0.939479 -294 TATTCAAGCAGTTAAAAACATCAAGAGATGTGTT 6 35 0 GAAAACATCA 0.988127 -266 TCATCCTACAGACAAAATCAACCAAAAGTGCGGT 6 235 0 GAAATCAACA 0.916699 -66 AGGATGATTAGCTATAATCATTTATATTCCAATA 6 262 1 GAAATCATTA 0.98171 -39 * * ******* * Masking position 7 Map Score: 2.28408 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 63 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 6 ********** No masking Map Score: -1.00654e-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 7 ********** No masking Map Score: -1.00654e-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 8 ********** No masking Map Score: -1.00654e-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