AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i013_Glycolysis_+_PPS_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 asnS 168 asparagine tRNA synthetase #2 pncB 265 nicotinate phosphoribosyltransferase #3 glk 203 glucokinase #4 pgi 300 glucosephosphate isomerase Motif number 1 TTTAATTCCGAAATCTTTCGCTGCATTTGCGAATTCTGCTT 1 47 1 ATGCCATGCG 0.99711 -122 GCCAGGTAACATAGGTATCCCCCCATTTACGGGTGGACAAG 1 102 1 ATCCCATACG 0.970836 -67 TGTTCAGTCTATTCCTGTTGCGTAAATCGCGCTATGCAGAA 2 43 1 ATGCAATGCG 0.993254 -223 TGTATGTTATAAAAATGTAGCAATAAAGGCGTTTGTACCTG 2 96 0 ATGCTAAGCG 0.850442 -170 ATATGGTGTGATCGGGGTTCAATAAATTGCGAAACAAGGTA 2 167 1 ATCAAATGCG 0.833625 -99 GGGGTCAGATACTTAGTTTGCCCAGCTTGCAAAAAGGCATC 3 27 1 ATGCAGTGCA 0.958052 -177 CAATTACTTTATCGTTTCAGCACCAATTGCAGCGATGCCTT 3 60 0 ACGCCATGCA 0.941502 -144 AGGCCAGAAGAGGCGCGTTGCCCAAGTAACGGTGTTGGAGG 4 33 0 ATGCAATACG 0.973314 -268 TTTATTTATAAATGTACTACCTGCGCTAGCGCAGGCCAGAA 4 65 0 ATCCCGTGCG 0.988259 -236 GAAAAATGTGATGGTTTTAGTGCCGTTAGCGTAATGTTGAG 4 211 0 ATGTCGTGCG 0.949697 -90 GTGACTTTGGAAGATTGTAGCGCCAGTCACAGAAAAATGTG 4 242 0 ATGCCATACA 0.954894 -59 * * ** ** * *** Masking position 1 Map Score: 10.4199 Number of sites scoring better than the average of aligned sites = 1141 Number in coding regions = 1051 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 2 AAGCAGAATTCGCAAATGCAGCGAAAGATTTCGG 1 54 0 CGCATGCGCA 0.986053 -115 CTTGTCCACCCGTAAATGGGGGGATACCTATGTT 1 109 0 CGTATGGGGA 0.981372 -60 ATTCCTGTTGCGTAAATCGCGCTATGCAGAATCT 2 53 1 CGTATCGGCA 0.969809 -213 GATGCCTTTTTGCAAGCTGGGCAAACTAAGTATC 3 34 0 TGCACTGGCA 0.951028 -170 AAGGCATCGCTGCAATTGGTGCTGAAACGATAAA 3 60 1 TGCATGGGCG 0.981284 -144 ATTATTTTGACTTTAGCGGAGCAGTTGAAGA 3 183 1 CTTACGGGCG 0.93606 -21 CCTCCAACACCGTTACTTGGGCAACGCGCCTCTT 4 33 1 CGTATTGGCA 0.974502 -268 TTCTGGCCTGCGCTAGCGCAGGTAGTACATTTAT 4 65 1 CGCACGCGGA 0.957491 -236 ATAAATAAAGGGTGAGCGGGGCGGTTGTCAACGA 4 97 1 GGTACGGGCG 0.968509 -204 CTCAACATTACGCTAACGGCACTAAAACCATCAC 4 211 1 CGCACGGACA 0.969108 -90 CACATTTTTCTGTGACTGGCGCTACAATCTTCCA 4 242 1 TGTATGGGCA 0.984222 -59 *** * *** ** * Masking position 5 Map Score: 12.2197 Number of sites scoring better than the average of aligned sites = 2581 Number in coding regions = 2442 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 3 AGCCGATTAGCTCCCTGATGATA 1 1 0 CTCCTGAATA 0.981778 -168 AGCTAATCGGCTCCCTTTTTTTACCTTTAATTC 1 22 1 CTCCTTTTTA 0.97534 -147 AATATTCTCTCTGTTAATAGTCGGAAAAA 1 150 0 CTCCTGTATA 0.995442 -19 GAAAGGCAGGCTCCCTGTAAATATCGATCTGGG 3 106 0 CTCCTGTATA 0.995442 -98 AATTCTTTCTCACACTGTAAATACCTGGGGGCA 3 153 0 CACCTGTATA 0.991529 -51 CCGCCCCGCTCACCCTTTATTTATAAATGTACT 4 88 0 CACCTTTTTA 0.954952 -213 *** **** *** Masking position 6 Map Score: 7.14637 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 15 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 4 CAGGGAGCTAATCGGCTCCCTTTTTTTACC 1 17 1 ATCGGCTCCC 0.94492 -152 GGTAACATAGGTATCCCCCCATTTACGGGT 1 106 1 GTATCCCCCC 0.976735 -63 CGATCACACCATATGCCACCTTTCTGGTCG 2 151 0 ATATGCCACC 0.947409 -115 CAAACTAAGTATCTGACCCCGCATAAGGAA 3 17 0 ATCTGACCCC 0.962257 -187 CGCCGGAAAGGCAGGCTCCCTGTAAATATC 3 114 0 GCAGGCTCCC 0.964222 -90 GGCGTTGTTGTTATGCCCCCAGGTATTTAC 3 140 1 TTATGCCCCC 0.982132 -64 TGAAAAATCCGCATGACCCCATCGTTGACA 4 122 0 GCATGACCCC 0.975662 -179 ********** Masking position 9 Map Score: 5.07846 Number of sites scoring better than the average of aligned sites = 332 Number in coding regions = 286 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 5 AAACATCTTCAGGAACTGCTGGAGTATACCT 2 203 0 AGGAACGCTG 0.971581 -63 GCTTGCAAAAAGGCATCGCTGCAATTGGTGC 3 51 1 AGGCATGCTG 0.958687 -153 CCTGCCTTTCCGGCGTTGTTGTTATGCCCCC 3 129 1 CGGCGTGTTG 0.990056 -75 TTGACTTTAGCGGAGCAGTTGAAGA 3 189 1 CGGAGCGTTG 0.993261 -15 AAAGGGTGAGCGGGGCGGTTGTCAACGATGG 4 103 1 CGGGGCGTTG 0.988566 -198 ACTGACCGCCAGGAGTGGATGAAAAATCCGC 4 140 0 AGGAGTGATG 0.95934 -161 ****** **** Masking position 10 Map Score: 3.97909 Number of sites scoring better than the average of aligned sites = 650 Number in coding regions = 627 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 6 TATAGAGTCTGGTGTTCAGTCTATTCCTGT 2 31 1 GGTGTTCAGT 0.958907 -235 TGGTGTGATCGGGGTTCAATAAATTGCGAA 2 170 1 GGGGTTCAAT 0.916873 -96 AGGTGCGCAGTAGCGTCCTCG 2 255 0 GGTGCGCAGT 0.968137 -11 ATTCCTTATGCGGGGTCAGATACTTAGTTT 3 16 1 CGGGGTCAGA 0.89634 -188 CTTTTTGCAAGCTGGGCAAACTAAGTATCT 3 33 0 GCTGGGCAAA 0.849357 -171 TTTGACTTTAGCGGAGCAGTTGAAGA 3 188 1 GCGGAGCAGT 0.963209 -16 TAAAGGGTGAGCGGGGCGGTTGTCAACGAT 4 102 1 GCGGGGCGGT 0.973626 -199 ATCCACTCCTGGCGGTCAGTAGTTCAGCTA 4 151 1 GGCGGTCAGT 0.975916 -150 ********** Masking position 4 Map Score: 3.59021 Number of sites scoring better than the average of aligned sites = 1128 Number in coding regions = 1051 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 7 TGGTGTTCAGTCTATTCCTGTTGCGTAAAT 2 40 1 TCTATTCCTG 0.728446 -226 GTATACTCCAGCAGTTCCTGAAGATGTTTA 2 205 1 GCAGTTCCTG 0.915189 -61 TATTGTACTAAACGCTCCTGTACGAGGACG 2 233 1 AACGCTCCTG 0.926113 -33 CCTGTACGAGGACGCTACTGCGCACCT 2 249 1 GACGCTACTG 0.913114 -17 CAGGGAGCCTGCCTTTCCGGCGTTGTTGTT 3 122 1 GCCTTTCCGG 0.934889 -82 TGTTGGAGGAGCCAGTCCTGTGATAACACC 4 12 0 GCCAGTCCTG 0.973008 -289 TGGGCAACGCGCCTCTTCTGGCCTGCGCTA 4 50 1 GCCTCTTCTG 0.972943 -251 GGATTTTTCATCCACTCCTGGCGGTCAGTA 4 142 1 TCCACTCCTG 0.983988 -159 TAGCAATACTCTTCTGATTTTGAGAA 4 285 0 TACTCTTCTG 0.821644 -16 ********** Masking position 6 Map Score: 4.73101 Number of sites scoring better than the average of aligned sites = 1450 Number in coding regions = 1335 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 8 ********** No masking Map Score: -3.23764e-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 9 ********** No masking Map Score: -3.23764e-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 10 ********** No masking Map Score: -3.23764e-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