AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -imodE_ecoli_opreg_100.orf -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 modA 166 molybdate-binding periplasmic protein; permease #2 moaA 300 molybdopterin biosynthesis, protein A #3 moaB 21 molybdopterin biosynthesis, protein B #4 dmsA 300 anaerobic dimethyl sulfoxide reductase subunit A Motif number 1 AGTCGGGCATTTTCTTTTTCTCAACTTCCTGC 1 29 1 TTCTTTTCTC 0.917145 -138 GTCGTTATATTGTCGCCTACATAACGTTACAT 1 132 1 TTCCCTACAT 0.832032 -35 AAAATGGCGGTTTTACTTTGATATACATCATC 2 47 0 TTTCTTTGAT 0.73944 -254 AAACCGCCATTTTCCCTTATTCTGTAGCGAAA 2 66 1 TTCCTTATTC 0.772016 -235 ATGGTAAAAATCTCATTTACACGCTAGTATCG 2 145 1 TTCTTTACAC 0.963375 -156 CTGATCTCTCCTTTTGACGTT 3 4 0 TTCTTTTGAC 0.972985 -18 GCTTTTTTTGTCTCCCTTTGATACCGAACAAT 4 23 1 TTCCTTTGAT 0.972985 -278 AATAATTACTCCTCACTTACACGTAATACTAC 4 52 1 CTCCTTACAC 0.904044 -249 AAAATCTACCTATCTCTTTGATTTTCAAATTA 4 93 1 TTCCTTTGAT 0.972985 -208 CATCAGGGATTTTCGTTTTCATAATGGCTCAC 4 214 0 TTCTTTTCAT 0.95911 -87 CGCCGATCGCTGTCGTTTTTACCAAACCACGG 4 271 0 TTCTTTTTAC 0.924071 -30 * ** ******* Masking position 8 Map Score: 9.57482 Number of sites scoring better than the average of aligned sites = 695 Number in coding regions = 602 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 2 TTTTCTTATCTACCTCACAAAGGTTAGCAAT 1 77 1 TACCTCAAAA 0.882105 -90 TCTACCTCTAAAGGACGATGCAC 2 3 1 TACCTCTAAG 0.961677 -298 TACTTTGATATACATCATCAGGGAGGCATAG 2 35 0 TACATCACAG 0.964823 -266 ACGGCCAAAGCACCGTATCAGTTGACCCAGG 2 207 0 CACCGTACAG 0.979112 -94 GTACACCTTTCCAGATACGGGAGG 2 287 0 CACCTTTCAG 0.968055 -14 CAGCAGCCAATACCGCATCAGGGATTTTCGT 4 230 0 TACCGCACAG 0.993021 -71 CACGGCGACTCACCTCAGCAGCCAATACCGC 4 245 0 CACCTCACAG 0.996083 -56 ******* *** Masking position 2 Map Score: 7.51314 Number of sites scoring better than the average of aligned sites = 450 Number in coding regions = 411 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 3 CCCGCTTAGTCGGGCATTTTCTTTTTCTCAACTT 1 22 1 CGATTTTCTT 0.962007 -145 GCTTTTCCTGCCGATATTTTTTCTTATCTACCTC 1 59 1 CGATTTTTCT 0.986612 -108 GGAATTTTCCCAGCAGTTATTGCTAACCTTTGTG 1 92 0 CGGTTATTCT 0.975982 -75 CAAAGTAAAACCGCCATTTTCCCTTATTCTGTAG 2 59 1 CGATTTTCCT 0.985698 -242 GATACGGGAGGCGAAGTCATTTCTTCCTTCGCCC 2 264 0 GGGTCATTCT 0.81683 -37 GCGCCTGCGGGCGCTTTTTTTGTCTCCCTTT 4 8 1 CGGCTTTTTT 0.826642 -293 TGTAAGTGAGGAGTAATTATTGTTCGGTATCAAA 4 39 0 GGATTATTTT 0.90294 -262 CAAAGAGATAGGTAGATTTTCACTCGAAAGTAGT 4 79 0 GTATTTTCCT 0.759877 -222 AAACCGTATTGTGTAATTATTTCTATAGCAGTTC 4 150 0 GGATTATTCT 0.962007 -151 AATACCGCATCAGGGATTTTCGTTTTCATAATGG 4 219 0 CGATTTTCTT 0.962007 -82 CCGCCGATCGCTGTCGTTTTTACCAAACCACGGC 4 270 0 CGGTTTTTCC 0.928463 -31 * * ****** ** Masking position 10 Map Score: 8.65767 Number of sites scoring better than the average of aligned sites = 1129 Number in coding regions = 971 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 4 TCCGAGTTAGTCGTTATATTGTCGCCTACA 1 123 1 TCGTTATATT 0.94018 -44 CGCCTACATAACGTTACATTAAGGGGTTAC 1 145 1 ACGTTACATT 0.874746 -22 TCGTGCTATTTCGCTACAGAATAAGGGAAA 2 76 0 TCGCTACAGA 0.963203 -225 CACGATCATGACGCTATATACATGATTACA 2 101 1 ACGCTATATA 0.978951 -200 ATCCACACTTTCGCTATGTAATCATGTATA 2 117 0 TCGCTATGTA 0.969445 -184 CTATAGCAGTTCGCTATATAGGCTTGTATA 4 132 0 TCGCTATATA 0.988603 -169 ********** Masking position 5 Map Score: 4.57927 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 66 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 TTCCCTGAATGCCCGCTTAGTCGGGCAT 1 8 1 AATGCCGCTT 0.909319 -159 AGAAAAAGAAAATGCCCGACTAAGCGGGCAT 1 19 0 AATGCCGACT 0.934919 -148 AACTTCCTGCTTTTCCTGCCGATATTTTTTC 1 51 1 TTTTCCGCCG 0.893151 -116 CGATGCACGCTATGCCTCCCTGATGATGTAT 2 26 1 TATGCCCCCT 0.983117 -275 GCTCGTAAAGATTGCCACCAGGGCGAAGGAA 2 244 1 ATTGCCCCAG 0.882882 -57 AAGAAATGACTTCGCCTCCCGTATCTGGAAA 2 273 1 TTCGCCCCCG 0.975922 -28 GGGCGCTTTTTTTGTCTCCCTTTGATACCGA 4 19 1 TTTGTCCCCT 0.885415 -282 GAACAATAATTACTCCTCACTTACACGTAAT 4 48 1 TACTCCCACT 0.581903 -253 TCGTTTTCATAATGGCTCACTCAAGCTTGCT 4 203 0 AATGGCCACT 0.883716 -98 CTGATGCGGTATTGGCTGCTGAGGTGAGTCG 4 240 1 ATTGGCGCTG 0.831797 -61 AACGACAGCGATCGGCGGCCTGGCA 4 286 1 ATCGGCGCCT 0.950393 -15 ****** **** Masking position 6 Map Score: 6.06137 Number of sites scoring better than the average of aligned sites = 4076 Number in coding regions = 3789 Number in noncoding regions = 287 Number of orfs with sites within 600 bp upstream = 272 Fraction of orfs with sites within 600 bp upstream = 0.0436878 Motif number 6 CTTTGATATACATCATCAGGGAGGCATAGC 2 34 0 CATCATCAGG 0.936105 -267 ACTCTAGCCTCTGCACCTGGGTCAACTGAT 2 192 1 CTGCACCTGG 0.963055 -109 GGCCAAAGCACCGTATCAGTTGACCCAGGT 2 206 0 CCGTATCAGT 0.965088 -95 ACTTCGCCTCCCGTATCTGGAAAGGTGTAC 2 281 1 CCGTATCTGG 0.987293 -20 GCAGCCAATACCGCATCAGGGATTTTCGTT 4 229 0 CCGCATCAGG 0.984443 -72 ********** Masking position 5 Map Score: 3.65297 Number of sites scoring better than the average of aligned sites = 854 Number in coding regions = 632 Number in noncoding regions = 222 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 7 ATTTCTTCCTTCGCCCTGGTGGCAATCTTT 2 250 0 TCGCCCTGGT 0.995346 -51 CTGAGGTGAGTCGCCGTGGTTTGGTAAAAA 4 258 1 TCGCCGTGGT 0.996867 -43 AGGCCGCCGATCGCTGTCGTTTTTACCAAA 4 277 0 TCGCTGTCGT 0.986647 -24 ********** Masking position 7 Map Score: 1.53398 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 50 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 ********** No masking Map Score: -1.36181e-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: -1.36181e-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: -1.36181e-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