AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i012_ecoli_bsub_100.orf -o012_ecoli_bsub_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -x5 -e 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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 malP 300 maltodextrin phosphorylase #2 glgB 272 1,4-alpha-glucan branching enzyme #3 glgD 23 ADP-glucose pyrophosphorylase #4 glgB 300 1,4-alpha-glucan branching enzyme Motif number 1 TGCGTATTTTCAAAAAGCGGAAGGTAACTCTAT 1 55 0 CAAAGGGAAG 0.93843 -246 TATCTAAGTGCAAAAAATGGCCGTTGCGTATTT 1 79 0 CAAAAGGCCG 0.769266 -222 CAAATCAATGCAATACAGCGCAGAAAATCTGTA 1 110 0 CATAACGCAG 0.803272 -191 GAGGAGTTGCGGGGATGAGCAAGGAAATGTGAT 1 183 0 GGGAGGCAAG 0.953549 -118 TCATCCTGCGGGGGATTAGGCAGGGAGGAGTTG 1 207 0 GGGATGGCAG 0.968164 -94 TAATCCCCCGCAGGATGAGGAAGGTCAACATCG 1 222 1 CGGAGGGAAG 0.990361 -79 GCGTAATACAGGAGTAAGCGCAGATGTTTCATG 2 54 1 GAGTACGCAG 0.795726 -219 TACCTGAAGTGAGGACGACGCAGAGAGGATGCA 2 157 1 GGGAGCGCAG 0.992734 -116 TTTTTTTGACCTGAACGGCGCAGCACTCTGTGC 2 187 0 CGAAGCGCAG 0.978711 -86 TTACTGAAGAGGGGGCAGAGTCA 3 6 1 GAGAGGGCAG 0.991953 -18 AAAAACCTTGCAGGATATGCAAGGCTTCTGGAT 4 78 0 CGGAAGCAAG 0.912646 -223 * *** * ***** Masking position 13 Map Score: 9.02976 Number of sites scoring better than the average of aligned sites = 2263 Number in coding regions = 2140 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 2 TTGATTTGATGCTAATCCTGTGGTTTGCAC 1 135 1 GCTAATCCTG 0.984604 -166 ACATTTCCTTGCTCATCCCCGCAACTCCTC 1 186 1 GCTCATCCCC 0.974802 -115 GCTCATCCCCGCAACTCCTCCCTGCCTAAT 1 196 1 GCAACTCCTC 0.950529 -105 CTCCTCCCTGCCTAATCCCCCGCAGGATGA 1 210 1 CCTAATCCCC 0.966474 -91 TGTTGACCTTCCTCATCCTGCGGGGGATTA 1 222 0 CCTCATCCTG 0.970081 -79 AACATCTGCGCTTACTCCTGTATTACGCAC 2 52 0 CTTACTCCTG 0.887605 -221 AATGCTCTATTTAACTCCCGGTAAATCATG 2 83 0 TTAACTCCCG 0.703007 -190 GCAGCACTCTGTGCATCCTCTCTGCGTCGT 2 171 0 GTGCATCCTC 0.871432 -102 TAACACGGGTTCGAATCCCGTACGGGTCAT 4 50 1 TCGAATCCCG 0.927109 -251 CAGAAGCCTTGCATATCCTGCAAGGTTTTT 4 81 1 GCATATCCTG 0.892202 -220 ********** Masking position 6 Map Score: 7.2483 Number of sites scoring better than the average of aligned sites = 1251 Number in coding regions = 1141 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 3 AAACAGTTTCATAAGTAAAATATCCA 1 4 0 AAATAAATAT 0.892253 -297 AGGTAACTCTATAAATTAAGTAAAGGAGTGAAA 1 34 0 AAATAAGTAA 0.894175 -267 CGTTGTGTTGAAAATCTAAGAAAAGTGGAACTC 1 276 1 AAACAAGAAA 0.954004 -25 TGTCACAACCAGAAGTCAAAAATCCAATTGGAT 2 220 1 AAATAAAAAT 0.940656 -53 CATGATTTATAAAAACAAAAAAACCTTGCAGGA 4 96 0 AAACAAAAAA 0.961752 -205 AATAAAGAACAAAATCTAAGACATATCATGATT 4 122 0 AAACAAGACA 0.910219 -179 TTTTCTGAAGAAAAACGAAATATATGGAGATTT 4 172 0 AAACAAATAT 0.914575 -129 ATTTATTCGAAGAAATAAAAAAAAGCCCTTTCC 4 239 0 AAATAAAAAA 0.951293 -62 AATAAATACTATAAATGAAAACTATGATGTCAG 4 265 1 AAATAAAACT 0.885688 -36 * ** * ****** Masking position 8 Map Score: 5.88571 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 119 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 4 CCTGCCTAATCCCCCGCAGGATGAGGAAGG 1 216 1 CCCCCGCAGG 0.952069 -85 AGAGTGCTGCGCCGTTCAGGTCAAAAAAAT 2 191 1 GCCGTTCAGG 0.980766 -82 TAAGACACCGCCCTTTCACGGCGGTAACAC 4 26 1 CCCTTTCACG 0.976109 -275 TTCTGGATGACCCGTACGGGATTCGAACCC 4 56 0 CCCGTACGGG 0.499416 -245 AAACAAAAAAACCTTGCAGGATATGCAAGG 4 87 0 ACCTTGCAGG 0.97368 -214 TAAGTATAAGCGCTTTCAGGAAAGGGCTTT 4 221 1 CGCTTTCAGG 0.976109 -80 ********** Masking position 7 Map Score: 2.02791 Number of sites scoring better than the average of aligned sites = 557 Number in coding regions = 503 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 5 TCCCCGCAACTCCTCCCTGCCTAATCCCCC 1 201 1 TCCTCCCTGC 0.917668 -100 AGGAGTTCCACTTTTCTTAGATTTTC 1 285 0 TCCACTTTTC 0.846864 -16 CTGCGCTTACTCCTGTATTACGCACTAACA 2 47 0 TCCTGTATTA 0.87945 -226 CGCAGATGTTTCATGATTTACCGGGAGTTA 2 72 1 TCATGATTTA 0.816838 -201 CTGTGAATACTCATGTATTCAGCCACCCTT 2 124 0 TCATGTATTC 0.87945 -149 CTCTGCGTCGTCCTCACTTCAGGTAAGGCT 2 152 0 TCCTCACTTC 0.960021 -121 ACTCTGTGCATCCTCTCTGCGTCGTCCTCA 2 166 0 TCCTCTCTGC 0.943066 -107 GCTTGTCTTCCTGTTTTATTGTGTCACC 2 255 0 TCCTGTTTTA 0.94373 -18 CTAAGACATATCATGATTTATAAAAACAAA 4 110 0 TCATGATTTA 0.816838 -191 GTAATCATCCTTTCTGACATCATA 4 287 0 TCATCCTTTC 0.918603 -14 ********** Masking position 8 Map Score: 6.89676 Number of sites scoring better than the average of aligned sites = 622 Number in coding regions = 508 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 6 ********** No masking Map Score: -6.44162e-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 7 ********** No masking Map Score: -6.44162e-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: -6.44162e-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