AlignACE version 2.2 July 7, 1998 alignACE -z/skink1/amcguire/genomes/ecoli.fna -a/home/amcguire/alignace/lib/ORF_ecoli.txt -b/home/amcguire/alignace/lib/bimes_ecoli.txt -k0 -l300 -jmalT.reg -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 = 146 Input sequences: #1 malP 300 bp malP 797 1-2394 CDS #2 malS 300 bp malS 676 1-2031 CDS #3 malE_malK 364 bp malE 396 1-1191 CDS malK 371 1-1116 CDS Motif number 1 AGTGCAAACCACAGGATTAGCATCAAATCA 1 136 0 ACAGGATTAG 0.805535 -165 GGAGGAGTTGCGGGGATGAGCAAGGAAATG 1 187 0 CGGGGATGAG 0.995415 -114 GGGGATTAGGCAGGGAGGAGTTGCGGGGAT 1 200 0 CAGGGAGGAG 0.991959 -101 CTCATCCTGCGGGGGATTAGGCAGGGAGGA 1 211 0 GGGGGATTAG 0.975222 -90 CTAATCCCCCGCAGGATGAGGAAGGTCAAC 1 221 1 GCAGGATGAG 0.985859 -80 AAGAGCACCCCAAGGAATAGTCCAAATCTG 2 83 1 CAAGGAATAG 0.683151 -218 GGATGAGAAGCAAGGGTGAGCGATCTCGCG 2 196 0 CAAGGGTGAG 0.924976 -105 CGGTAAGTCCACAGGATGAGAAGCAAGGGT 2 209 0 ACAGGATGAG 0.958068 -92 ACTTACCGCTCAGGGATGAGTTTTGTTTGG 2 231 1 CAGGGATGAG 0.992681 -70 GGCGGATGAGTCCTTATTGC 2 291 0 GGCGGATGAG 0.972922 -10 GGCGTAGGGGCAAGGAGGATGGAAAGAGGT 3 80 0 CAAGGAGGAT 0.813074 -285 GGAGGAGGCGGGAGGATGAGAACACGGCTT 3 236 0 GGAGGATGAG 0.992662 -129 GCTTTTTTATGGGGGAGGAGGCGGGAGGAT 3 249 0 GGGGGAGGAG 0.994961 -116 AAAAAAGCCAGGGGGTGGAGGATTTAAGCC 3 271 1 GGGGGTGGAG 0.951062 -94 GGTTGTTACAAAGGGAGAAGGGC 3 352 1 AAGGGAGAAG 0.743661 -13 ********** Masking position 9 Map Score: 29.7728 Number of sites scoring better than the average of aligned sites = 405 Number in coding regions = 343 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 2 CGTTGCGTATTTTCAAAAAGCGGAAGGTAACT 1 59 0 TTTCAAAACG 0.890212 -242 CTGTATCTAAGTGCAAAAAATGGCCGTTGCGT 1 83 0 GTGCAAAATG 0.971708 -218 ATGCAATACAGCGCAGAAAATCTGTATCTAAG 1 104 0 GCGCAAAATC 0.969623 -197 TGGCGCTAAATCGCAGAAAATGTGGGGGTTAT 2 142 1 TCGCAAAATG 0.987864 -159 GAGCGATCTCGCGCAAAAAACGGCTGAATTTT 2 177 0 GCGCAAAACG 0.995167 -124 GTAACAGAGATCACACAAAGCGACGGTGGGGC 3 107 0 TCACAAAACG 0.984255 -258 GTGGAGATGCGCACATAAAATCGCCACGATTT 3 154 1 GCACAAAATC 0.9258 -211 GTGATGTTGCTTGCAAAAATCGTGGCGATTTT 3 170 0 TTGCAAAACG 0.981278 -195 TCGGTTTAGTTCACAGAAGCCGTGTTCTCATC 3 220 1 TCACAAAGCG 0.935921 -145 ***** *** ** Masking position 7 Map Score: 11.373 Number of sites scoring better than the average of aligned sites = 824 Number in coding regions = 764 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 3 TTTCCTTGCTCATCCCCGCAACTCCTCCCT 1 189 1 CATCCCCGCA 0.951157 -112 CCCCGCAACTCCTCCCTGCCTAATCCCCCG 1 202 1 CCTCCCTGCC 0.984326 -99 CGAGATCGCTCACCCTTGCTTCTCATCCTG 2 198 1 CACCCTTGCT 0.970247 -103 AAACAAAACTCATCCCTGAGCGGTAAGTCC 2 229 0 CATCCCTGAG 0.702557 -72 CTCTTTCCATCCTCCTTGCCCCTACGCCCC 3 82 1 CCTCCTTGCC 0.988789 -283 CCCTACGCCCCACCGTCGCTTTGTGTGATC 3 101 1 CACCGTCGCT 0.89243 -264 GCCGTGTTCTCATCCTCCCGCCTCCTCCCC 3 238 1 CATCCTCCCG 0.970673 -127 CATCCTCCCGCCTCCTCCCCCATAAAAAAG 3 248 1 CCTCCTCCCC 0.98716 -117 AAATCCTCCACCCCCTGGCTTTTTTATGGG 3 266 0 CCCCCTGGCT 0.959061 -99 GCCCTTCTCCCTTTGTAACAAC 3 353 0 CCTTCTCCCT 0.847617 -12 ********** Masking position 1 Map Score: 8.88889 Number of sites scoring better than the average of aligned sites = 1169 Number in coding regions = 1039 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 4 TACAGATTTTCTGCGCTGTATTGCATTGATTTGA 1 110 1 CTGCGTTAGC 0.976252 -191 CTAGCTTTAAGTGGTTGAGATCACATTTCCTTGC 1 164 1 GTGGTGGAAC 0.855458 -137 CTTCCTCATCCTGCGGGGGATTAGGCAGGGAGGA 1 211 0 CTGCGGGAAG 0.902159 -90 ATTCCTTGGGGTGCTCTTGACAGCTATTTTTGAT 2 67 0 GTGCTTGAGC 0.986234 -234 CCCACATTTTCTGCGATTTAGCGCCAATCTGAAT 2 134 0 CTGCGTTAGC 0.975428 -167 CGCAGAAAATGTGGGGGTTATCGCAAAATTCAGC 2 153 1 GTGGGGTAGC 0.948071 -148 CAGCCGTTTTTTGCGCGAGATCGCTCACCCTTGC 2 183 1 TTGCGGGAGC 0.979953 -118 GTCCTTATTGCTGCGATTTCAGACAGTTTGCCAG 2 268 0 CTGCGTTCAC 0.892413 -33 TGTTGGTGAAGTGCTCGTGAAAACACCTAAACGG 3 24 1 GTGCTGGAAC 0.980198 -341 AAGGAATTTCGTGATGTTGCTTGCAAAAATCGTG 3 178 0 GTGATTGCGC 0.732772 -187 ATCATGAATGTTGCTGTCGATGACAGGTTGTTAC 3 327 1 TTGCTTGAAC 0.912649 -38 ***** * ** ** Masking position 2 Map Score: 8.02319 Number of sites scoring better than the average of aligned sites = 1835 Number in coding regions = 1734 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 5 GAGCAAGGAAATGTGATCTCAACCACTTAA 1 170 0 ATGTGATCTC 0.91665 -131 TTTCAACACAACGTTATCGCTAGTTTGCCA 1 259 0 ACGTTATCGC 0.940228 -42 GAAAATGTGGGGGTTATCGCAAAATTCAGC 2 157 1 GGGTTATCGC 0.950705 -144 CGTTTTTTGCGCGAGATCGCTCACCCTTGC 2 187 1 GCGAGATCGC 0.642163 -114 AGTTTTGTTTGGCTTATCGCTGGCAAACTG 2 249 1 GGCTTATCGC 0.938306 -52 CCGTCGCTTTGTGTGATCTCTGTTACAGAA 3 113 1 GTGTGATCTC 0.957684 -252 ATGCGTCATCAGGAGATGGCTTAAATCCTC 3 288 0 AGGAGATGGC 0.883492 -77 ********** Masking position 6 Map Score: 4.74539 Number of sites scoring better than the average of aligned sites = 1114 Number in coding regions = 1076 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 6 TTTACTTATGAAACTGTTTCACTCCTTTAC 1 18 1 AAACTGTTTC 0.863169 -283 CAGCGCAGAAAATCTGTATCTAAGTGCAAA 1 98 0 AATCTGTATC 0.985566 -203 GAATAGTCCAAATCTGAAACTATGTCACGT 2 97 1 AATCTGAAAC 0.970809 -204 ATTTAGCGCCAATCTGAATCGTTAACACGT 2 123 0 AATCTGAATC 0.979446 -178 ATTACCGCCAATTCTGTAACAGAGATCACA 3 124 0 ATTCTGTAAC 0.935419 -241 ********** Masking position 5 Map Score: 3.3114 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 26 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 CGTTATCGCTAGTTTGCCAGGCTCGATGTT 1 248 0 AGTTTGCCAG 0.981109 -53 AAACGGCTGAATTTTGCGATAACCCCCACA 2 162 0 ATTTTGCGAT 0.888459 -139 GATTTCAGACAGTTTGCCAGCGATAAGCCA 2 258 0 AGTTTGCCAG 0.981109 -43 GGATGGAAAGAGGTTGCCGTATAAAGAAAC 3 64 0 AGGTTGCCGT 0.982475 -301 CCCATCATGAATGTTGCTGTCGATGACAGG 3 324 1 ATGTTGCTGT 0.862312 -41 ********** Masking position 5 Map Score: 0.185592 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 220 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 ********** No masking Map Score: -9.92328e-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: -9.92328e-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 10 ********** No masking Map Score: -9.92328e-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