AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00471_bsub_reg_100.orf -o00471_bsub_100.ace -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 mraY 112 phospho-N-acetylmuramoyl-pentapeptide transferase #2 yrpC 300 similar to glutamate racemase #3 ysmB 243 similar to transcriptional regulator (MarR family) #4 murC 249 UDP-N-acetyl muramate-alanine ligase Motif number 1 TGTCCTTTTCTCCTCCTGTTTCTTTCAAACGA 1 91 0 TTCTCGTTTC 0.951854 -22 AAATCTAAATACTCCTACATTTTCAAAGCTAATT 2 43 1 ATCTCTTTTC 0.988187 -258 ATTTCGATCTTATCTCCCCTTCTCAAGTTTTGCT 2 153 1 TTCCCTTCTC 0.932581 -148 CTTCTCAAGTTTTGCTCCCTATTCGAATAATCGA 2 171 1 TTGTCTATTC 0.822386 -130 TGAATAGTAAAATGGTTCTTTTTCGTTTGATTCA 2 223 1 ATGTCTTTTC 0.966709 -78 ACGCTTTCTGTCTCATTCTTTTTTTATCATATGA 2 269 0 TTCTCTTTTT 0.957765 -32 CACTTCTCACGCTTTCTGTCTCATTCTT 2 283 0 TTCCCTTCTG 0.859888 -18 CCTTGCCGGTATTCCTTCTTTTGGAAGGAGCCGG 3 12 1 ATCTCTTTGG 0.864344 -232 AATTTATGACTTGCCTACGTTTTGCACAGCATTC 3 84 0 TGCTCTTTTG 0.946547 -160 CTCTCCTGCGAGTCTTGCATTTTCTTCAAAAAAG 3 160 1 ATCTCTTTTC 0.988187 -84 CCGTGTCTATTTTCCTTCTTTTTTGAAGAAAATG 3 177 0 TTCTCTTTTT 0.957765 -67 TATGGGTTCATTTTCACACCAAACA 4 2 1 AGGTCTTTTC 0.909615 -248 * ** * * ***** Masking position 8 Map Score: 10.9359 Number of sites scoring better than the average of aligned sites = 1480 Number in coding regions = 1223 Number in noncoding regions = 257 Number of orfs with sites within 600 bp upstream = 300 Fraction of orfs with sites within 600 bp upstream = 0.048185 Motif number 2 AAAAGATTTTTCATATGGAAAAAAATCATGAATA 1 42 1 TCAATGAAAA 0.986579 -71 ACTACGTATGTCGTTTGAAAGAAACAGGAGGAGA 1 81 1 TCGTTGAAAA 0.919055 -32 ATCATCTGAATCAAACGAAAAAGAACCATTTTAC 2 229 0 TCAACGAAGA 0.90676 -72 TTCGTTTGATTCAGATGATATAAAGTCATATGAT 2 244 1 TCAATGAAAA 0.986581 -57 TGATATAAAGTCATATGATAAAAAAAGAATGAGA 2 259 1 TCAATGAAAA 0.986581 -42 AAATATGGTTTCGAATGTTCCAAACAAACAGCAA 3 49 0 TCGATGCAAA 0.983455 -195 AATGCAAGACTCGCAGGAGAGAAATAGAGGACTT 3 147 0 TCGAGGAAAA 0.956847 -97 CTCAAGGATCTCTTACGCACAAAAGCGTTCCGTG 3 206 0 TCTACGCAAA 0.893746 -38 GGCATAGCTGTTAAATGCTCTAAACACTATCATA 4 39 0 TTAATGCAAA 0.856012 -211 *** *** * *** Masking position 12 Map Score: 8.31398 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 183 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 3 CCTGTTTCTTTCAAACGACATACGTAGTTA 1 79 0 TCAAACGACA 0.98904 -34 AATCGGGTTATCAATCATCACATTGATACG 2 79 1 TCAATCATCA 0.908097 -222 ATCATCTGAATCAAACGAAAAAGAACCATT 2 233 0 TCAAACGAAA 0.933158 -68 AATGTTCCAAACAAACAGCAATAACCGGCT 3 40 0 ACAAACAGCA 0.947487 -204 AGGACTTTAGTCAAACAACATCAAGAAATA 3 124 0 TCAAACAACA 0.982874 -120 TGTACCTCCAACAAACGTCTATCTGTTCCC 4 227 0 ACAAACGTCT 0.892789 -23 ********** Masking position 4 Map Score: 3.06167 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 250 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 4 ATTCAAATTAGCTTTGAAAATGTAGGAGTA 2 52 0 GCTTTGAAAA 0.962384 -249 TATTTGGAATGCTGTGCAAAACGTAGGCAA 3 78 1 GCTGTGCAAA 0.993107 -166 TACCATGTTTGGTGTGAAAATGAACCCATA 4 11 0 GGTGTGAAAA 0.974306 -239 AAGCGGCATAGCTGTTAAATGCTCTAAACA 4 47 0 GCTGTTAAAT 0.886058 -203 CTTTACAGCAGCTGTGCATAGACAAATCTT 4 74 1 GCTGTGCATA 0.97768 -176 ********** Masking position 5 Map Score: 2.74549 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 187 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 TGAAAAAGATTTTTCATATGGAAAAAAATC 1 39 1 TTTTCATATG 0.978042 -74 ACATACGTAGTTATCATATTCATGATTTTT 1 62 0 TTATCATATT 0.873266 -51 TACTATTCAAATTTAATATGGGAGCTATCG 2 202 0 ATTTAATATG 0.895124 -99 ATATGACTTTATATCATCTGAATCAAACGA 2 245 0 ATATCATCTG 0.94215 -56 CATTCTTTTTTTATCATATGACTTTATATC 2 260 0 TTATCATATG 0.978042 -41 TTAGCGGCGTATTTTATATGTTTTGTTATG 4 145 0 ATTTTATATG 0.895124 -105 ********** Masking position 6 Map Score: 2.50169 Number of sites scoring better than the average of aligned sites = 434 Number in coding regions = 367 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 6 TTTCAAAGCTAATTTGAATCGGGTTATCAAT 2 63 1 AATTTGAATG 0.93956 -238 GAAATTATCAAGATCGCATCGTATCAATGTG 2 97 0 AGATCGCATG 0.836828 -204 AGGGGAGATAAGATCGAAATGTTGGTAATGT 2 142 0 AGATCGAAAG 0.933145 -159 AGCTATCGATTATTCGAATAGGGAGCAAAAC 2 179 0 TATTCGAATG 0.939162 -122 TCCCATATTAAATTTGAATAGTAAAATGGTT 2 209 1 AATTTGAATG 0.939798 -92 TTCGAAACCATATTTGGAATGCTGTGCAAAA 3 68 1 TATTTGGAAG 0.866889 -176 TATCTGGGTTTAATCGGAAAGAAATAACCTG 4 106 1 TAATCGGAAG 0.912184 -144 CCGCGGTCGCAAATTGAAATGAGCGTCATAT 4 192 1 AAATTGAAAG 0.93936 -58 ********* * Masking position 8 Map Score: 2.70578 Number of sites scoring better than the average of aligned sites = 375 Number in coding regions = 322 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 7 TCATATGGAAAAAAATCATGAATATGATAA 1 52 1 AAAAATCATG 0.75118 -61 CGAATAGGGAGCAAAACTTGAGAAGGGGAG 2 166 0 GCAAAACTTG 0.9487 -135 GGAATGCTGTGCAAAACGTAGGCAAGTCAT 3 83 1 GCAAAACGTA 0.907405 -161 CAAAACGTAGGCAAGTCATAAATTAAATTT 3 94 1 GCAAGTCATA 0.816087 -150 TCATTTTCACACCAAACATGGTATGATAGT 4 18 1 ACCAAACATG 0.930289 -232 CTGTGCATAGACAAATCTTGATATCTGGGT 4 85 1 ACAAATCTTG 0.921636 -165 ATAACCTGATACTAAACATAACAAAACATA 4 129 1 ACTAAACATA 0.850224 -121 ACTAAACATAACAAAACATATAAAATACGC 4 139 1 ACAAAACATA 0.964718 -111 ********** Masking position 4 Map Score: 2.7662 Number of sites scoring better than the average of aligned sites = 462 Number in coding regions = 378 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 8 TTATCAAGATCGCATCGTATCAATGTGATG 2 94 0 CGCATCGTAT 0.926539 -207 GCTGCTGTAAAGCGGCATAGCTGTTAAATG 4 56 0 AGCGGCATAG 0.980431 -194 AGCCTCCCTTAGCGGCGTATTTTATATGTT 4 153 0 AGCGGCGTAT 0.992482 -97 AATTGAAATGAGCGTCATATACTGGGGAAC 4 203 1 AGCGTCATAT 0.982215 -47 ********** Masking position 8 Map Score: 0.323768 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 77 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 ********** No masking Map Score: 1.21035e-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: 1.21035e-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 11 ********** No masking Map Score: 1.21035e-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