AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i173_1_17_4_2_ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 nrdG 50 anaerobic ribonucleotide reductase activating protein #2 BIME230 22 BIME #3 nrdD 300 anaerobic ribonucleoside-triphosphate reductase #4 HI1155 247 anaerobic ribonucleoside-triphosphate reductase activating protein (nrdG) #5 HI1157 71 ATP-binding protein protein (cydD) #6 HI1158 73 thioredoxin reductase (trxB) #7 HI1159 284 conserved hypothetical protein #8 HI1161 300 conserved hypothetical protein Motif number 1 GCAATCGCCATCCGCTTATCCACAACGCCG 3 193 0 TCCGCTTATC 0.673811 -108 TGGGAAGGTTTCCGCCCAACTTCCTTTTC 4 10 0 TCCGCCCAAC 0.90455 -238 TCTAACCAATTCCCCTCTTTTAACTCTTTT 5 15 1 TCCCCTCTTT 0.95184 -57 TAGAAAAAGTTCCCCTCTTTAAAAGAGTTA 5 35 0 TCCCCTCTTT 0.95184 -37 TCTAAAATCTTCCGCACTTTGCTAAAATCA 7 32 1 TCCGCACTTT 0.82009 -253 TGCCAAAAAATCCGCCGATTCTTTATGCGT 7 193 0 TCCGCCGATT 0.905082 -92 TCCCCCCATAAATGGGTGGA 8 1 1 TCCCCCCATA 0.989659 -300 TAATCTTGGCTCCACCCATTTATGGGGGGA 8 11 0 TCCACCCATT 0.965023 -290 TTCGGGCACCTTCCCCCACAAGCAGGGGAA 8 103 0 TTCCCCCACA 0.778957 -198 TATCCCTATATCCCCCTTCCCTTCGGGCAC 8 124 0 TCCCCCTTCC 0.851547 -177 TGAACATTTATCCCCCCTCACCTTCGGCAG 8 228 1 TCCCCCCTCA 0.971581 -73 CTTCGGCAGCTCCCCCCATAAATGGGTGGA 8 249 1 TCCCCCCATA 0.989659 -52 TTATCTTGGCTCCACCCATTTATGGGGGGA 8 259 0 TCCACCCATT 0.965023 -42 ********** Masking position 1 Map Score: 18.0314 Number of sites scoring better than the average of aligned sites = 384 Number in coding regions = 324 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 2 GTACGCTCTGCTTTTTACTTTGAGCTACATCA 3 43 1 CTTTTCTTTG 0.911507 -258 GATGTTTGAGCTTTTTTTGATGTAGCTCAAAG 3 60 0 CTTTTTGATG 0.716482 -241 ATTAATACAACATATTGGGTTGGGACGCATTT 3 122 0 CTATTGGTTG 0.834675 -179 CAACGCCGCACCTTTTTCGTGGGGAGCTGTAG 3 169 0 CTTTTCGTGG 0.988089 -132 TTTTTCGTTTCGTTTTCCGGTGCTTTCCGCAA 3 219 0 CTTTTCGGTG 0.985288 -82 TTGGGAAAGGCGTTTTCCGGTTTTTTCGTTTC 3 240 0 CTTTTCGGTT 0.8152 -61 ACGCCTTTCCCAATTTCTGTGGATAACCTGTT 3 259 1 CATTTTGTGG 0.839857 -42 GCTGATTTTCCTTTTATCGTTGAGATCAACGA 7 93 1 CTTTACGTTG 0.974152 -192 TCCGCCGATTCTTTATGCGTTGGCGCGTAAAA 7 181 0 CTTATCGTTG 0.896518 -104 TGGCTCCACCCATTTATGGGGGGA 8 3 0 CTTTAGGGGG 0.948484 -298 GTACCTAAAACAATTTAGGTTGAAATTGAACA 8 202 1 CATTTGGTTG 0.938383 -99 TGGCTCCACCCATTTATGGGGGGAGCTGCCGA 8 251 0 CTTTAGGGGG 0.948484 -50 TCCATATTATCAATTATCTTGGCTCCACCCAT 8 270 0 CATTACTTGG 0.609367 -31 * **** ***** Masking position 1 Map Score: 11.6998 Number of sites scoring better than the average of aligned sites = 931 Number in coding regions = 822 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 3 AAAGCACTATATATAGACTTTAAAATGCGTCCCAA 3 100 1 ATAGATAAAA 0.951979 -201 TTCATAAGAATCCTAAAAATGTGGCTTA 4 230 0 ATAAATAAAA 0.948578 -18 GTTCCCCTCTTTAAAAGAGTTAAAAGAGGGGAATT 5 22 0 TTAAGTAAAA 0.952327 -50 GCAAAAAGTTTATAATCAGTAAAATGCAACTTAT 6 10 1 TTAATTAAAA 0.869376 -64 TAATAGAAATGGTAAAACGTTTCTAAA 7 3 1 ATAAATAAAA 0.948578 -282 CATTATTTTTTTCACAAGGATAAAACATGGCTGAT 7 64 1 TTCAATAAAA 0.856279 -221 TTGTTCGTTGATCTCAACGATAAAAGGAAAATCAG 7 94 0 ATCAATAAAA 0.876236 -191 GGAGCCAAGATTAGAGGTTCTAAAATAAATAATGA 8 28 1 TTAGGTAAAA 0.955453 -273 CTTCTGCTTATTAGAGGTTTTAAAAACTTGCCTTC 8 71 1 TTAGGTAAAA 0.955484 -230 GGATATAGGGATATGCGAAATAAAATTTTGGAGTG 8 141 1 ATACGTAAAA 0.879629 -160 AAAAACATAGATAATGTACCTAAAACAATTTAGGT 8 187 1 ATAGTTAAAA 0.896847 -114 *** ** ***** Masking position 12 Map Score: 7.40216 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 119 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 4 GCTACTACAGCTCCCCACGAAAAAGGTGCG 3 165 1 CTCCCCACGA 0.937247 -136 TCCCCCCATAAATGGGTGGAG 8 2 1 CCCCCCATAA 0.992716 -299 TCGGGCACCTTCCCCCACAAGCAGGGGAAG 8 102 0 TCCCCCACAA 0.986379 -199 TATCCCTATATCCCCCTTCCCTTCGGGCAC 8 124 0 TCCCCCTTCC 0.902137 -177 GAACATTTATCCCCCCTCACCTTCGGCAGC 8 229 1 CCCCCCTCAC 0.989608 -72 TTCGGCAGCTCCCCCCATAAATGGGTGGAG 8 250 1 CCCCCCATAA 0.992716 -51 ********** Masking position 5 Map Score: 5.37672 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 69 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 5 GTTGTGGATAAGCGGATGGCGATTGCGGAA 3 197 1 AGCGGATGGC 0.973079 -104 GGATGGCGATTGCGGAAAGCACCGGAAAAC 3 210 1 TGCGGAAAGC 0.98387 -91 TGCGGAAAGCACCGGAAAACGAAACGAAAA 3 220 1 ACCGGAAAAC 0.926967 -81 AAACGAAAAAACCGGAAAACGCCTTTCCCA 3 241 1 ACCGGAAAAC 0.926967 -60 CCACAGAAATTGGGAAAGGCGTTTTCCGGT 3 251 0 TGGGAAAGGC 0.847498 -50 CTCGGTCAGGTCCGGAAGGAAGCAGCCAAA 4 69 0 TCCGGAAGGA 0.914598 -179 TTTAGCAAAGTGCGGAAGATTTTAGAAACG 7 28 0 TGCGGAAGAT 0.87198 -257 ACCTCTAATAAGCAGAAGGCAAGTTATCAT 8 59 0 AGCAGAAGGC 0.957407 -242 CCCCACAAGCAGGGGAAGGCAAGTTTTTAA 8 90 0 AGGGGAAGGC 0.985884 -211 ********** Masking position 6 Map Score: 8.45308 Number of sites scoring better than the average of aligned sites = 1290 Number in coding regions = 1208 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 6 GGTCCGGAAGGAAGCAGCCAAAGTCGGAAT 4 61 0 GAAGCAGCCA 0.973588 -187 CTGACCGAGTAAACCAGACACCGTTGCGAG 4 90 1 AAACCAGACA 0.940048 -158 CACTTTGCTAAAATCAGCCATTATTTTTTT 7 46 1 AAATCAGCCA 0.992882 -239 GATAAAAGGAAAATCAGCCATGTTTTATCC 7 81 0 AAATCAGCCA 0.992882 -204 TAGTGCCAAAAAATCCGCCGATTCTTTATG 7 196 0 AAATCCGCCG 0.965881 -89 ********** Masking position 3 Map Score: 2.52705 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 214 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 7 AGGTGCGGCGTTGTGGATAAGCGGATGGCG 3 188 1 TTGTGGATAA 0.974547 -113 TTCCCAATTTCTGTGGATAACCTGTTCTTA 3 265 1 CTGTGGATAA 0.958834 -36 TGTTTTATCCTTGTGAAAAAAATAATGGCT 7 61 0 TTGTGAAAAA 0.96165 -224 GAAAAGTAAATTGTGAAAAAGAGCGA 7 269 1 TTGTGAAAAA 0.96165 -16 ********** Masking position 4 Map Score: 1.00393 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 18 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 ATCCACAACGCCGCACCTTTTTCGTGGGGA 3 176 0 CCGCACCTTT 0.96464 -125 AAGGCGTTTTCCGGTTTTTTCGTTTCGTTT 3 236 0 CCGGTTTTTT 0.850394 -65 ACACAGTAATTCCGACTTTGGCTGCTTCCT 4 53 1 TCCGACTTTG 0.709085 -195 GCCAAATTCACCGCACTTTTGAATTAGTCT 4 193 0 CCGCACTTTT 0.991508 -55 AGAATTTAAGCCACATTTTTAGGATTCTTA 4 224 1 CCACATTTTT 0.780551 -24 CTAACCAATTCCCCTCTTTTAACTCTTTTA 5 16 1 CCCCTCTTTT 0.983123 -56 AGAAAAAGTTCCCCTCTTTAAAAGAGTTAA 5 34 0 CCCCTCTTTA 0.923625 -38 CTAAAATCTTCCGCACTTTGCTAAAATCAG 7 33 1 CCGCACTTTG 0.985101 -252 TCGCTCTTTTTCACAATTTA 7 275 0 TCGCTCTTTT 0.94914 -10 ********** Masking position 8 Map Score: 8.13545 Number of sites scoring better than the average of aligned sites = 534 Number in coding regions = 450 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 9 GTAGTTAAGTAATAATATAATGCAATAAGTTG 6 37 0 AATAATAATG 0.953831 -37 TATCCTTGTGAAAAAAATAATGGCTGATTTTA 7 54 0 AAAAATAATG 0.969181 -231 ACAAAATCTTACTGAAATACTGCAACAATCCT 7 125 1 ACTAATACTG 0.914358 -160 AGAGGTTCTAAAATAAATAATGATAACTTGCC 8 40 1 AAAAATAATG 0.969001 -261 ATATTAAAAAACATAGATAATGTACCTAAAAC 8 181 1 ACAAATAATG 0.971385 -120 *** * ****** Masking position 7 Map Score: 0.186453 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 28 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 10 ********** No masking Map Score: -1.07049e-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: -1.07049e-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 12 TATTAATCGACTATAATTGCTACTACAGCTCCC 3 147 1 CTAATTCTAC 0.960994 -154 TCTCGGCACACAGTAATTCCGACTTTGGCTGCT 4 46 1 CTAATTCGAC 0.980726 -202 TGCAATACGGCGGTAATTTCTGCATAATAGTGC 4 159 0 CTAATTCTGC 0.967481 -89 GGAACTTTTTCTATAATCACGACCAAAACA 5 52 1 CTAATCCGAC 0.983986 -20 AACCACTTGTCATCAATTTTTACGCGCCAACGC 7 164 1 CCAATTTTAC 0.785887 -121 ATTTTAGAACCTCTAATCTTGGCTCCACCCATT 8 21 0 CTAATCTGGC 0.97292 -280 TCCATATTATCAATTATCTTGGCTCCACCCATT 8 269 0 CTTATCTGGC 0.88178 -32 * ***** **** Masking position 6 Map Score: 1.27689 Number of sites scoring better than the average of aligned sites = 371 Number in coding regions = 348 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 13 ********** No masking Map Score: -1.07049e-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 14 ********** No masking Map Score: -1.07049e-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 15 ********** No masking Map Score: -1.07049e-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