AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -inarL_hpyl_opreg_300.orf -g0.389 -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 = 0.389 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HP0144 300 cytochrome c oxidase, heme b and copper-binding subunit, membrane-bound (fixN) #2 HP0193 214 fumarate reductase, cytochrome b subunit (frdC) #3 HP0376 55 ferrochelatase (hemH) #4 HP0377 76 thiol:disulfide interchange protein (dsbC), putative Motif number 1 CATGAAAATACAAAAATAAAGCCAAGCGTT 1 25 1 CAAAAATAAA 0.932227 -276 CGGTGCGCCTAAAAAATACAACAGCGTTGC 1 70 1 AAAAAATACA 0.932227 -231 ATGTTACAGAAAAAGATTAAAAATTAAGCT 1 213 1 AAAAGATTAA 0.978025 -88 ATCTTTTTCAAAAAGCTTAATTTTTAATCT 1 226 0 AAAAGCTTAA 0.961349 -75 AGCTTTTTGAAAAAGATAAAATTTTATAAT 1 239 1 AAAAGATAAA 0.986926 -62 GTAAATTCAACAAAGATAAACATAATTATA 1 263 0 CAAAGATAAA 0.963183 -38 CTAAATTGAGAAAAAATTCAATTCAAAGGG 2 93 0 AAAAAATTCA 0.890231 -122 TCTTATAAACAAAACCTAAATTGAGAAAAA 2 108 0 AAAACCTAAA 0.890266 -107 AACTGCTCCTAAAAACTCAAAATTAACCTA 2 192 0 AAAAACTCAA 0.854931 -23 AACGATTAATAAAAAATAAATCGTTAGAAA 3 18 0 AAAAAATAAA 0.975423 -38 TGCTAAAATAAAACGATTAATAAAAAATAA 3 29 0 AAACGATTAA 0.884267 -27 CAAATCTATTAAAAGATAAAGGTTATTAC 4 58 1 AAAAGATAAA 0.986926 -19 ********** Masking position 3 Map Score: 21.6059 Number of sites scoring better than the average of aligned sites = 551 Number in coding regions = 413 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 2 CGCTGTTGTATTTTTTAGGCGCACCGGATG 1 66 0 TTTTTTAGGC 0.877832 -235 TTCTTGCCCCTTTTTTTATCGCAACGCTGT 1 90 0 TTTTTTTATC 0.942209 -211 TGATGAGGGTTTGTTTAATCATGTTTAACC 1 120 1 TTGTTTAATC 0.931113 -181 TTGTTTAATCATGTTTAACCTTTAGCCAAA 1 130 1 ATGTTTAACC 0.782139 -171 TTTGAATGGCATTTTTAAGCCAAATTGCTA 1 165 0 ATTTTTAAGC 0.970532 -136 AAAAAGCTTAATTTTTAATCTTTTTCTGTA 1 217 0 ATTTTTAATC 0.968152 -84 CATAATTATAAAATTTTATCTTTTTCAAAA 1 243 0 AAATTTTATC 0.416299 -58 AAAATTTACATTTTTTAAACGCTATTAGAT 2 53 0 TTTTTTAAAC 0.928016 -162 AAAAAATGTAAATTTTAAACAATAGCCCCT 2 67 1 AATTTTAAAC 0.694466 -148 TTTGAATTGAATTTTTTCTCAATTTAGGTT 2 96 1 ATTTTTTCTC 0.726052 -119 CGATTTATTTTTTATTAATCGTTTTATTTT 3 25 1 TTTATTAATC 0.789376 -31 ATTAATCGTTTTATTTTAGCATGCACCA 3 38 1 TTATTTTAGC 0.814221 -18 CAATAATCGCTTTTTTATGCGCATTTTA 4 9 0 TTTTTTATGC 0.829003 -68 ********** Masking position 5 Map Score: 11.0283 Number of sites scoring better than the average of aligned sites = 1550 Number in coding regions = 1323 Number in noncoding regions = 227 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 3 TTGTATTTTCATGGGCATGATTATAGG 1 3 0 ATCATATTTA 0.977665 -298 AGACCTAACGCTTGGCTTTATTTTTGTATTTTCAT 1 26 0 CTCTTATTTT 0.908303 -275 GATTAAACAAACCCTCATCATTCTTGCCCCTTTTT 1 105 0 ACCATATTTT 0.94839 -196 ATCTTTTTCAAAAAGCTTAATTTTTAATCTTTTTC 1 221 0 AACTTATTTT 0.822226 -80 TTCAACAAAGATAAACATAATTATAAAATTTTATC 1 253 0 ATCATATTTA 0.977665 -48 GCAATACTCCTATTTGTAGTAAATTCAA 1 283 0 ATCCTTTTTA 0.929158 -18 TGAACGATCCTTATTTTATAGGTGGTAA 2 4 1 ACCCTATTTA 0.974118 -211 TAGGTGGTAACTATCCCTTATTATATCTAATAGCG 2 29 1 CTCCTATTTA 0.953025 -186 ATTGTTTAAAATTTACATTTTTTAAACGCTATTAG 2 55 0 ATCATTTTAA 0.579837 -160 ACGCAAAAACACTGCCTTAATTCTACTACATTTGA 2 147 0 ACCTTATTTA 0.968912 -68 GTAATAACCTTTATCTTTTAATAGATTT 4 59 0 ATCTTATCTT 0.829362 -18 ** *** *** ** Masking position 8 Map Score: 7.24405 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 201 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 4 TGGCATTTTTAAGCCAAATTGCTACTATCT 1 159 0 AAGCCAAATT 0.818751 -142 ATCCCATTTGAATGGCATTTTTAAGCCAAA 1 171 0 AATGGCATTT 0.882711 -130 GTAATAACTCAATCCCATTTGAATGGCATT 1 182 0 AATCCCATTT 0.960976 -119 TACATTTTTTAAACGCTATTAGATATAATA 2 47 0 AAACGCTATT 0.750901 -168 AGCCCCTTTGAATTGAATTTTTTCTCAATT 2 90 1 AATTGAATTT 0.765277 -125 TTTTTGCGTCAAGCGATTTTAGGTTAATTT 2 173 1 AAGCGATTTT 0.955975 -42 TCGCTTTTTTATGCGCATTTTA 4 3 0 ATGCGCATTT 0.940857 -74 TTACTACAATAATCGCTTTTTTATGCGCAT 4 15 0 AATCGCTTTT 0.964748 -62 ********** Masking position 1 Map Score: 3.97814 Number of sites scoring better than the average of aligned sites = 1563 Number in coding regions = 1412 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 5 TTAGCCAAAGATAGTAGCAATTTGGCTTAAAAA 1 151 1 ATAGAGAATT 0.948993 -150 TTTCTGTAACATTGTAATAACTCAATCCCATTT 1 192 0 ATTGAAAATC 0.893551 -109 TTACAATGTTACAGAAAAAGATTAAAAATTAAG 1 208 1 ACAGAAAGTT 0.740718 -93 AATTAAGCTTTTTGAAAAAGATAAAATTTTATA 1 234 1 TTTGAAAGTA 0.762356 -67 AATACTCCTATTTGTAGTAAATTCAACAAAGAT 1 276 0 TTTGAGAATT 0.964587 -25 AAACCTAAATTGAGAAAAAATTCAATTCAAAGG 2 94 0 TGAGAAAATC 0.741692 -121 TTCTACTACATTTGAAATAATTTTTCTTATAAA 2 129 0 TTTGAAAATT 0.961747 -86 TTTTGAGTTTTTAGGAGCAGTTTTT 2 200 1 TTAGAGAGTT 0.950966 -15 AAATAAATCGTTAGAAAGAAGTTA 3 2 0 TTAGAAAATT 0.961747 -54 AAAAGCGATTATTGTAGTAAGATACCTAGTTTT 4 25 1 ATTGAGAAAT 0.723595 -52 **** ** ** ** Masking position 6 Map Score: 3.83357 Number of sites scoring better than the average of aligned sites = 379 Number in coding regions = 325 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 6 TCATCATTCTTGCCCCTTTTTTTATCGCAA 1 96 0 TGCCCCTTTT 0.957414 -205 GGCATTTTTAAGCCAAATTGCTACTATCTT 1 158 0 AGCCAAATTG 0.669651 -143 TCCCATTTGAATGGCATTTTTAAGCCAAAT 1 170 0 ATGGCATTTT 0.815414 -131 TAATAACTCAATCCCATTTGAATGGCATTT 1 181 0 ATCCCATTTG 0.973296 -120 TTTAAACAATAGCCCCTTTGAATTGAATTT 2 80 1 AGCCCCTTTG 0.984229 -135 CGCTTTTTTATGCGCATTTTA 4 2 0 TGCGCATTTT 0.953802 -75 TACTACAATAATCGCTTTTTTATGCGCATT 4 14 0 ATCGCTTTTT 0.874753 -63 ********** Masking position 8 Map Score: 1.49261 Number of sites scoring better than the average of aligned sites = 1031 Number in coding regions = 947 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 7 ********** No masking Map Score: 1.57984e-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 8 ********** No masking Map Score: 1.57984e-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: 1.57984e-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