AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -inarL_hpyl_opreg_100.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 AACGCTTGGCTTTATTTTTGTATTTTCATG 1 25 0 TTTATTTTTG 0.941538 -276 GCAACGCTGTTGTATTTTTTAGGCGCACCG 1 70 0 TGTATTTTTT 0.941538 -231 AGCTTAATTTTTAATCTTTTTCTGTAACAT 1 213 0 TTAATCTTTT 0.981171 -88 AGATTAAAAATTAAGCTTTTTGAAAAAGAT 1 226 1 TTAAGCTTTT 0.966797 -75 ATTATAAAATTTTATCTTTTTCAAAAAGCT 1 239 0 TTTATCTTTT 0.988812 -62 TATAATTATGTTTATCTTTGTTGAATTTAC 1 263 1 TTTATCTTTG 0.968386 -38 CCCTTTGAATTGAATTTTTTCTCAATTTAG 2 93 1 TGAATTTTTT 0.904722 -122 TTTTTCTCAATTTAGGTTTTGTTTATAAGA 2 108 1 TTTAGGTTTT 0.904753 -107 TAGGTTAATTTTGAGTTTTTAGGAGCAGTT 2 192 1 TTGAGTTTTT 0.87342 -23 TTTCTAACGATTTATTTTTTATTAATCGTT 3 18 1 TTTATTTTTT 0.978934 -38 TTATTTTTTATTAATCGTTTTATTTTAGCA 3 29 1 TTAATCGTTT 0.899457 -27 GTAATAACCTTTATCTTTTAATAGATTTG 4 58 0 TTTATCTTTT 0.988812 -19 ********** Masking position 4 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 TATTTTTGTATTTTCATGGGCATGATTATAGG 1 11 0 TTTTCAGGCA 0.976715 -290 GCTGTTGTATTTTTTAGGCGCACCGGATGGGT 1 63 0 TTTTTAGGCA 0.994481 -238 CTTGCCCCTTTTTTTATCGCAACGCTGTTGTA 1 86 0 TTTTTACCAA 0.867705 -215 TTGAATGGCATTTTTAAGCCAAATTGCTACTA 1 162 0 TTTTTAGCAA 0.971524 -139 AAATTTACATTTTTTAAACGCTATTAGATATA 2 50 0 TTTTTAAGCT 0.892601 -165 ATTTAGGTTTTGTTTATAAGAAAAATTATTTC 2 117 1 TGTTTAAGAA 0.804418 -98 TAAGGCAGTGTTTTTGCGTCAAGCGATTTTAG 2 163 1 TTTTTGGCAA 0.936137 -52 TAATTTTGAGTTTTTAGGAGCAGTTTTT 2 197 1 TTTTTAGGCA 0.994446 -18 AATCGTTTTATTTTAGCATGCACCA 3 41 1 TTTTAGAGCA 0.800142 -15 AATAATCGCTTTTTTATGCGCATTTTA 4 6 0 TTTTTAGGCA 0.994453 -71 ****** * *** Masking position 4 Map Score: 11.4243 Number of sites scoring better than the average of aligned sites = 588 Number in coding regions = 527 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 3 AGGGTTTGTTTAATCATGTTTAACCTTTAGC 1 125 1 TAATATGTTT 0.973907 -176 TAAAATTTTATAATTATGTTTATCTTTGTTG 1 255 1 TAATATGTTT 0.973907 -46 TTATTATATCTAATAGCGTTTAAAAAATGTA 2 46 1 TAATGCGTTT 0.981687 -169 ACTACATTTGAAATAATTTTTCTTATAAACA 2 127 0 AAATATTTTT 0.830255 -88 TATTTTTTATTAATCGTTTTATTTTAGCATG 3 30 1 TAATGTTTTA 0.856149 -26 CTTACTACAATAATCGCTTTTTTATGCGCAT 4 15 0 TAATGCTTTT 0.971924 -62 GTAATAACCTTTATCTTTTAAT 4 65 0 TAATACCTTT 0.943632 -12 **** ****** Masking position 3 Map Score: 4.89628 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 160 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 4 TTAGCCAAAGATAGTAGCAATTTGGCTTAA 1 151 1 ATAGTAGCAA 0.92789 -150 TTTCTGTAACATTGTAATAACTCAATCCCA 1 195 0 ATTGTAATAA 0.947491 -106 AATACTCCTATTTGTAGTAAATTCAACAAA 1 279 0 TTTGTAGTAA 0.965284 -22 AATTATTTCAAATGTAGTAGAATTAAGGCA 2 140 1 AATGTAGTAG 0.928118 -75 AAAAGCGATTATTGTAGTAAGATACCTAGT 4 25 1 ATTGTAGTAA 0.989433 -52 ********** Masking position 5 Map Score: 2.50753 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 11 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 5 CATCATTCTTGCCCCTTTTTTTATCGCAAC 1 95 0 GCCCCTTTTT 0.967371 -206 CCCATTTGAATGGCATTTTTAAGCCAAATT 1 169 0 TGGCATTTTT 0.787755 -132 AATAACTCAATCCCATTTGAATGGCATTTT 1 180 0 TCCCATTTGA 0.972744 -121 GCAATACTCCTATTTGTAGTAAATTCA 1 284 0 TCCTATTTGT 0.799728 -17 GTGGTAACTATCCCTTATTATATCTAATAG 2 32 1 TCCCTTATTA 0.77799 -183 TTAAACAATAGCCCCTTTGAATTGAATTTT 2 81 1 GCCCCTTTGA 0.966733 -134 GCTTTTTTATGCGCATTTTA 4 1 0 GCGCATTTTA 0.956485 -76 ACTACAATAATCGCTTTTTTATGCGCATTT 4 13 0 TCGCTTTTTT 0.92319 -64 ********** Masking position 6 Map Score: 3.93519 Number of sites scoring better than the average of aligned sites = 1129 Number in coding regions = 998 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 6 ********** 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 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