AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -icpxR6_hinf_opreg_100.orf -g0.38 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HI0079 102 peptidyl-prolyl cis-trans isomerase B (ppiB) #2 HI0837 53 response regulator (cpxR) #3 HI0839 116 conserved hypothetical protein #4 HI0845 86 conserved hypothetical protein #5 HI1004 272 peptidyl-prolyl cis-trans isomerse, putative #6 HI1259 193 periplasmic serine protease Motif number 1 GTTTGTTTTTATTTCATTTTACGAGCTTAA 1 13 0 ATTTCATTTT 0.974405 -90 TCTTTTTATTTTCACCACACTA 2 3 1 TTTTTATTTT 0.952418 -51 TGGAGATTCCTTTTACCAATTATT 2 40 0 GATTCCTTTT 0.770564 -14 AGCCAAATTTTTTTTATTTTTAACATT 3 8 0 TTTTTATTTT 0.952418 -109 GAACCTAAATAATTTCTTTTTTCTTGCTGA 3 60 1 AATTTCTTTT 0.93689 -57 TTTCATTGCTATTTCCTTTTTAATCGTAAA 4 51 0 ATTTCCTTTT 0.96901 -36 TGCTATTTCCTTTTTATTTCATTG 4 73 0 ATTTCCTTTT 0.96901 -14 GAGGATGGAGTTTTCACTTTTTAAGATGCT 5 109 1 TTTTCACTTT 0.85357 -164 AGATGCTAATTTTTTACGTTTAGATTATAA 5 132 1 TTTTTACGTT 0.629308 -141 AATCGGGAAAATTTTATATTTATAACAAGG 5 160 1 ATTTTATATT 0.802546 -113 AAGATTTCTAAATTTATCTTAGGTTTGATT 5 234 1 AATTTATCTT 0.756255 -39 AAATTCTATAAATTTATGTTCTAATACGCG 6 41 0 AATTTATGTT 0.85096 -153 TACTGCTCCGATTTCCTTTTAAACAAGATA 6 93 1 ATTTCCTTTT 0.96901 -101 TTGAACATTTTTTTTATTTTTTTGTCTTAC 6 139 1 TTTTTATTTT 0.952418 -55 CGTTATCTGAAATTTATTTTGGAGTATTT 6 175 1 AATTTATTTT 0.947556 -19 ********** Masking position 4 Map Score: 21.8837 Number of sites scoring better than the average of aligned sites = 912 Number in coding regions = 653 Number in noncoding regions = 259 Number of orfs with sites within 600 bp upstream = 225 Fraction of orfs with sites within 600 bp upstream = 0.0361388 Motif number 2 TTTTAAGCTCGTAAAATGAAATAAAAA 1 2 1 TTTTCTAAAT 0.938167 -101 TTTGTTTTCCCTCTAAAAAATTAAGGGTTG 1 83 0 TTTTCAAAAA 0.963333 -20 TTATTCTTATTGTAGTGTGGTGAAAATAAAAAGA 2 9 0 TGTTGTAAAA 0.873531 -45 AAAGAAATTATTTAGGTTCTACCAAATAATCGGGTA 3 43 0 TTTTCACAAA 0.938429 -74 AATAATTTCTTTTTTCTTGCTGAAAAAGTGCGGTTA 3 67 1 TTTTGTAAAA 0.953009 -50 TGCTATTTCCTTTTTAATCGTAAAAAATAGGCAAAT 4 39 0 TTTTCTAAAA 0.960432 -48 CCGCTTTTGATTTAAATTTTGCCAAAAAATGACCGC 5 23 0 TTTTTGCAAA 0.612133 -250 GCTAATAGCAATTCCTATCAACAAAACACCACCAAA 5 64 0 ATTTCAAAAA 0.932072 -209 AACGTAAAAAATTAGCATCTTAAAAAGTGAAAACTC 5 116 0 ATTTCTAAAA 0.955502 -157 TTACGTTTAGATTATAATCGGGAAAATTTTATATTT 5 145 1 ATTTCGAAAA 0.902269 -128 GGTTATAGAATGTTAATTGAAAAAATGCACAATTTA 5 189 1 TGTTGAAAAT 0.542609 -84 TTTAGAAATCTTTGAGTTTGTTAAATTGTGCATTTT 5 210 0 TTTTTTAAAT 0.700302 -63 TACGCGCAATTTTCTAGTCAATAAAAAGGTCAAAAA 6 11 0 TTTTCAAAAA 0.972439 -183 AGGAGAGCAAATTATCTTGTTTAAAAGGAAATCGGA 6 99 0 ATTTGTAAAA 0.90739 -95 TTTTTTTTATTTTTTTGTCTTACAGACCACGTTATC 6 146 1 TTTTCTCAGA 0.763741 -48 *** ** * **** Masking position 14 Map Score: 15.2597 Number of sites scoring better than the average of aligned sites = 750 Number in coding regions = 551 Number in noncoding regions = 199 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 3 AAGTGCTATAAAAGTGCGGTTTGTTTTTAT 1 31 0 AAAGTGCGGT 0.990258 -72 AATCGAGGTAAAAGTGCTATAAAAGTGCGG 1 42 0 AAAGTGCTAT 0.961569 -61 TCTTGCTGAAAAAGTGCGGTTATAATTTGC 3 81 1 AAAGTGCGGT 0.990258 -36 GTGCGGTTATAATTTGCGGCAAATTTTTCA 3 94 1 AATTTGCGGC 0.959114 -23 GAAGCGTAAAGTGCGGTCATTTTTTGG 5 8 1 AAAGTGCGGT 0.990258 -265 TTGTTGATAGGAATTGCTATTAGCTGGCTT 5 76 1 GAATTGCTAT 0.819726 -197 ATTGACTAGAAAATTGCGCGTATTAGAACA 6 25 1 AAATTGCGCG 0.927012 -169 AAATTTATAGAATTTGCTACTTGTAAGACC 6 56 1 AATTTGCTAC 0.85253 -138 TAAACAAGATAATTTGCTCTCCTCTTATTG 6 112 1 AATTTGCTCT 0.91681 -82 ********** Masking position 5 Map Score: 11.3961 Number of sites scoring better than the average of aligned sites = 1583 Number in coding regions = 1072 Number in noncoding regions = 511 Number of orfs with sites within 600 bp upstream = 327 Fraction of orfs with sites within 600 bp upstream = 0.0525217 Motif number 4 CTATAAAAGTGCGGTTTGTTTTTATTTCATTT 1 24 0 GCGGTTTTTT 0.984422 -79 CTGAAAAAGTGCGGTTATAATTTGCGGCAAAT 3 86 1 GCGGTAAATT 0.941734 -31 GTTATAATTTGCGGCAAATTTTTCAAAG 3 99 1 GCGGCATTTT 0.994331 -18 AGCGTAAAGTGCGGTCATTTTTTGGCAAAATT 5 13 1 GCGGTATTTT 0.993163 -260 TAAATCAAAAGCGGCAATATTTGGTGGTGTTT 5 45 1 GCGGCAATTT 0.989475 -228 CACTTTTTAAGATGCTAATTTTTTACGTTTAG 5 123 1 GATGCATTTT 0.861242 -150 AGGTTTGATTGCTGTATCGTTTTTAGTTG 5 254 1 GCTGTTGTTT 0.885917 -19 ***** * **** Masking position 11 Map Score: 5.9329 Number of sites scoring better than the average of aligned sites = 826 Number in coding regions = 559 Number in noncoding regions = 267 Number of orfs with sites within 600 bp upstream = 201 Fraction of orfs with sites within 600 bp upstream = 0.032284 Motif number 5 ATAATCGGGTATCATAAGCCAAATTTTTTTTAT 3 21 0 ATCATACAAA 0.90186 -96 ACTTGAAATAATGATAGATTAAAAT 4 3 0 ATGATATAAA 0.968797 -84 AAATAGGCAAATGATACTTGAAATAATGATAGA 4 18 0 ATGATATAAA 0.968797 -69 TTTTTGGCAAAATTTAAATCAAAAGCGGCAATA 5 31 1 AATTTATAAA 0.685343 -242 AATTTTCCCGATTATAATCTAAACGTAAAAAAT 5 140 0 ATTATACAAA 0.855904 -133 GGGTTATAGAATGTTAATTGAAAAAATGCACAA 5 188 1 ATGTTATAAA 0.968797 -85 AGAGCAAATTATCTTGTTTAAAAGGAAATCGGA 6 99 0 ATCTTGTAAA 0.811686 -95 CTTACAGACCACGTTATCTGAAATTTATTTTGG 6 164 1 ACGTTATAAA 0.905245 -30 ****** * *** Masking position 11 Map Score: 1.33198 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 104 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 GCCAAATTTTTTTTATTTTTAACATT 3 7 0 TTTTATTTTT 0.881814 -110 ATAATTTCTTTTTTCTTGCTGAAAAAGTGC 3 68 1 TTTTCTTGCT 0.973739 -49 TTCATTGCTATTTCCTTTTTAATCGTAAAA 4 50 0 TTTCCTTTTT 0.946531 -37 TTCCTTTTTATTTCATTGCTATTTCCTTTT 4 61 0 TTTCATTGCT 0.957967 -26 TGCTATTTCCTTTTTATTTCATTGC 4 72 0 TTTCCTTTTT 0.946531 -15 GGAATTGCTATTAGCTGGCTTTGTGAGGAT 5 85 1 TTAGCTGGCT 0.694156 -188 TTATCTTAGGTTTGATTGCTGTATCGTTTT 5 247 1 TTTGATTGCT 0.939926 -26 GGAGAGCAAATTATCTTGTTTAAAAGGAAA 6 104 0 TTATCTTGTT 0.901002 -90 TGAACATTTTTTTTATTTTTTTGTCTTACA 6 140 1 TTTTATTTTT 0.881814 -54 ********** Masking position 6 Map Score: 7.57704 Number of sites scoring better than the average of aligned sites = 579 Number in coding regions = 442 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 7 ********** No masking Map Score: 1.07535e-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: 1.07535e-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: 1.07535e-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