AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i250_fts_cell_wall_hinf_reg_100.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -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 HI0033 53 conserved hypothetical protein #2 HI0034 124 conserved hypothetical protein #3 HI0266 82 conserved hypothetical protein #4 HI0267 41 nitrate/nitrite sensor protein (narQ) #5 HI1129 201 conserved hypothetical protein #6 HI1130 30 conserved hypothetical protein #7 HI1136 122 UDP-N-acetylmuramoylalanine--D-glutamate ligase (murD) #8 HI1137 21 cell division protein (ftsW) #9 HI1139 137 UDP-N-acetylmuramate--alanine ligase (murC) #10 HI1140 71 D-alanine--D-alanine ligase (ddlB) #11 HI1143 83 cell division protein (ftsZ) Motif number 1 TTATTTTTTACCGCACTTTACTAAAAT 1 8 0 CCGCACTTTA 0.986262 -46 TAAAAAATAACCGCACTTTTTAGATAAGGA 1 28 1 CCGCACTTTT 0.998044 -26 GCGAAATTAACCGCGCTTTTTATGTCTAAA 2 26 0 CCGCGCTTTT 0.995463 -99 GCGGTTAATTTCGCGCTTATTTTTTGCGTG 2 42 1 TCGCGCTTAT 0.920013 -83 TGATAGAATTCCGCACCTTTATTGCTAAGT 2 96 1 CCGCACCTTT 0.988712 -29 AAATTTTACCGCACTTTTCTAAATTTCC 4 9 1 CCGCACTTTT 0.998044 -33 CTCCACAAAACACCACTTTTCTCCACTTCT 5 136 0 CACCACTTTT 0.922946 -66 AAAATAATGTAGTACTTTTATCTTAAATT 6 10 1 TAGTACTTTT 0.785319 -21 ATAGCTAGGTTCGCTCTTTCACTTTTGAAA 7 16 1 TCGCTCTTTC 0.960997 -107 GTAAAAAAGGTCGCTCTTTCAAAAGTGAAA 7 32 0 TCGCTCTTTC 0.960997 -91 TTTCTAATATTAGCACTTTTGGATATAAAA 9 51 0 TAGCACTTTT 0.980763 -87 CGAATTTTAACCGCACTTTTAGTTGAGTTT 9 92 1 CCGCACTTTT 0.998044 -46 ********** Masking position 8 Map Score: 29.5288 Number of sites scoring better than the average of aligned sites = 1545 Number in coding regions = 1028 Number in noncoding regions = 517 Number of orfs with sites within 600 bp upstream = 331 Fraction of orfs with sites within 600 bp upstream = 0.0531642 Motif number 2 ATTTTAGTAAAGTGCGGTAAAAAATAACCG 1 11 1 AGTGCGGTAA 0.997471 -43 TTATCTAAAAAGTGCGGTTATTTTTTACCG 1 25 0 AGTGCGGTTA 0.998233 -29 AGACATAAAAAGCGCGGTTAATTTCGCGCT 2 29 1 AGCGCGGTTA 0.996087 -96 AATTTAGAAAAGTGCGGTAAAATTT 4 6 0 AGTGCGGTAA 0.997471 -36 CTCAACTAAAAGTGCGGTTAAAATTCGCAA 9 89 0 AGTGCGGTTA 0.998233 -49 ********** Masking position 8 Map Score: 16.0197 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 152 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 3 GTCATCCTTATCTAAAAAGTGCGGTTATTT 1 32 0 TCTAAAAAGT 0.594862 -22 GCTTTTTATGTCTAAATTGAAATTATTTTT 2 12 0 TCTAAATTGA 0.692074 -113 AAGGTTTCCTCTAAAATTATTGTAGGCGT 3 10 1 TCTAAAATTA 0.846615 -73 ACCGCACTTTTCTAAATTTCCACTGGAGTT 4 18 1 TCTAAATTTC 0.935444 -24 TCAAACGGCTTTTTTATTTTGATAAAAATC 5 51 1 TTTTTATTTT 0.742967 -151 TTCTGGCAAGTTTATAATTTGTTCGCTCAA 5 110 0 TTTATAATTT 0.822207 -92 TTAGAAAATCTCTAAAAATCTCCACAAAAC 5 155 0 TCTAAAAATC 0.848002 -47 TTAGAGATTTTCTAAAAATAAGTTCAATTT 5 170 1 TCTAAAAATA 0.704111 -32 AGTACTTTTATCTTAAATTT 6 21 1 TCTTAAATTT 0.839305 -10 GTAAAGGAAATTTATATTTCCATCAATGAT 7 66 1 TTTATATTTC 0.877422 -57 ATGATATAATTTTAAAATTTATAGCAATTA 7 91 1 TTTAAAATTT 0.867064 -32 TTTCTTTCTTCTTAATTGCTATAAATTTT 7 104 0 TCTTAATTGC 0.746216 -19 GTTGTGGCGTTTTATAAATAGCCTCAGTCA 9 13 1 TTTATAAATA 0.540187 -125 TCATAAGTATTTTTTATATCCAAAAGTGCT 9 40 1 TTTTTATATC 0.632702 -98 ATTCGCAACGTTTTTATTTCTAATATTAGC 9 67 0 TTTTTATTTC 0.799743 -71 TTATTTTAATTTTTCATCTACAA 11 4 1 TTTTAATTTT 0.803027 -80 ATAAAGGGAATTTATATTTTATATATTTAG 11 33 1 TTTATATTTT 0.838214 -51 ********** Masking position 6 Map Score: 12.9994 Number of sites scoring better than the average of aligned sites = 1017 Number in coding regions = 736 Number in noncoding regions = 281 Number of orfs with sites within 600 bp upstream = 215 Fraction of orfs with sites within 600 bp upstream = 0.0345326 Motif number 4 TTTTTATGTCTAAATTGAAATTATTTTTA 2 10 0 TAAATTGAAA 0.738809 -115 TACAATAATTTTAGAGGAAACCTT 3 5 0 TTAGAGGAAA 0.967309 -78 AAACTTGCCAGAAGTGGAGAAAAGTGGTGT 5 127 1 GAAGTGGAGA 0.842815 -75 AAATTTAAGATAAAAGTACTACATT 6 16 0 TAAGATAAAA 0.728076 -15 TTTTACGTTAGTAAAGGAAATTTATATTTC 7 56 1 GTAAAGGAAA 0.925845 -67 TTATAGCAATTAAGAAGAAAGAAA 7 109 1 TAAGAAGAAA 0.950151 -14 GTCATTGGGAGAAAAGGAAAAATAA 9 123 1 GAAAAGGAAA 0.95968 -15 GTATCATCAGTAAGAAGAAAAACAGGATAG 10 49 1 TAAGAAGAAA 0.950151 -23 TCCCTTTATTGTAGATGAAAAATTAAAATA 11 12 0 GTAGATGAAA 0.948572 -72 ********** Masking position 3 Map Score: 6.07663 Number of sites scoring better than the average of aligned sites = 458 Number in coding regions = 370 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 5 GTGCGGTAAAAAATAACCGCACTTTTTAGAT 1 22 1 AAATACCGCA 0.854597 -32 ATTCAATGATAGAATTCCGCACCTTTATTGC 2 90 1 AGAATCCGCA 0.891624 -35 GCACTTTTCTAAATTTCCACTGGAGTTTCCT 4 21 1 AAATTCCACT 0.911779 -21 AATTTTATGAAAAAAGCCGTTTGAATTGTTT 5 18 1 AAAAGCCGTT 0.974994 -184 TATCAAAATAAAAAAGCCGTTTGAATAAACA 5 44 0 AAAAGCCGTT 0.974994 -158 TTATTTTGATAAAAATCAGTTGCTTTAATGT 5 64 1 AAAATCAGTT 0.809502 -138 AAATCTCCACAAAACACCACTTTTCTCCACT 5 139 0 AAAAACCACT 0.952215 -63 ACTAACGTAAAAAAGGTCGCTCTTTCAAAAG 7 37 0 AAAAGTCGCT 0.923508 -86 GGCTATTTATAAAACGCCACAACCC 9 5 0 AAAAGCCACA 0.963903 -133 TCCCAATGACAAAACTCAACTAAAAGTGCGG 9 102 0 AAAATCAACT 0.865362 -36 **** ****** Masking position 3 Map Score: 7.47023 Number of sites scoring better than the average of aligned sites = 630 Number in coding regions = 507 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 6 GAGGGTATTCAATGATAGAATTCCGCACCTT 2 84 1 AATGATGAAT 0.709611 -41 TCTACCCAAAATTGATAGCATACGCCTACAA 3 30 0 ATTGATGCAT 0.949158 -53 TTAATGTGGAATTACTTGCAAGTTGAGCGAA 5 88 1 ATTACTGCAA 0.868007 -114 ACTTTTCTCCACTTCTGGCAAGTTTATAATT 5 121 0 ACTTCTGCAA 0.836408 -81 AATTGAACTTATTTTTAGAAAATCTCTAAAA 5 168 0 ATTTTTGAAA 0.793413 -34 AAATTATATCATTGATGGAAATATAAATTTC 7 72 0 ATTGATGAAA 0.969826 -51 TAATTTTAAAATTTATAGCAATTAAGAAGAA 7 97 1 ATTTATGCAA 0.961079 -26 TGCCAGATGGATTGATTGAAAATCTTAGTAT 10 11 1 ATTGATGAAA 0.96982 -61 ****** **** Masking position 10 Map Score: 3.37748 Number of sites scoring better than the average of aligned sites = 305 Number in coding regions = 275 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 7 AGCGCGGTTAATTTCGCGCTTATTTTTTGC 2 39 1 ATTTCGCGCT 0.960706 -86 TTTTGCGTGGATTTTGCGCAAGAGGGTATT 2 63 1 ATTTTGCGCA 0.815827 -62 AAGGTTTCCTCTAAAATTATTG 3 3 1 GGTTTCCTCT 0.879555 -80 GTTTATAATTTGTTCGCTCAACTTGCAAGT 5 101 0 TGTTCGCTCA 0.948661 -101 AATATAGCTAGGTTCGCTCTTTCACTTTTG 7 13 1 GGTTCGCTCT 0.989463 -110 AACGTAAAAAAGGTCGCTCTTTCAAAAGTG 7 35 0 AGGTCGCTCT 0.969093 -88 ********** Masking position 4 Map Score: 0.734623 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 79 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 TGAATAAACAATTCAAACGGCTTTTTTCATAA 5 22 0 ATTAACGGCT 0.992487 -180 TGAATTGTTTATTCAAACGGCTTTTTTATTTT 5 39 1 ATTAACGGCT 0.992487 -163 GTAATTCCACATTAAAGCAACTGATTTTTATC 5 71 0 ATTAACAACT 0.955559 -131 TATTTTATATATTTAGTCAGCTTATCTGGCAG 11 47 1 ATTAGCAGCT 0.98042 -37 *** ** ***** Masking position 5 Map Score: 0.258098 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 22 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 9 ********** No masking Map Score: 1.37435e-13 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: 1.37435e-13 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: 1.37435e-13 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