AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i250_fts_cell_wall_mtub_reg_300.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -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 = 0.66 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 murB 26 murB #2 ftsZ 172 ftsZ #3 murE 22 murE #4 hypothetical 267 hypothetical protein Rv2160c #5 Rv2161c 102 hypothetical protein Rv2161c #6 PE_PGRS 209 PE_PGRS #7 Rv2166c 300 hypothetical protein Rv2166c #8 ddlA 77 ddlA #9 gpdA2 118 gpdA2 Motif number 1 AGCAGGTCAGGCTACCCTTACG 1 3 1 CAGGTCAGGC 0.781405 -24 CGCGCCGATACGCGGCGGGCATTTTTTCGG 2 11 0 CGCGGCGGGC 0.951248 -162 GCTAACCGTGCAGGCGCGCCGATACGCGGC 2 25 0 CAGGCGCGCC 0.956564 -148 GGTTAGCAACCGTCGTAGCCATACGGTTCT 2 48 1 CGTCGTAGCC 0.920236 -125 ACACACCGAAGAACCGAGCCCCACCAGGGA 2 141 1 GAACCGAGCC 0.775496 -32 CGCCGACGTCGGCCGCCAAACCC 4 4 1 CGACGTCGGC 0.955883 -264 GATCTGCGCCCGGGTTTGGCGGCCGACGTC 4 15 0 CGGGTTTGGC 0.855657 -253 GGGCGCAGATCCTGCGCGCCGCGATGGATA 4 34 1 CCTGCGCGCC 0.950297 -234 GATGGACAGCCCCGAGAGCCCCTTCACCGA 4 69 0 CCCGAGAGCC 0.709005 -199 CTCATGCCCAGCCGCCCGGCAAGCTCGCCG 4 98 0 GCCGCCCGGC 0.494081 -170 TGGGCATGAGCAAGTCGGGCCTGTTCCGGC 4 118 1 CAAGTCGGGC 0.807943 -150 AGCTGCAGCTGCTCCTTGGCGCCGAAATGC 4 146 0 GCTCCTTGGC 0.480815 -122 TGGCGACCGTCGAGGCCGCCGTGAGCGTGT 4 175 1 CGAGGCCGCC 0.983888 -93 GCGGGAGCCACGACCTCGGCTTCGAACACG 4 200 0 CGACCTCGGC 0.963757 -68 GCGCTGCCATCGCGGGAGCCACGACCTCGG 4 211 0 CGCGGGAGCC 0.981164 -57 CCACCCCGGGCGGCGCTGCCATCGCGGGAG 4 223 0 CGGCGCTGCC 0.97293 -45 GGGTGGACCGGGTGCGCGCCCTCATGCATG 4 247 1 GGTGCGCGCC 0.84074 -21 GTGACCGCTCGCTCGGGGCCCGGG 5 5 0 GCTCGGGGCC 0.698835 -98 ATTGACAGCACGCCCCAGGCGGACCATCGT 5 45 1 CGCCCCAGGC 0.980142 -58 CGGCGGCGGCTTTCATTAAG 5 93 0 CGGCGGCGGC 0.983275 -10 CCGTTACCGGCGCCGCCGCC 6 1 0 CGCCGCCGCC 0.926116 -209 CGCCGGTAACGGCGCGCGCCGGTTCGTTTC 6 19 1 GGCGCGCGCC 0.499573 -191 AGACCTGCGACACCGTCGGCAGGGCTTTCG 6 150 0 CACCGTCGGC 0.881745 -60 CCAGCCGGGTCGTCACCGGCTGTCGGCGAT 7 54 1 CGTCACCGGC 0.861217 -247 AAGTGGGGCACAACTGGGGCTCAAACCGGA 7 90 0 CAACTGGGGC 0.826409 -211 CAAGTGGGGCCAAGTGGGGCACAACTGGGG 7 101 0 CAAGTGGGGC 0.826409 -200 AAATGGGTGGCAAGTGGGGCCAAGTGGGGC 7 111 0 CAAGTGGGGC 0.826409 -190 AGGTCGTAGCCGGGCTAGCCGCGCGCTTCA 7 164 1 CGGGCTAGCC 0.94833 -137 CCACAATCCCCCACTTTGCCCCATAACTGG 7 229 0 CCACTTTGCC 0.670691 -72 CTCACCCAAACACCTCAGCCACCATACCCC 7 257 0 CACCTCAGCC 0.855117 -44 GGGGCACCTCCCTGCCAAATCCATCT 7 285 0 CCTCCCTGCC 0.906682 -16 CGTGCCGGCCCGTGCGAGGC 8 1 0 CGTGCGAGGC 0.969583 -77 AGTTTTCGGTCGTGCCGGCCCGTGCGAGGC 8 11 0 CGTGCCGGCC 0.975204 -67 AACTGCAGCTCGTGGGAGCCCGTCTGCCTG 8 37 1 CGTGGGAGCC 0.969116 -41 CAGAGGCTACCGGGTCAGGCAGACGGGCTC 8 52 0 CGGGTCAGGC 0.934426 -26 CCGCGTGGATCGACGCTGGCAGGATGACTT 9 12 0 CGACGCTGGC 0.967349 -107 CAATGCCGTCGAAGTGTGCCGCGTGGATCG 9 30 0 GAAGTGTGCC 0.574152 -89 CACACTTCGACGGCATTGCCGCCACGGTCG 9 42 1 CGGCATTGCC 0.696956 -77 GCCCCGGCCACGACCGTGGCGGCAATGCCG 9 52 0 CGACCGTGGC 0.976276 -67 ACCGTGCCTGGGCCCCGGCCACGACCGTGG 9 63 0 GGCCCCGGCC 0.499759 -56 GTTGCCGTCGGGACCGTGCCTGGGCCCCGG 9 75 0 GGACCGTGCC 0.931459 -44 TAATCTGCGCCGCGGTTGCCGTCGGGACCG 9 89 0 CGCGGTTGCC 0.953195 -30 ********** Masking position 8 Map Score: 72.2594 Number of sites scoring better than the average of aligned sites = 89309 Number in coding regions = 84379 Number in noncoding regions = 4930 Number of orfs with sites within 600 bp upstream = 1524 Fraction of orfs with sites within 600 bp upstream = 0.24478 Motif number 2 CGCCGCGTATCGGCGCGCCTGCACGGTTAG 2 24 1 CGGCGCGCCT 0.656892 -149 AACCGTATGGCTACGACGGTTGCTAACCGT 2 46 0 CTACGACGGT 0.294373 -127 CTCCCTGGTGGGGCTCGGTTCTTCGGTGTG 2 142 0 GGGCTCGGTT 0.481078 -31 CGTTCGGCTTCCTCCCTGGTGGGG 2 159 0 CGGCTTCCTC 0.779732 -14 GTGTGCGCGCCCTGTCGGTAGG 3 5 1 GCGCGCCCTG 0.940102 -18 CGCCGACGTCGGCCGCCAAA 4 1 1 CGCCGACGTC 0.959584 -267 CGCGCAGGATCTGCGCCCGGGTTTGGCGGC 4 22 0 CTGCGCCCGG 0.929296 -246 AGATCCTGCGCGCCGCGATGGATATCGCCT 4 40 1 CGCCGCGATG 0.94942 -228 CGATGGATATCGCCTCGGTGAAGGGGCTCT 4 55 1 CGCCTCGGTG 0.868591 -213 CGATGGACAGCCCCGAGAGCCCCTTCACCG 4 70 0 CCCCGAGAGC 0.612494 -198 GGCTGTCCATCGGCGAGCTTGCCGGGCGGC 4 88 1 CGGCGAGCTT 0.960122 -180 GCTCATGCCCAGCCGCCCGGCAAGCTCGCC 4 99 0 AGCCGCCCGG 0.736081 -169 GGAACAGGCCCGACTTGCTCATGCCCAGCC 4 115 0 CGACTTGCTC 0.512812 -153 TCCGGCATTTCGGCGCCAAGGAGCAGCTGC 4 142 1 CGGCGCCAAG 0.668452 -126 CGACCGTCGAGGCCGCCGTGAGCGTGTTCG 4 178 1 GGCCGCCGTG 0.93931 -90 ATCGCGGGAGCCACGACCTCGGCTTCGAAC 4 203 0 CCACGACCTC 0.902957 -65 GCGATGGCAGCGCCGCCCGGGGTGGACCGG 4 228 1 CGCCGCCCGG 0.975624 -40 TGGACCGGGTGCGCGCCCTCATGCATGC 4 250 1 GCGCGCCCTC 0.940208 -18 GATTGCGTGACCGCTCGCTCGGGGCCCGGG 5 11 0 CCGCTCGCTC 0.819595 -92 GGTCCGCCTGGGGCGTGCTGTCAATGCCGG 5 40 0 GGGCGTGCTG 0.844842 -63 CGGCGGCGGCTTTCATTAAG 5 93 0 CGGCGGCGGC 0.821768 -10 GGCGGCGGCGCCGGTAACGGCGCGC 6 6 1 CGGCGCCGGT 0.965888 -204 GCGCCGGTAACGGCGCGCGCCGGTTCGTTT 6 18 1 CGGCGCGCGC 0.641771 -192 TGCGCAACATGTGCGCGCTGACGATCGGGT 6 64 1 GTGCGCGCTG 0.768232 -146 AAGGAAAGTGCGACATCCTGTTTTCAGATT 6 110 1 CGACATCCTG 0.368653 -100 CCCAGACCTGCGACACCGTCGGCAGGGCTT 6 153 0 CGACACCGTC 0.665553 -57 CCCGCACCTCCGACCAGCTCAGCACAACTT 6 190 0 CGACCAGCTC 0.650189 -20 CTGGGTGAACCGCCCCGGTGAGTCCGGAGA 7 28 0 CGCCCCGGTG 0.830943 -273 GACTCAATATCGCCGACAGCCGGTGACGAC 7 62 0 CGCCGACAGC 0.843976 -239 CCCATTTGCCCGGCGACATGCGGTTTTCTG 7 134 1 CGGCGACATG 0.928384 -167 GCTAGCCCGGCTACGACCTCAGAAAACCGC 7 153 0 CTACGACCTC 0.750076 -148 GCCGGGCTAGCCGCGCGCTTCAGTGGTACA 7 172 1 CCGCGCGCTT 0.931491 -129 AGACGGGCTCCCACGAGCTGCAGTTTTCGG 8 32 0 CCACGAGCTG 0.892984 -46 TGGGCCCCGGCCACGACCGTGGCGGCAATG 9 55 0 CCACGACCGT 0.719309 -64 CACTAATCTGCGCCGCGGTTGCCGTCGGGA 9 92 0 CGCCGCGGTT 0.954284 -27 ********** Masking position 4 Map Score: 46.2253 Number of sites scoring better than the average of aligned sites = 82396 Number in coding regions = 77389 Number in noncoding regions = 5007 Number of orfs with sites within 600 bp upstream = 1544 Fraction of orfs with sites within 600 bp upstream = 0.247992 Motif number 3 CGCCGACGTCGGCCGCCAAACCCGGG 4 6 1 ACGTCGCCGC 0.838752 -262 GCAAGCTCGCCGATGGACAGCCCCGAGAGCC 4 79 0 CGATGGCAGC 0.953001 -189 GCGGCCTCGACGGTCGCCAGCTGCAGCTGCT 4 163 0 CGGTCGCAGC 0.992925 -105 ACCGTCGAGGCCGCCGTGAGCGTGTTCGAAG 4 180 1 CCGCCGGAGC 0.923173 -88 GCGCCGCCCGGGGTGGACCGGGTGCGCGCCC 4 237 1 GGGTGGCCGG 0.973621 -31 CCCGGGCCCCGAGCGAGCGGTCACGCAATC 5 10 1 CGAGCGGCGG 0.863296 -93 TCGTGTTTAACGATGGTCCGCCTGGGGCGTG 5 53 0 CGATGGCCGC 0.973125 -50 GGCGGCGGCGCCGGTAACGGCGC 6 3 1 CGGCGGGCCG 0.831342 -207 CCGAAACGAACCGGCGCGCGCCGTTACCGGC 6 20 0 CCGGCGGCGC 0.927253 -190 TCCGCCAACCCGATCGTCAGCGCGCACATGT 6 70 0 CGATCGCAGC 0.967929 -140 GATTGTTATAGGATCGAAAGCCCTGCCGACG 6 136 1 GGATCGAAGC 0.685736 -74 ACCTGCGACACCGTCGGCAGGGCTTTCGATC 6 147 0 CCGTCGCAGG 0.957419 -63 CTGAGCTGGTCGGAGGTGCGGG 6 198 1 CGGAGGGCGG 0.927542 -12 CGACCCGGCTGGGTGAACCGCCCCGGTGAGT 7 35 0 GGGTGACCGC 0.76836 -266 TCACCCAGCCGGGTCGTCACCGGCTGTCGGC 7 50 1 GGGTCGCACC 0.966481 -251 CCGGGCAAATGGGTGGCAAGTGGGGCCAAGT 7 116 0 GGGTGGAAGT 0.294034 -185 GGATTTGGCAGGGAGGTGCCCC 7 289 1 GGGAGGGCCC 0.848109 -12 CTGCAGTTTTCGGTCGTGCCGGCCCGTGCGA 8 14 0 CGGTCGGCCG 0.980652 -64 ATTGCCGCCACGGTCGTGGCCGGGGCCCAGG 9 56 1 CGGTCGGGCC 0.927612 -63 GCCGCGGTTGCCGTCGGGACCGTGCCTGGGC 9 80 0 CCGTCGGACC 0.954283 -39 ****** **** Masking position 6 Map Score: 28.2589 Number of sites scoring better than the average of aligned sites = 26613 Number in coding regions = 24800 Number in noncoding regions = 1813 Number of orfs with sites within 600 bp upstream = 1006 Fraction of orfs with sites within 600 bp upstream = 0.16158 Motif number 4 AGCAGGTCAGGCTACCCTTACG 1 2 1 GCGGTCAGGC 0.967893 -25 GGCCCGTAAGGGTAGCCTGACC 1 15 0 GCCGTAAGGG 0.947747 -12 AAAATGCCCGCCGCGTATCGGCGCGCCTGCA 2 16 1 CCCGTATCGG 0.906068 -157 TTCCTCCCTGGTGGGGCTCGGTTCTTCGGTG 2 144 0 GTGGGCTCGG 0.645518 -29 GGATCTGCGCCCGGGTTTGGCGGCCGACGTC 4 15 0 CCGGTTTGGC 0.927909 -253 GGCGGCGGCGCCGGTAACGGCGCGCGCCGG 6 10 1 GCGGTAACGG 0.976474 -200 GCGCGCGCCGGTTCGTTTCGGCTCCAACAAC 6 30 1 GTCGTTTCGG 0.755137 -180 AGTGCGACATCCTGTTTTCAGATTGTTATAG 6 116 1 CCGTTTTCAG 0.627611 -94 CGACGGTGTCGCAGGTCTGGGATTCGTGAAG 6 162 1 GCGGTCTGGG 0.994589 -48 GTTGTGCTGAGCTGGTCGGAGGTGCGGG 6 192 1 GCGGTCGGAG 0.82917 -18 CCGGCGACATGCGGTTTTCTGAGGTCGTAGC 7 143 1 GCGTTTTCTG 0.838887 -158 GGCTAGCCGCGCGCTTCAGTGGTACAGAGAC 7 176 1 GCCTTCAGTG 0.712765 -125 CTTTGATACCCCAGTTATGGGGCAAAGTGGG 7 219 1 CCGTTATGGG 0.920817 -82 CCCACGAGCTGCAGTTTTCGGTCGTGCCGGC 8 22 0 GCGTTTTCGG 0.966352 -56 GCAGAGGCTACCGGGTCAGGCAGACGGGCTC 8 52 0 CCGGTCAGGC 0.931863 -26 CAACCGCGGCGCAGATTAGTGTGTGTGG 9 101 1 GCGATTAGTG 0.526693 -18 ** ******** Masking position 6 Map Score: 10.8456 Number of sites scoring better than the average of aligned sites = 14296 Number in coding regions = 13194 Number in noncoding regions = 1102 Number of orfs with sites within 600 bp upstream = 752 Fraction of orfs with sites within 600 bp upstream = 0.120784 Motif number 5 GGCCCGTAAGGGTAGCCTGACC 1 15 0 CCCGTAAGGG 0.406661 -12 CCGAAAAAATGCCCGCCGCGTATCGGCGCG 2 11 1 GCCCGCCGCG 0.688265 -162 GTATCGGCGCGCCTGCACGGTTAGCAACCG 2 30 1 GCCTGCACGG 0.97154 -143 TCGGCTTCCTCCCTGGTGGGGCTCGGTTCT 2 150 0 CCCTGGTGGG 0.765233 -23 GTGTGCGCGCCCTGTCGGTAGG 3 9 1 GCCCTGTCGG 0.869272 -14 AGGATCTGCGCCCGGGTTTGGCGGCCGACG 4 17 0 CCCGGGTTTG 0.376304 -251 GATCCTGCGCGCCGCGATGGATATCGCCTC 4 41 1 GCCGCGATGG 0.892377 -227 CCCCGAGAGCCCCTTCACCGAGGCGATATC 4 60 0 CCCTTCACCG 0.693944 -208 CCGATGGACAGCCCCGAGAGCCCCTTCACC 4 71 0 GCCCCGAGAG 0.641696 -197 GAGCTTGCCGGGCGGCTGGGCATGAGCAAG 4 102 1 GGCGGCTGGG 0.86208 -166 AGCAAGTCGGGCCTGTTCCGGCATTTCGGC 4 126 1 GCCTGTTCCG 0.676066 -142 GCTCACGGCGGCCTCGACGGTCGCCAGCTG 4 171 0 GCCTCGACGG 0.943893 -97 CGTCGAGGCCGCCGTGAGCGTGTTCGAAGC 4 182 1 GCCGTGAGCG 0.934408 -86 GGTCGTGGCTCCCGCGATGGCAGCGCCGCC 4 215 1 CCCGCGATGG 0.810829 -53 ACCCGGTCCACCCCGGGCGGCGCTGCCATC 4 230 0 CCCCGGGCGG 0.893377 -38 CCCGGGGTGGACCGGGTGCGCGCCCTCATG 4 243 1 ACCGGGTGCG 0.906501 -25 CCCGGGCCCCGAGCGAGCGGTCACG 5 6 1 GCCCCGAGCG 0.907016 -97 ACGATGGTCCGCCTGGGGCGTGCTGTCAAT 5 45 0 GCCTGGGGCG 0.872718 -58 CTTAATGAAAGCCGCCGCCG 5 93 1 GCCGCCGCCG 0.938264 -10 ACCGGCGCGCGCCGTTACCGGCGCCGCCGC 6 12 0 GCCGTTACCG 0.683853 -198 AACGGCGCGCGCCGGTTCGTTTCGGCTCCA 6 26 1 GCCGGTTCGT 0.270825 -184 CTGCGACACCGTCGGCAGGGCTTTCGATCC 6 146 0 GTCGGCAGGG 0.748215 -64 AGTTGTGCTGAGCTGGTCGGAGGTGCGGG 6 191 1 AGCTGGTCGG 0.247867 -19 CTCCGGACTCACCGGGGCGGTTCACCCAGC 7 29 1 ACCGGGGCGG 0.911765 -272 CCGGTGACGACCCGGCTGGGTGAACCGCCC 7 43 0 CCCGGCTGGG 0.921348 -258 GCGCGGCTAGCCCGGCTACGACCTCAGAAA 7 158 0 CCCGGCTACG 0.638949 -143 GCGGCGTTTTGCCGTCTCTGTACCACTGAA 7 190 0 GCCGTCTCTG 0.611752 -111 GCCTCGCACGGGCCGGCACGA 8 2 1 CCTCGCACGG 0.519549 -76 CCTCGCACGGGCCGGCACGACCGAAAACTG 8 12 1 GCCGGCACGA 0.864453 -66 TGCAGAGGCTACCGGGTCAGGCAGACGGGC 8 54 0 ACCGGGTCAG 0.68057 -24 AACCTGCAGAGGCTACCGGGT 8 67 0 ACCTGCAGAG 0.336879 -11 GAAGTCATCCTGCCAGCGTCGATCCACG 9 9 1 CCTGCCAGCG 0.445593 -110 GTCGAAGTGTGCCGCGTGGATCGACGCTGG 9 23 0 GCCGCGTGGA 0.6626 -96 CGACGGCATTGCCGCCACGGTCGTGGCCGG 9 49 1 GCCGCCACGG 0.985006 -70 TGGCCGGGGCCCAGGCACGGTCCCGACGGC 9 72 1 CCAGGCACGG 0.677276 -47 ********** Masking position 3 Map Score: 41.1652 Number of sites scoring better than the average of aligned sites = 60733 Number in coding regions = 56798 Number in noncoding regions = 3935 Number of orfs with sites within 600 bp upstream = 1397 Fraction of orfs with sites within 600 bp upstream = 0.224382 Motif number 6 GAGTTTGCCAGCAGACACACCGAAGAACCG 2 127 1 GCAGACACAC 0.9697 -46 TACCGACAGGGCGCGCACAC 3 1 0 GCGCGCACAC 0.955169 -22 CCCCGAGCGAGCGGTCACGCAATCCGGCAT 5 17 1 GCGGTCACGC 0.958072 -86 CAGAGAGTCTCCGGACTCACCGGGGCGGTT 7 21 1 CCGGACTCAC 0.9853 -280 GGGGCTCAAACCGGACTCAATATCGCCGAC 7 75 0 CCGGACTCAA 0.948152 -226 TGCCTGGGCCCCGGCCACGACCGTGGCGGC 9 59 0 CCGGCCACGA 0.927231 -60 CCACACACACTAATCTGCGC 9 109 0 CCACACACAC 0.946633 -10 ********** Masking position 6 Map Score: 3.7783 Number of sites scoring better than the average of aligned sites = 2311 Number in coding regions = 2120 Number in noncoding regions = 191 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 7 ********** No masking Map Score: 2.07722e-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: 2.07722e-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: 2.07722e-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