AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i181_bsub_mtub_300.orf -o181_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -x5 -e 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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 panB 245 ketopantoate hydroxymethyltransferase #2 ypjH 31 alternate gene name: jojH; similar to lipopolysaccharide biosynthesis-related protein #3 ypjD 300 alternate gene name: jojD #4 panB 300 panB #5 Rv3603c 184 hypothetical protein Rv3603c #6 ftsH 66 ftsH Motif number 1 AATAATAGGTGCAGTTCGCAGGCGATACTGCCCAATGGA 1 45 0 GCAGCGGCTT 0.952475 -201 GATAGACATTGCAGCAGTCTGCCTTGATCCAAAAAAGGA 1 90 1 GCAGCGCCGC 0.981699 -156 TTCAGCGCACTGCTGGCAAGCTTTTTCCGAAAC 4 5 1 GCGCCGGCGT 0.975098 -296 ACGCCTTTGACCGGCTGCGTGACGCGTTCTGACTCCAGA 4 60 0 CCGGGGACGC 0.964063 -241 CCGGTCAAAGGCGTAACCCATGCTCGAGCAAACATGCAT 4 85 1 GCGTCTGCGC 0.969288 -216 CGCGCATGCAGCGGCTCAGTGGCCTGGACGCCAGTTGCT 4 149 0 GCGGGGGCGC 0.998235 -152 GTATGCCGATGGGGGCCCCGGGCGCGTCTGAGGGGAAGA 4 191 1 GGGGCGGCGT 0.98901 -110 TAGGGTCCCCGGGTTCGTCGGACCCTGACAGTCTGCCAC 4 231 0 GGGTCGACTC 0.862497 -70 GGGACCCTAACGGGCCACGAGGATCGACCCGACCACCAT 4 261 1 CGGGGGGAGC 0.909413 -40 TCGGTTGCCGGCGGCAATCGGGCGGGTACACCCTGGCAC 5 22 0 GCGGCGGCGC 0.999484 -163 GACCAAATCAGCAGTGCCCCGGGTGGGTCTTGACGTGCA 5 76 1 GCAGCGGGGC 0.983361 -109 AGTCCCATGCCCGGGTACCGGACGGTCACCAAGACTGTA 5 122 0 CCGGCGACTC 0.960318 -63 CGGTACCCGGGCATGGGACTGGAACGAACCAAGAAACCT 5 141 1 GCATCGGAGC 0.971638 -44 GAGCGGTAACCTGGACTTTCCAGCTGCGTGT 6 3 1 GCGGCGGATC 0.991714 -64 CTTTCCAGCTGCGTGTATCGGGAAGGACCTGGCCGGCAC 6 26 1 GCGTCGGAGC 0.993097 -41 **** * *** * * Masking position 11 Map Score: 26.9648 Number of sites scoring better than the average of aligned sites = 1024 Number in coding regions = 957 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 2 CCAAATGAAAAAATTGCCGCTCCGATTAAAATAA 3 104 1 ATGCCGCCCG 0.981825 -197 GCTTTTTCCGAAACCGCGGCCTCGCCTTGATCTG 4 30 1 ACGCGGCTCG 0.968341 -271 CCAGACACAGCAACTGGCGTCCAGGCCACTGAGC 4 141 1 CCGGCGTCAG 0.965381 -160 ACCATCGCGCATGCAGCGGCTCAGTGGCCTGGAC 4 159 0 ACGCGGCCAG 0.990419 -142 GATGGTATGCCGATGGGGGCCCCGGGCGCGTCTG 4 187 1 CTGGGGCCCG 0.992727 -114 CCTCGTGGCCCGTTAGGGTCCCCGGGTTCGTCGG 4 249 0 CTGGGTCCCG 0.973826 -52 TACACCCTGGCACAAGCGGCGCCG 5 1 0 CAGCGGCCCG 0.9844 -184 CGTCAAGACCCACCCGGGGCACTGCTGATTTGGT 5 77 0 CCGGGGCCTG 0.985262 -108 TTCCAGTCCCATGCCCGGGTACCGGACGGTCACC 5 131 0 ACCGGGTCCG 0.940523 -54 AGCAGACGGCCTCACAGGTTTCTTGGT 5 168 0 ACGCCTCCAG 0.922349 -17 GCAGCTGGAAAGTCCAGGTTACCGCTC 6 4 0 ACAGGTTCCG 0.705143 -63 CGATCATCGGCCGTGCCGGCCAGGTCCT 6 49 0 CCGCCGTCCG 0.988493 -18 * * ***** *** Masking position 14 Map Score: 15.7751 Number of sites scoring better than the average of aligned sites = 951 Number in coding regions = 891 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 3 TTGGATCAAGGCAGACTGCTGCAATGTCTATCTA 1 88 0 GCAGACTGCA 0.806566 -158 AACGCGTCACGCAGCCGGTCAAAGGCGTAACCCA 4 71 1 GCAGCCGGAG 0.970651 -230 CAGTGGCCTGGACGCCAGTTGCTGTGTCTGGAAA 4 138 0 GACGCCAGCG 0.880308 -163 AGGCCACTGAGCCGCTGCATGCGCGATGGTATGC 4 163 1 GCCGCTGCCC 0.942539 -138 GCGATGGTATGCCGATGGGGGCCCCGGGCGCGTC 4 185 1 GCCGATGGCC 0.986991 -116 GGAAGAAGTGGCAGACTGTCAGGGTCCGACGAAC 4 224 1 GCAGACTGGG 0.91303 -77 AGGGTCCGACGAACCCGGGGACCCTAACGGGCCA 4 244 1 GAACCCGGCC 0.923163 -57 CGGCGCCGCTTGTGCCAGGGTGTACCCG 5 5 1 GCCGCTTGCG 0.980056 -180 CCGCCCGATTGCCGCCGGCAACCGACACTGTTGG 5 36 1 GCCGCCGGCG 0.998151 -149 AATCAGCAGTGCCCCGGGTGGGTCTTGACGTGCA 5 81 1 GCCCCGGGGC 0.898778 -104 AGCAGACGGCCTCACAGGTTTCTTG 5 170 0 GCAGACGGCC 0.992353 -15 CCCGATACACGCAGCTGGAAAGTCCAGGTTACCG 6 14 0 GCAGCTGGGC 0.982928 -53 ******** * * Masking position 1 Map Score: 12.0867 Number of sites scoring better than the average of aligned sites = 1910 Number in coding regions = 1796 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 4 TATTAAAATAGATAGACATTGCAGCAGTCTGC 1 80 1 GATAGAATGC 0.809485 -166 GGGACAGAGGGATGAAACTCGCCGAACTTTAG 1 131 1 GATGAACTGC 0.971189 -115 TTTAGAAAGTGAAGAATCCTTCTCGTTGTAAC 1 158 1 GAAGAACCTC 0.670893 -88 TTGGCTTGCAGAAGAAAACGGCAGATCATCTC 1 200 1 GAAGAAACGC 0.980648 -46 TCAATATGCAGAACAATCTGGCTGAGGGCGGT 3 61 0 GAACAACTGC 0.978609 -240 AGTGGATGAAAAAGAAAACAGCAAACGTGCTT 3 216 1 AAAGAAACGC 0.815758 -85 TGAACGAAACCTCCTATCATCCT 3 288 0 GAACGAACTC 0.869154 -13 CGCGGTTTCGGAAAAAGCTTGCCAGCAGTGCG 4 16 0 GAAAAACTGC 0.952969 -285 GGGCCACGAGGATCGACCCGACCACCATTAGG 4 272 1 GATCGACCAC 0.799915 -29 CGTGTATCGGGAAGGACCTGGCCGGCACGGCC 6 37 1 GAAGGACTGC 0.987495 -30 ****** ** ** Masking position 6 Map Score: 6.81406 Number of sites scoring better than the average of aligned sites = 974 Number in coding regions = 891 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 5 TTTGGATCAAGGCAGACTGCTGCAATGTCT 1 93 0 GGCAGACTGC 0.925726 -153 AAAGGACTGGGACAGAGGGATGAAACTCGC 1 123 1 GACAGAGGGA 0.860996 -123 GGGCTGATGTGGAAAAGGGCATAAAGCAAA 3 14 1 GGAAAAGGGC 0.903468 -287 AGAACAATCTGGCTGAGGGCGGTTTTACAG 3 54 0 GGCTGAGGGC 0.991719 -247 TCTAATGGAAGGAAAAGGGGTTTTGTGTGA 3 171 0 GGAAAAGGGG 0.947811 -130 GCCTTTGACCGGCTGCGTGACGCGTTCTGA 4 67 0 GGCTGCGTGA 0.80291 -234 CACGCAGCCGGTCAAAGGCGTAACCCATGC 4 78 1 GTCAAAGGCG 0.704129 -223 AACATGCATGGGCTGAGTGGACGTTTCCAG 4 115 1 GGCTGAGTGG 0.988427 -186 CGCATGCAGCGGCTCAGTGGCCTGGACGCC 4 156 0 GGCTCAGTGG 0.942591 -145 CCCCGGGCGCGTCTGAGGGGAAGAAGTGGC 4 206 1 GTCTGAGGGG 0.975719 -95 GGTTGCCGGCGGCAATCGGGCGGGTACACC 5 29 0 GGCAATCGGG 0.798095 -156 ********** Masking position 1 Map Score: 8.90187 Number of sites scoring better than the average of aligned sites = 1051 Number in coding regions = 917 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 6 TGTGTTGGTACAAGCCCGTTGATTTTGGTATAC 1 11 1 CAGCCGTGAT 0.982897 -235 GACAAATGTTTAAGCACGTTTGCTGTTTTCTTT 3 226 0 TAGCCGTTGC 0.963282 -75 CCACTCAGCCCATGCATGTTTGCTCGAGCATGG 4 102 0 CAGCTGTTGC 0.981376 -199 TGAGCCGCTGCATGCGCGATGGTATGCCGATGG 4 170 1 CAGCCGTGGT 0.991221 -131 CCAGGGTGTACCCGCCCGATTGCCGCCGGCAAC 5 25 1 CCGCCGTTGC 0.984258 -160 ACTACACCAACAGTGTCGGTTGCCGGCGGCAAT 5 43 0 CATGCGTTGC 0.94135 -142 AAATCGACTACAGTCTTGGTGACCGTCCGGTAC 5 114 1 CATCTGTGAC 0.871784 -71 GTTCCAGTCCCATGCCCGGGTACCGGACGGTCA 5 133 0 CAGCCGGTAC 0.969534 -52 ACCTGGCCGGCACGGCCGATGATCG 6 52 1 CAGGCGTGAT 0.945961 -15 ** ** ** **** Masking position 8 Map Score: 7.97848 Number of sites scoring better than the average of aligned sites = 493 Number in coding regions = 474 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 AAAACGGCAGATCATCTCCTCTAAACATGAG 1 214 1 ATCTCTCCTC 0.975813 -32 GTTTTCTCCTCCTCATGTTTAGAG 1 232 0 TTCCCTCCTC 0.977554 -14 TGTTCGCCCCCAAGCACATCATG 2 19 0 TTCCCCCCAA 0.900412 -13 CCTTTTCCACATCAGCCCCTC 3 1 0 ATCGCCCCTC 0.985212 -300 TGTTTTCTTTTTCATCCACTATAATATAAAC 3 205 0 TTCTCCACTA 0.934771 -96 TGTGTCTGGAAACGTCCACTCAGCCCATGCA 4 119 0 AACTCCACTC 0.893341 -182 AGTCTGCCACTTCTTCCCCTCAGACGCGCCC 4 210 0 TTCTCCCCTC 0.994834 -91 *** ******* Masking position 6 Map Score: 4.22149 Number of sites scoring better than the average of aligned sites = 226 Number in coding regions = 160 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 8 GACGCGCCCGGGGCCCCCATCGGCATACCATCG 4 186 0 GGGCCCACGG 0.997943 -115 CCGGGTTCGTCGGACCCTGACAGTCTGCCACTT 4 229 0 CGGCCCGCAG 0.886576 -72 GACGAACCCGGGGACCCTAACGGGCCACGAGGA 4 251 1 GGGCCCACGG 0.99794 -50 CACTGTCCCTAATGGTGGTCGGGTC 4 286 0 CTGCCCATGG 0.983558 -15 CGGGTACACCCTGGCACAAGCGGCGCCG 5 6 0 CTGCACACGG 0.967269 -179 TGTTGGTGTAGTGACCAAATCAGCAGTGCCCCG 5 64 1 GTGCCAACAG 0.892317 -121 CAAATCAGCAGTGCCCCGGGTGGGTCTTGACGT 5 79 1 GTGCCCGTGG 0.986201 -106 TCCCATGCCCGGGTACCGGACGGTCACCAAGAC 5 126 0 GGGACCGCGG 0.978912 -59 CGGGAAGGACCTGGCCGGCACGGCCGATGATCG 6 44 1 CTGCCGCCGG 0.883644 -23 *** *** * *** Masking position 3 Map Score: 13.2756 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 107 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 9 ********** No masking Map Score: 8.55083e-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: 8.55083e-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: 8.55083e-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