AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i076_bsub_mtub_300.orf -o076_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 yveM 258 similar to capsular polysaccharide biosynthesis #2 yveK 245 similar to capsular polysaccharide biosynthesis #3 Rv0225 35 hypothetical protein Rv0225 #4 gmdA 300 gmdA Motif number 1 CCAGCATCTAAGGCAGCAACTTCAGCTGCCC 1 68 0 AGCAGCAACT 0.760142 -191 CACGCCCCGCCAGCGACGACCAGCATCTAAG 1 87 0 CGCGACGACC 0.991713 -172 TCCAAAAAATCGGCAGCAGCTAAACCGACAA 1 163 0 CGCAGCAGCT 0.974559 -96 GAGACGAAAACCGCCGCAGCTAAACCGATAA 1 194 1 CGCCGCAGCT 0.9905 -65 CGCGGGAAGCCAGCCGCGGGAAGGCTGAAGG 2 215 1 CGCCGCGGGA 0.972685 -31 CTGGCACACCCTACGGCCCGC 3 1 1 CGGCACACCC 0.936689 -35 GGCTCTCAGCGACAGCTGTCTGACCTG 4 7 1 CGCGACAGCT 0.956311 -294 CAATCCCGCACAGCCACGACCAACTTGGGAA 4 46 0 CGCCACGACC 0.994004 -255 GAGAATCCATACGACGCGACCCCCACGCCAC 4 80 0 AGACGCGACC 0.917305 -221 CCGCGCGAAACGGCCGCAGGCGCAATGGTCA 4 121 1 CGCCGCAGGC 0.989824 -180 AGGCTAGACTCCACCGCGGCCAAGTTGGTGA 4 149 0 CACCGCGGCC 0.98246 -152 TCCTGGTTGTCGGGGGCGACCAGGAAAATGT 4 181 0 CGGGGCGACC 0.991546 -120 AACGCCCGTTCTGCAGCGACCTCCTGGTTGT 4 202 0 CGCAGCGACC 0.995248 -99 AGATGTGGGTAGGGAACGCCCGTTCTGCAGC 4 216 0 AGGAACGCCC 0.687775 -85 TATGAAGCGACAGCGGCGCCCCGCTGTGATG 4 249 1 CGCGGCGCCC 0.99704 -52 GCATGACCGACAGAGGCGGGAAGACA 4 285 1 CGAGGCGGGA 0.764828 -16 * ********* Masking position 7 Map Score: 30.7242 Number of sites scoring better than the average of aligned sites = 2757 Number in coding regions = 2585 Number in noncoding regions = 172 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 2 AATGGAGGCACTCGGCTCTGCTGTGGGCAGC 1 44 1 CTCGGCTCGC 0.986511 -215 AGGACGTATTGTCGGTTTAGCTGCTGCCGAT 1 155 1 GTCGGTTTGC 0.994888 -104 TAATTCTTTTATCGGTTTAGCTGCGGCGGTT 1 202 0 ATCGGTTTGC 0.967861 -57 ACACCCTACGGCCCGCTAGGCTATCGACCA 3 16 1 GCCCGCTAGC 0.969397 -20 GATTCTCCTCCTCGGTTCCGCGCGAAACGGC 4 104 1 CTCGGTTCGC 0.992316 -197 TTGCGCCTGCGGCCGTTTCGCGCGGAACCGA 4 115 0 GGCCGTTTGC 0.977653 -186 GGTAGGGAACGCCCGTTCTGCAGCGACCTCC 4 209 0 GCCCGTTCGC 0.992078 -92 TCCCGCCTCTGTCGGTCATGCTCAGCCATCA 4 275 0 GTCGGTCAGC 0.972982 -26 ******** ** Masking position 5 Map Score: 11.5424 Number of sites scoring better than the average of aligned sites = 305 Number in coding regions = 284 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 3 CACTCGGCTCTGCTGTGGGCAGCTGAAGTT 1 52 1 TGCTGTGGGC 0.956495 -207 GTCGCTGGCGGGGCGTGAGGATGGGTTAAA 1 101 1 GGGCGTGAGG 0.963221 -158 TAACAGAAAGGGGCGCGGGAAGCCAGCCGC 2 202 1 GGGCGCGGGA 0.984093 -44 GCGGGAAGCCAGCCGCGGGAAGGCTGAAGG 2 216 1 AGCCGCGGGA 0.941418 -30 GCCGCGGGAAGGCTGAAGGCTATGAATAC 2 227 1 GGCTGAAGGC 0.88208 -19 TAGCCTAGCGGGCCGTAGGGTGTGCCAG 3 9 0 GGCCGTAGGG 0.994765 -27 AGTTGGTCGTGGCTGTGCGGGATTGGAGGT 4 52 1 GGCTGTGCGG 0.969823 -249 GGATTGGAGGTGGCGTGGGGGTCGCGTCGT 4 71 1 TGGCGTGGGG 0.981065 -230 CGCGCGAAACGGCCGCAGGCGCAATGGTCA 4 122 1 GGCCGCAGGC 0.950744 -179 TCACCAACTTGGCCGCGGTGGAGTCTAGCC 4 149 1 GGCCGCGGTG 0.980249 -152 GCGACCTCCTGGTTGTCGGGGGCGACCAGG 4 188 0 GGTTGTCGGG 0.821042 -113 ********** Masking position 5 Map Score: 16.9876 Number of sites scoring better than the average of aligned sites = 580 Number in coding regions = 535 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 4 CGCCAGCGACGACCAGCATCTAAGGCAGCA 1 81 0 GACCAGCATC 0.939584 -178 TTTTTGGAGAGACGAAAACCGCCGCAGCTA 1 186 1 GACGAAAACC 0.973692 -73 GACAGGAATAGAGGAGAATTTCATATT 2 8 0 GAGGAGAATT 0.926196 -238 CAGTAAATTAGAGGAAAATCATGATTTTGT 2 101 1 GAGGAAAATC 0.987664 -145 TCTCTTTAGAGAACAAAATCATGATTTTCC 2 113 0 GAACAAAATC 0.964376 -133 ACCAACTTGGGAACAAAACCACAGGTCAGA 4 29 0 GAACAAAACC 0.947962 -272 CGGAACCGAGGAGGAGAATCCATACGACGC 4 94 0 GAGGAGAATC 0.989761 -207 ********** Masking position 5 Map Score: 7.0751 Number of sites scoring better than the average of aligned sites = 259 Number in coding regions = 229 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 5 CCATCCTCACGCCCCGCCAGCGACGACCAGC 1 94 0 GCCCGCCAGC 0.997848 -165 AAAGGGGCGCGGGAAGCCAGCCGCGGGAAGG 2 208 1 GGAAGCCAGC 0.971836 -38 CACACCCTACGGCCCGCTAGGCTATCGACCA 3 15 1 GGCCGCTAGG 0.933349 -21 CAAAACCACAGGTCAGACAGCTGTCGCTGAG 4 15 0 GGCAGACAGC 0.988636 -286 CTCCAATCCCGCACAGCCACGACCAACTTGG 4 49 0 GCCAGCCACG 0.959694 -252 CGCCCGTTCTGCAGCGACCTCCTGGTTGTCG 4 200 0 GCGCGACCTC 0.847598 -101 CATCTACTATGAAGCGACAGCGGCGCCCCGC 4 242 1 GAGCGACAGC 0.936283 -59 TGTCGGTCATGCTCAGCCATCACAGCGGGGC 4 266 0 GCCAGCCATC 0.987627 -35 ** ******** Masking position 6 Map Score: 5.14871 Number of sites scoring better than the average of aligned sites = 1010 Number in coding regions = 957 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 6 AACCTTTTCCCCCCTAATTCTTTTATCGGT 1 217 0 CCCCTAATTC 0.95985 -42 ATGAAATTCTCCTCTATTCCTGTCGTTATT 2 14 1 CCTCTATTCC 0.988158 -232 TCATGATTTTCCTCTAATTTACTGCACTTC 2 95 0 CCTCTAATTT 0.910468 -151 CCCCACGCCACCTCCAATCCCGCACAGCCA 4 61 0 CCTCCAATCC 0.985943 -240 GGATTCTCCTCCTCGGTTCCGCGCGAAACG 4 103 1 CCTCGGTTCC 0.956617 -198 ********** Masking position 8 Map Score: 1.2088 Number of sites scoring better than the average of aligned sites = 145 Number in coding regions = 123 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 CACAGCCACGACCAACTTGGGAACAAAACC 4 39 0 ACCAACTTGG 0.995269 -262 CGCAATGGTCACCAACTTGGCCGCGGTGGA 4 141 1 ACCAACTTGG 0.995269 -160 ********** Masking position 5 Map Score: 0.278166 Number of sites scoring better than the average of aligned sites = 1 Number in coding regions = 1 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 TCAGGAGACATCACCTTTACAAAAA 1 6 0 TCACCTTTAC 0.973346 -253 TCCGGTAACTCAACCTTTTCCCCCCTAATT 1 228 0 CAACCTTTTC 0.961635 -31 TTTTAAATAATAACGTTTTCTTTTATAATC 2 165 1 TAACGTTTTC 0.926569 -81 GAGTCTAGCCTCACATTTTCCTGGTCGCCC 4 169 1 TCACATTTTC 0.971276 -132 CGTTCCCTACCCACATCTACTATGAAGCGA 4 229 1 CCACATCTAC 0.919876 -72 ********** Masking position 6 Map Score: 0.107817 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 188 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 9 ********** No masking Map Score: -8.2833e-14 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: -8.2833e-14 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: -8.2833e-14 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