AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00780_bsub_reg_100.orf -o00780_bsub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ylxY 117 alternate gene name: ymxI; similar to deacetylase #2 ymxG 39 similar to processing protease #3 yqhS 86 similar to 3-dehydroquinate dehydratase #4 yqhR 226 yqhR #5 yteI 185 similar to protease IV #6 bioW 251 6-carboxyhexanoate-CoA ligase Motif number 1 CTTGTCCTTCTCCTTCATAATGTGAGGTGAG 1 84 1 TCCTTCATAT 0.703669 -34 ATTTGTTCCTCCTATTCAAAGACAAG 2 24 0 TTCCTCCTTT 0.946053 -16 TTCGCGAGGGTTTCTCATGTAAAAAATGTTC 3 53 0 TTTCTCATTA 0.93375 -34 ACAATCTCTCCTTTTCGCGAGGGTT 3 72 0 TCTCTCCTTT 0.986753 -15 GGTTTAGCGGTGTTTCCTGTACAATAGAGTG 4 56 0 TGTTTCCTTA 0.888658 -171 AAGCCGGAGCTTTCTCATGAAGTGAAACATT 5 114 1 TTTCTCATAA 0.900041 -72 AAGTGAAACATTTTTCATATTGAATCGTATA 5 133 1 TTTTTCATTT 0.897596 -53 TTTCCTAAACTCTCTCATTATACGATTCAAT 5 151 0 TCTCTCATAT 0.949786 -35 TTTCTCCTCCTTTTTCCTAAACTCTCTCATT 5 163 0 TTTTTCCTAA 0.900061 -23 ACGGTCTTTTTGTTTCCTTTTAACCAACTGC 6 49 1 TGTTTCCTTT 0.925874 -203 AAATCGATCCTTTCTTCTATTGACAGAAACA 6 83 1 TTTCTTCTTT 0.785227 -169 AATATATTATTCTCTCCTGTTTCTGTCAATA 6 100 0 TCTCTCCTTT 0.986753 -152 GTGTAGCGCTTCTCACCTAAATTGTTAACCA 6 156 0 TCTCACCTAA 0.763968 -96 ******** ** Masking position 8 Map Score: 13.8659 Number of sites scoring better than the average of aligned sites = 1713 Number in coding regions = 1230 Number in noncoding regions = 483 Number of orfs with sites within 600 bp upstream = 517 Fraction of orfs with sites within 600 bp upstream = 0.0830389 Motif number 2 TGAAAACATAAAAGGAGCCTGGGAGACCCGG 1 12 1 AAAGGAGCTG 0.951102 -106 GCTTCAAAATAAAGAAGCCGGGTCTCCCAGG 1 29 0 AAAGAAGCGG 0.990195 -89 AAGCTTTTCAAAAGCAGGCGGGTTCTACCTT 1 56 1 AAAGCAGCGG 0.978491 -62 CTCACATTATGAAGGAGAAGGACAAGGTAGA 1 79 0 GAAGGAGAGG 0.954669 -39 TAGCAATCCTAAAGAAATAGGCAGGTTGATA 4 13 0 AAAGAAAAGG 0.969908 -214 CAATAGAGTGAAAGGAAATGGTTAGCAATCC 4 35 0 AAAGGAATGG 0.95061 -192 AGTTTAGGAAAAAGGAGGAGAAAAA 5 171 1 AAAGGAGAGA 0.966094 -15 CTGTAAAAAGAAATCGAAAAAGACCGT 6 7 1 AAAGAAACGA 0.946999 -245 CAGTTGGTTAAAAGGAAACAAAAAGACCGTT 6 48 0 AAAGGAACAA 0.774849 -204 TCTTCTATTGACAGAAACAGGAGAGAATAAT 6 95 1 ACAGAAAAGG 0.870495 -157 ******* *** Masking position 6 Map Score: 11.1207 Number of sites scoring better than the average of aligned sites = 1381 Number in coding regions = 1173 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 214 Fraction of orfs with sites within 600 bp upstream = 0.034372 Motif number 3 CTTCTTTATTTTGAAGCTTTTCAAAAGCAGG 1 43 1 TTGAACTTTT 0.954546 -75 TTCACTTCTCGTGAACATTTTATCATACTGG 3 25 0 GTGAAATTTT 0.959373 -62 TTCACGAGAAGTGAACATTTTTTACATGAGA 3 41 1 GTGAAATTTT 0.959373 -46 CTTTAGGATTGCTAACCATTTCCTTTCACTC 4 30 1 GCTAACATTT 0.720738 -197 TACCCGTTATTTTCAAATTTTACTCGCAGCT 4 142 1 TTTCAATTTT 0.788736 -85 GCCAAAAAGTGTGAGCTTTTTTATTGACATT 4 173 1 GTGAGTTTTT 0.756882 -54 TTTATTGACATTTCATTTTTTGGGCACACTT 4 192 1 TTTCATTTTT 0.741414 -35 TGCTGTCATATTTAAGTTTTTCTGCCATCCA 5 26 1 TTTAATTTTT 0.836833 -160 TTCTCATGAAGTGAAACATTTTTCATATTGA 5 125 1 GTGAACATTT 0.9601 -61 TATTCTAATTGTTAACCTTTGAATATAATTG 6 127 1 GTTAACTTTG 0.832667 -125 AATATAATTGGTTAACAATTTAGGTGAGAAG 6 148 1 GTTAAAATTT 0.88442 -104 AAGTTTCTTCTTGCATCATTTCTCGCCCTTT 6 205 0 TTGCACATTT 0.858937 -47 ***** ***** Masking position 9 Map Score: 7.16383 Number of sites scoring better than the average of aligned sites = 1017 Number in coding regions = 816 Number in noncoding regions = 201 Number of orfs with sites within 600 bp upstream = 218 Fraction of orfs with sites within 600 bp upstream = 0.0350145 Motif number 4 TTCAAAAGCAGGCGGGTTCTACCTTGTCCT 1 62 1 GGCGGGTTCT 0.938569 -56 CAGATGAAGGCAGCTTGTCTTTGAATAG 2 9 1 GGCAGCTTGT 0.991897 -31 TAAAGAAATAGGCAGGTTGATAAT 4 5 0 GGCAGGTTGA 0.986317 -222 CCTCTAGATTGACAGGCTGAAAAAATTGCC 4 85 1 GACAGGCTGA 0.820204 -142 CACACTTTTTGGCAGCTGCGAGTAAAATTT 4 156 0 GGCAGCTGCG 0.882395 -71 GGCACCTCCAGTTAAAGTGT 4 217 0 GGCACCTCCA 0.887143 -10 CACGTTTGCCGGCAGCCCGTTAAGCCGGAG 5 93 1 GGCAGCCCGT 0.983012 -93 ATCGATTTATGGCAGTTGGTTAAAAGGAAA 6 61 0 GGCAGTTGGT 0.951389 -191 ********** Masking position 3 Map Score: 4.61322 Number of sites scoring better than the average of aligned sites = 1008 Number in coding regions = 911 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 5 GGCGGGTTCTACCTTGTCCTTCTCCTTCATA 1 72 1 ACTTGTCCTT 0.756545 -46 AGATGAAGGCAGCTTGTCTTTGAATAGGAGG 2 12 1 ACTTGTCTTT 0.930071 -28 AAATTGCCATAGCCTTGCTTTTCCTACATGC 4 107 1 ACCTTGCTTT 0.889287 -120 CATGCATTATACCCGTTATTTTCAAATTTTA 4 133 1 ACCGTTATTT 0.914804 -94 TTTTTCTGCCATCCAGTATTTGTGATAAAAT 5 42 1 ACCAGTATTT 0.801686 -144 TTTTCACACAAAACGGTCTTTTTCGATTTCT 6 19 0 AACGGTCTTT 0.972302 -233 TTTTGTGTGAAAACGGTCTTTTTGTTTCCTT 6 37 1 AACGGTCTTT 0.972302 -215 CCATAAATCGATCCTTTCTTCTATTGACAGA 6 79 1 ACCTTTCTTC 0.943834 -173 GAGAAGCGCTACACGTTCTTCAGTTATCAGT 6 173 1 AACGTTCTTC 0.897285 -79 * ********* Masking position 10 Map Score: 4.09985 Number of sites scoring better than the average of aligned sites = 1174 Number in coding regions = 999 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 163 Fraction of orfs with sites within 600 bp upstream = 0.0261805 Motif number 6 AGAAATAGGCAGGTTGATAAT 4 2 0 AGGTTGATAA 0.874884 -225 TGAAAGGAAATGGTTAGCAATCCTAAAGAA 4 28 0 TGGTTAGCAA 0.948565 -199 CTAGATTGACAGGCTGAAAAAATTGCCATA 4 88 1 AGGCTGAAAA 0.818467 -139 TCACAAATACTGGATGGCAGAAAAACTTAA 5 37 0 TGGATGGCAG 0.841472 -149 TTATGGCAGTTGGTTAAAAGGAAACAAAAA 6 55 0 TGGTTAAAAG 0.899391 -197 TTATATTCAAAGGTTAACAATTAGAATATA 6 125 0 AGGTTAACAA 0.965489 -127 TGAATATAATTGGTTAACAATTTAGGTGAG 6 146 1 TGGTTAACAA 0.935739 -106 ********** Masking position 9 Map Score: 2.1614 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 268 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 7 TTTTATCATACTGGAAAAGGATTATACA 3 9 0 CTGGAAAAGG 0.961498 -78 CTGTACAATAGAGTGAAAGGAAATGGTTAG 4 41 0 GAGTGAAAGG 0.950442 -186 TATAATGCATGTAGGAAAAGCAAGGCTATG 4 114 0 GTAGGAAAAG 0.875576 -113 TGAGAGAGTTTAGGAAAAAGGAGGAGAAAA 5 165 1 TAGGAAAAAG 0.752676 -21 CTGTAAAAAGAAATCGAAAA 6 1 1 CTGTAAAAAG 0.962876 -251 AGACCGTTTTGTGTGAAAACGGTCTTTTTG 6 31 1 GTGTGAAAAC 0.838574 -221 CTTCAGTTATCAGTGAAAGGGCGAGAAATG 6 190 1 CAGTGAAAGG 0.961818 -62 CATTCTGACACTATAAAAAGTTTCTTCTTG 6 223 0 CTATAAAAAG 0.855948 -29 ********** Masking position 6 Map Score: 3.34697 Number of sites scoring better than the average of aligned sites = 956 Number in coding regions = 794 Number in noncoding regions = 162 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 8 ********** No masking Map Score: -1.24102e-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: -1.24102e-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 10 ********** No masking Map Score: -1.24102e-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