AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -icysB_bsub_opreg_300.orf -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 spoIIE 300 serine phosphatase #2 yabS 84 similar to hypothetical proteins #3 yabT 88 yabT #4 yacA 103 similar to cell-cycle protein #5 ftsH 97 cell-division protein and general stress protein (class III heat-shock) #6 yacB 194 similar to hypothetical proteins #7 yacC 85 similar to hypothetical proteins #8 yacD 46 similar to protein secretion PrsA homolog #9 cysK 75 cysteine synthetase A #10 gltC 146 transcriptional regulator (LysR family) #11 ytkP 148 similar to cysteine synthase #12 yvbU 99 similar to transcriptional regulator (LysR family) Motif number 1 AGAATTTCCGGAATGTTGTCTAAAAATGAAAAAAATCGGC 1 140 0 GTTCTAAGAA 0.871449 -161 TTTCTGCCTTGATATTCGTTTATGAAAAGAATTTCCGGAA 1 167 0 GTTTTAAAGA 0.98326 -134 CGAAAGCACAGATAGGATTTTGTCAAAAGAAGGTAACAAT 1 227 0 GGTTTAAAGA 0.9171 -74 TAGTACCATAGAAAATCATTCCAATACAAACAATAACCAT 5 30 0 GTTTCTAAAA 0.814214 -68 GCGTCAGCCGGCAGTTTTTTTAGAAAGAAAGCGAA 6 6 0 GTTTTAAAAA 0.98945 -189 CCGCAGCTGAGCCAATCATTTACATAAAAAAACTGCCAGC 6 44 0 GTTTTTAAAA 0.9588 -151 TACACGATCAGCGGCTCATTTGTAAACAAATCGATACCAG 6 103 0 GTTTTAAAAA 0.989451 -92 TAAAAGGGCTGGAATTGATTTATGAAAGAAACCGCGTAGG 7 35 1 GTTTTAAGAA 0.972971 -51 TCTTTAGCGGGTTTTTAATTTGAGAAAAGGGGCTGAAAGC 8 13 1 GTTTTAAAGG 0.917099 -34 TTCTTTGACAGCTATTATTTTATCAATAAAGAGGCTGTGC 11 26 1 GTTTTAAAAA 0.989424 -123 TGTCATTCCTTTCTGAATAAAACAAGTGTCA 11 128 0 GTTTTAAAAA 0.98945 -21 * * *** ** *** Masking position 16 Map Score: 10.8989 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 126 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 2 AAATATGGTAGCGGCGGAGGGGATC 1 3 0 GGGGGAGGGA 0.997724 -298 ATAACAGGTGGGAGATGAGAGGA 1 288 1 GAGTGAGGGA 0.975116 -13 TCGTATTCTCCAGGAGGAATGAAT 2 71 1 CGGGGAAGAA 0.937982 -14 CAATCAAAGGCAAGTGGAATGGAAACACTTATA 3 28 1 CAGGGAAGGA 0.963859 -61 CTTACTGTGGGAGGAGGTAAGGA 5 85 1 GGGGGTAGGA 0.990211 -13 TTTGAGAAAAGGGGCTGAAAGCAGGT 8 31 1 GGGTGAAGCA 0.954055 -16 CGGAAATTGATCGGGGGAGAGGAATT 10 4 0 TGGGGAGGGA 0.985466 -143 TATCAATAAAGAGGCTGTGCGGATAGAGGAACA 11 46 1 GGGTGTGGGA 0.984306 -103 * ** **** *** Masking position 13 Map Score: 7.79118 Number of sites scoring better than the average of aligned sites = 225 Number in coding regions = 176 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 3 CAAGCGGTTAAGACACCGCCCTTTCACGGC 1 51 1 AGACACCGCC 0.968606 -250 CTTCTGCAAGAGAAACCGATTTGTTAGGAT 1 111 0 AGAAACCGAT 0.935997 -190 TTTCTCTTGCAGAAGCCGATTTTTTTCATT 1 126 1 AGAAGCCGAT 0.89225 -175 ATATCAAGGCAGAAACCGTCGAAGATTTCT 1 192 1 AGAAACCGTC 0.944839 -109 TTCTTTCTAAAAAAACTGCCGGCTGACGCT 6 17 1 AAAAACTGCC 0.929751 -178 ATTTACATAAAAAAACTGCCAGCGTCAGCC 6 37 0 AAAAACTGCC 0.929751 -158 GGATGATTGTAAAAGCCGCAGCTGAGCCAA 6 69 0 AAAAGCCGCA 0.879421 -126 GATTTATGAAAGAAACCGCGTAGGAAGTGT 7 51 1 AGAAACCGCG 0.974029 -35 TCTCAAATTAAAAACCCGCTAAAGAGC 8 8 0 AAAACCCGCT 0.909202 -39 ********** Masking position 3 Map Score: 7.46983 Number of sites scoring better than the average of aligned sites = 704 Number in coding regions = 592 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 4 GATCCCCTCCGCCGCTACCATATTTG 1 5 1 CCTCGCCGCT 0.997072 -296 AATTCCATTGGCCCCTTTACCAAGCT 3 73 0 CCTTGCCCCT 0.970917 -16 ATGGTGCAAACTGCAGAGCCTATGCTTCTTC 4 10 1 ACGCGAGCCT 0.841216 -94 TATCCTAACACTTTCAACCCCTCCAAGCAAAG 4 41 0 CTTCACCCCT 0.884205 -63 AAAAAAACTGCCGGCTGACGCTGGCAGTTTTT 6 25 1 CCGCGACGCT 0.989253 -170 AATGATTGGCTCAGCTGCGGCTTTTACAATCA 6 64 1 TCGCGCGGCT 0.941742 -131 ATACCATACACGATCAGCGGCTCATTTGTAAA 6 117 0 CGTCGCGGCT 0.971213 -78 ACCTGCTTTCAGCCCCTTTTCTCAAAT 8 30 0 CTTCGCCCCT 0.987324 -17 CCGTCTGACACTCCCTTCTTTG 11 1 1 CCTCGACACT 0.955331 -148 ** ** ****** Masking position 12 Map Score: 5.83526 Number of sites scoring better than the average of aligned sites = 913 Number in coding regions = 807 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 5 CCGTACGGGTCATCCTAACAAATCGGTTTC 1 100 1 CATCCTAACA 0.984368 -201 AAGATATTCATATCCTAACACTTTCAACCC 4 53 0 TATCCTAACA 0.975635 -51 AATGTCCTCCTCACAATGAGCAGGT 4 89 0 CCTCCTCACA 0.987964 -15 TCCTTACCTCCTCCCACAGTAAGCAC 5 82 0 CCTCCTCCCA 0.967758 -16 ACTGTTCCTCTATCCGCACAGCCTCTTTAT 11 51 0 TATCCGCACA 0.958287 -98 TGTCATATAATATCCTAACATAATAAACGT 11 103 0 TATCCTAACA 0.975635 -46 ********** Masking position 3 Map Score: 6.89783 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 29 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 TTGTCTAAAAATGAAAAAAATCGGCTTCTGCAAGAGA 1 128 0 ATAAAATCGT 0.735155 -173 AGGTAACAATACCAAAGAAATCTTCGACGGTTTCTGC 1 200 0 ACAAGATCTA 0.901939 -101 CTCCTGGAGAATACGAGGATTCTCAGATTCATATATT 2 50 0 ATGAGATCTA 0.820013 -35 CCAATCATTTACATAAAAAAACTGCCAGCGTCAGCCG 6 36 0 ACAAAAACTA 0.735155 -159 ACTTTACTTTTTACAAACATTCTACAATACCATACAC 6 138 0 TTAAAATCTA 0.888913 -57 TATTGGTATTATGTATATAATCTATCAATTTCAAAAT 9 21 0 ATATAATCTA 0.889002 -55 CATAATACCAATACAAATAGTCGGAAATTGAGGTGTC 9 45 1 ATAAAATCGA 0.959944 -31 CGGTCATAAAATCTAACAACTCTATAATCATTGTAGG 10 44 1 ATAACATCTA 0.935152 -103 TTTCAAAACGATATAAACAATATATAATTTAGATCAA 10 82 1 ATAAAATATA 0.832217 -65 TATAATTTAGATCAAAAGAATCTCAAAATGAGATAGA 10 104 1 ATAAAATCTA 0.985733 -43 GGAACAGTGTATGAAAACACTCTCGCACAAACGTTTA 11 73 1 ATAAAATCTA 0.985744 -76 GTATCATATGATGGAAAAGTTCTACAAGGAGTGAATG 12 15 0 ATAAAGTCTA 0.922293 -85 ** *** * *** * Masking position 11 Map Score: 4.88953 Number of sites scoring better than the average of aligned sites = 424 Number in coding regions = 337 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 7 ATGACCCGTACGGGATTCGAACCCGTGTTA 1 83 0 CGGGATTCGA 0.94199 -218 TCATCCAATTCTGGTATCGATTTGTTTACA 6 93 1 CTGGTATCGA 0.911719 -102 CCTAAAAGGGCTGGAATTGATTTATGAAAG 7 33 1 CTGGAATTGA 0.980582 -53 ACAAAAAATTTTGAAATTGATAGATTATAT 9 14 1 TTGAAATTGA 0.832427 -62 TACAAATAGTCGGAAATTGAGGTGTCGAGA 9 56 1 CGGAAATTGA 0.980581 -20 CCGGTATTATCGGAAATTGATCGGGGGAGA 10 17 0 CGGAAATTGA 0.980581 -130 ********** Masking position 7 Map Score: 3.59036 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 173 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 ATATGGTAGCGGCGGAGGGGATC 1 4 0 GGCGGAGGGG 0.989163 -297 GGCAGAAACCGTCGAAGATTTCTTTGGTAT 1 199 1 GTCGAAGATT 0.772247 -102 AATATAACAGGTGGGAGATGAGAGGA 1 285 1 GTGGGAGATG 0.984817 -16 AATTTCTTCTGGCGAAGATGGGAATATATG 2 28 1 GGCGAAGATG 0.971802 -57 TGTGCTTACTGTGGGAGGAGGTAAGGA 5 81 1 GTGGGAGGAG 0.955122 -17 GAAATTGATCGGGGGAGAGGAATT 10 5 0 GGGGGAGAGG 0.990999 -142 ********** Masking position 6 Map Score: 3.55616 Number of sites scoring better than the average of aligned sites = 295 Number in coding regions = 269 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 9 TGCAGAGCCTATGCTTCTTCTTTGCTTGGAGGG 4 22 1 ATGTCTTTTT 0.974529 -82 TGCTTCCGAGATGGTTATTGTTTGTATTGGAAT 5 20 1 ATGTATTTTT 0.948783 -78 GACTATTTGTATTGGTATTATGTATATAATCTA 9 34 0 ATTTATTTGT 0.859207 -42 TCTCGCACAAACGTTTATTATGTTAGGATATTA 11 93 1 ACGTATTTGT 0.873151 -56 AGGATATTATATGACACTTGTTTTATTCAGAAA 11 117 1 ATGACTTTTT 0.888183 -32 GATTCATTTTATTTATCTTATGTTCTACCGTAT 12 48 0 ATTTCTTTGT 0.926492 -52 GATAAATAAAATGAATCTTTTTTATAAGGAGCA 12 64 1 ATGTCTTTTT 0.974529 -36 *** **** *** Masking position 1 Map Score: 0.823744 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 123 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 10 AAAGAAGGTAACAATACCAAAGAAATCTTC 1 212 0 ACAATACCAA 0.973515 -89 ACTATGTTCAATAGTACCATAGAAAATCAT 5 51 0 ATAGTACCAT 0.894303 -47 CAAACATTCTACAATACCATACACGATCAG 6 132 0 ACAATACCAT 0.973381 -63 GATTATATACATAATACCAATACAAATAGT 9 36 1 ATAATACCAA 0.959491 -40 ********** Masking position 5 Map Score: 0.752992 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 13 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 11 ********** No masking Map Score: 1.23224e-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 12 ********** No masking Map Score: 1.23224e-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 13 ********** No masking Map Score: 1.23224e-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