AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -ioxyR_bsub_opreg_100.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 ycgK 192 similar to transcriptional regulator (LysR family) #2 gltC 146 transcriptional regulator (LysR family) #3 dps 262 alternate gene name: ytkB; stress- and starvation-induced gene controlled by sigma-B #4 yvbU 99 similar to transcriptional regulator (LysR family) #5 ywqM 122 similar to transcriptional regulator (LysR family) #6 ywbI 105 alternate gene name: ipa-24d; similar to transcriptional regulator (LysR family) #7 yybE 228 similar to transcriptional regulator (LysR family) Motif number 1 AGCTCCTTCTTTTCGTAAATGATGATATGGATTATGTTAGCA 1 93 1 TTAATGAGAT 0.970715 -100 TTTTTATATCTTGGACGAATCATAACAGAAATTGCTAACATA 1 125 0 TTAATAAAAT 0.934283 -68 TTCGTCCAAGATATAAAAATGATGAAAATGATAGGTTCAACC 1 148 1 ATAATGAGAT 0.944667 -45 CTCTCCCCCGATCAATTTCCGATAATACCGGTCATAAAATCT 2 16 1 ATCATAAGGT 0.834685 -131 TCATTGTAGGTTTTCAAAACGATATAAACAATATATAATTTA 2 71 1 TTAATAAAAT 0.934283 -76 TTAGATCAAAAGAATCTCAAAATGAGATAGATGGATGTGAGA 2 110 1 AGAATGAGAT 0.745601 -37 TAAAAGCCTATAATGTAAAGCATACCATTGATCCACCACAAG 3 33 0 TAAATAAGAT 0.941348 -230 TTTTTTAACAATTGTAGCATAATAGAAGAAATCGTGACAGAT 3 161 1 ATAATAAAAT 0.879838 -102 AAAAAGAGGTTTTAGCGTACGATATTAAGGGTATACATAGTC 3 210 1 TTAATAAGGT 0.958656 -53 CATCATATGATACGGTAGAACATAAGATAAATAAAATGAATC 4 39 1 TAAATAAAAT 0.806227 -61 AACAATTTACTTATGCTCCTTATAAAAAAGATTCATTTTATT 4 68 0 TTCATAAGAT 0.958655 -32 TTACGAATGATTTTCTTCATCATATAATGGATTCATCAATCA 5 30 1 TTAATAAGAT 0.982092 -93 TAGGTAAAATATATATTAAGAATAAGAAGTATTCCTTTTGTC 6 55 1 ATAATAATAT 0.689971 -51 TTTATATGCATTATACAACATATATCAACGGTGCTAAGATAA 7 114 0 TTCATAAGGT 0.907438 -115 CTCTCCTTATTACATATAAGCATGAAAAGGATATTTTATATG 7 148 0 TAAATGAGAT 0.906553 -81 ** * *** * *** Masking position 12 Map Score: 12.9768 Number of sites scoring better than the average of aligned sites = 511 Number in coding regions = 392 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 2 ATTTGAACCAGCTCCTTCTTTTCGTAAATG 1 84 1 GCTCCTTCTT 0.957152 -109 ACATAATCCATATCATCATTTACGAAAAGA 1 100 0 TATCATCATT 0.672992 -93 ATGTCATGACGCTTCTCATTACGATAAGTA 3 120 0 GCTTCTCATT 0.859031 -143 GGTATCTCCTCCTTGTTATATGAC 3 249 0 TCTCCTCCTT 0.992879 -14 ACAATTTACTTATGCTCCTTATAAAAAAGA 4 79 0 TATGCTCCTT 0.920546 -21 GATGCATCTGCTCCTTTGTTTACGAA 5 7 1 TCTGCTCCTT 0.983288 -116 TTGTTCTCTTCCTTTCTAAATCGG 5 109 0 TCTCTTCCTT 0.947607 -14 AAGGAATACTTCTTATTCTTAATATATATT 6 62 0 TCTTATTCTT 0.740356 -44 AATTATCATCTCTCCTTATTACATATAAGC 7 169 0 TCTCCTTATT 0.937412 -60 ********** Masking position 6 Map Score: 8.54937 Number of sites scoring better than the average of aligned sites = 771 Number in coding regions = 534 Number in noncoding regions = 237 Number of orfs with sites within 600 bp upstream = 271 Fraction of orfs with sites within 600 bp upstream = 0.0435271 Motif number 3 ATCTAACAACTCTATAATCATTGTAGGTTTTCAAA 2 54 1 TTATAATTTA 0.98152 -93 TGATCTAAATTATATATTGTTTATATCGTTTTGAA 2 83 0 TTATATTTTA 0.921804 -64 CACCTCCCGTTTTTTAACAATTGTAGCATAATAGA 3 152 1 TTTTAATTTA 0.916865 -111 TATATGACTATGTATACCCTTAATATCGTACGCTA 3 222 0 TTATATTATA 0.827218 -41 ATGCCTCCCTTATATACTTATTGTACATAAGGTCT 6 15 1 TTATAATTTA 0.981439 -91 CTTCTTATTCTTAATATATATTTTACCTATAGAGA 6 49 0 TAATAATTTA 0.916851 -57 AAAAGGATATTTTATATGCATTATACAACATATAT 7 131 0 TTATAATTTA 0.98145 -98 * **** *** ** Masking position 6 Map Score: 3.55296 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 8 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 4 TTTTATATCTTGGACGAATCATAACAGAAA 1 136 0 TGGACGAATC 0.98437 -57 TTGTGTGAATCAGAGTGATTT 3 2 1 TGTGTGAATC 0.869638 -261 TTTCTTGTGGTGGATCAATGGTATGCTTTA 3 30 1 TGGATCAATG 0.925107 -233 TGTAACCATTTGGACGACTGTAAAAGCCTA 3 65 0 TGGACGACTG 0.943591 -198 TGCTCCTTTGTTTACGAATGATTTTCTTCA 5 19 1 TTTACGAATG 0.905864 -104 TCTGTATTGATTGATGAATCCATTATATGA 5 49 0 TTGATGAATC 0.961709 -74 TTTTAGCGATTGGATTAATCGAAATAATCA 5 79 0 TGGATTAATC 0.892868 -44 AGGATGATTGTTTATGAATGGCAGTGCTCC 7 41 0 TTTATGAATG 0.907558 -188 ********** Masking position 7 Map Score: 4.07397 Number of sites scoring better than the average of aligned sites = 478 Number in coding regions = 424 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 5 CCCCCTCGGCAAATACCTTTTCATCCCGATA 1 16 1 AAATACCTTT 0.868655 -177 ATTACAAATGAAACACCGTTTTCTAAAAACG 1 55 0 AAACACCTTT 0.943197 -138 ACATAATCCATATCATCATTTACGAAAAGAA 1 99 0 TATCATCTTT 0.816003 -94 TCGTACGCTAAAACCTCTTTTTTACCCTTAT 3 201 0 AAACCTCTTT 0.889931 -62 GATTAATCGAAATAATCATCTGTATTGATTG 5 66 0 AATAATCTCT 0.782127 -57 ATTCATAAACAATCATCCTTTATTTCTTACG 7 52 1 AATCATCTTT 0.965673 -177 TTACGAATTCAAACATCCTCGAGTCTGTTTA 7 78 1 AAACATCTCG 0.869785 -151 AATGCATATAAAATATCCTTTTCATGCTTAT 7 144 1 AAATATCTTT 0.931224 -85 TTCCCATTCCAATTATCATCTCTCCTTATTA 7 178 0 AATTATCTCT 0.9007 -51 ******* *** Masking position 9 Map Score: 4.42155 Number of sites scoring better than the average of aligned sites = 433 Number in coding regions = 366 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 6 TAGCAATTTCTGTTATGATTCGTCCAAGAT 1 130 1 TGTTATGATT 0.832819 -63 TGAATCAGAGTGATTTTCTTGTGGTGGATC 3 16 1 TGATTTTCTT 0.867438 -247 TTGTGCTGGCTGTTTTGCTTGTAACCATTT 3 84 0 TGTTTTGCTT 0.97601 -179 TTACGATAAGTATTTTGATTGTGCTGGCTG 3 102 0 TATTTTGATT 0.911946 -161 AGATTCATTTTATTTATCTTATGTTCTACC 4 52 0 TATTTATCTT 0.713012 -48 TGTTTACGAATGATTTTCTTCATCATATAA 5 27 1 TGATTTTCTT 0.867438 -96 AATAATCATCTGTATTGATTGATGAATCCA 5 57 0 TGTATTGATT 0.832819 -66 TACAGATGATTATTTCGATTAATCCAATCG 5 73 1 TATTTCGATT 0.761152 -50 TCCTCGAGTCTGTTTATATTATTATCTTAG 7 93 1 TGTTTATATT 0.854822 -136 ********** Masking position 9 Map Score: 2.83676 Number of sites scoring better than the average of aligned sites = 1108 Number in coding regions = 962 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 7 ACACCGTTTTCTAAAAACGCCGAGATGTAT 1 44 0 CTAAAAACGC 0.981349 -149 GTCATAAAATCTAACAACTCTATAATCATT 2 46 1 CTAACAACTC 0.952275 -101 ATATCGTACGCTAAAACCTCTTTTTTACCC 3 205 0 CTAAAACCTC 0.981349 -58 AATCCAATCGCTAAAACCGATTTAGAAAGG 5 93 1 CTAAAACCGA 0.953457 -30 ********** Masking position 6 Map Score: 0.486891 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 46 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 GATAGGTTCAACCTATGGAGGCTGAA 1 177 1 ACCTATGGAG 0.958417 -16 CGTTTTGAAAACCTACAATGATTATAGAGT 2 62 0 ACCTACAATG 0.937155 -85 GACTGTAAAAGCCTATAATGTAAAGCATAC 3 50 0 GCCTATAATG 0.93714 -213 TATATATTTTACCTATAGAGAGACCTTATG 6 40 0 ACCTATAGAG 0.980392 -66 ATGATGAGGGACCGATAAAGTCCCG 7 6 0 ACCGATAAAG 0.955292 -223 ********** Masking position 5 Map Score: 0.305383 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 25 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 9 ********** No masking Map Score: -9.71011e-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: -9.71011e-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: -9.71011e-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