AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -iargR_aful_opreg_100.orf -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 AF0079 69 A. fulgidus predicted coding region AF0079 #2 AF0080 27 acetylornithine aminotransferase (argD-1) #3 AF0522 39 acetylornithine deacetylase (argE) #4 AF0883 71 argininosuccinate lyase (argH) #5 AF1255 27 ornithine carbamoyltransferase (argF) #6 AF1259 36 inosine monophosphate dehydrogenase, putative #7 AF1260 207 phosphoribosylformylglycinamidine synthase I (purQ) #8 AF1269 300 A. fulgidus predicted coding region AF1269 #9 AF1270 33 transcriptional regulatory protein, ArsR family #10 AF1280 272 acetylglutamate kinase (argB) #11 AF1814 83 A. fulgidus predicted coding region AF1814 #12 AF1815 36 acetylornithine aminotransferase (argD-2) #13 AF2071 60 N-acetyl-gamma-glutamyl-phosphate reductase (argC) #14 AF2252 78 argininosuccinate synthetase (argG) Motif number 1 TAACTTATACCTTAAAATTTTTTACGGTAACCTTTTTG 1 32 0 CTATTTTAGT 0.879112 -38 TTAATTAACCGGAAATTTTTAACCGGT 5 10 1 CGATTTACGT 0.933251 -18 TTTTAGCTTGCCGTCATTTTTCTTCTGTA 6 18 1 CGATTTTTGT 0.958159 -19 AATTAAAGATCTGCCAGCTTTGAAAGTTTAGGTTTTTC 7 11 1 CGATTTAATT 0.986243 -197 AAGCAATCAACCGCAATCTTTTAAGCTTTTTCCGTGTC 7 176 0 CGATTTAATT 0.986243 -32 AGAGGATCGTCAAGGAGATTTATACTTTGCGCTGCAAA 8 227 0 CAATTTTATT 0.886053 -74 AACCCTTTAACAGGAAATTTTCTACTGTCTATCCCAAC 8 266 0 CGATTTTAGT 0.989281 -35 TTTGGGAATCCAGGCAGTTTTTAACACTTGCCTCCAGC 10 199 1 CGATTTAACT 0.950102 -74 ATTCCTCCGTCAGCTAAATTTGTTTCTTTACAACTGAA 11 52 1 CGATTTTTTT 0.960738 -32 TTCGCCATCTCAGAAAACTCTTTATTTTGCCTCTTAAC 13 24 1 CGATCTTATT 0.944264 -37 TCTGAAAACCCAGGAAGTTTTTTAACTTTTGTTTAATC 14 15 1 CGATTTTATT 0.989969 -64 TCCCGTCATGCGGAGAGGTTTAAATCTTTTGAGATTAA 14 47 0 CGATTTAATT 0.986243 -32 * * * *** ** ** Masking position 6 Map Score: 16.8117 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 34 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 2 GGAAAAAATTTTGCTGAGTAATT 2 15 0 GAAAAATTTG 0.766132 -13 GCCATCATCTCCAAAACATAAATACATTTGCG 4 16 1 CCAAAATAAA 0.841017 -56 CAAAAGTTTTTAGCTTGCCGTC 6 1 1 CAAAAGTTTA 0.738198 -36 AGTAAAAAAAGAAAAACCTAAACTTTCAAAGC 7 27 0 GAAAAATAAA 0.9384 -181 CCTGTCTAGGGAAAAGTAAAAAAAGAAAAACC 7 41 0 GAAAAGAAAA 0.826797 -167 TGCCGACACGGAAAAAGCTTAAAAGATTGCGG 7 172 1 GAAAAATTAA 0.903133 -36 CAGATAACCACAAAAGACTATGTGCTAGTTTA 8 45 1 CAAAAGTATG 0.759559 -256 ACTTTGCGCTGCAAAATATAGGCGACGGAGAG 8 210 0 GCAAAATAGG 0.798663 -91 ATTTTGCAGCGCAAAGTATAAATCTCCTTGAC 8 225 1 GCAAAGTAAA 0.934945 -76 TAGTAGCCTTGAAAAATCTTTAGATTGGAGCG 10 113 0 GAAAAATTTA 0.85623 -160 AGGAAAAATATTTAATGATTTATT 12 3 1 GAAAAATTTA 0.85623 -34 GCAAAAAATAGAAATAAATCAT 12 25 0 GCAAAATAGA 0.877204 -12 AGGTTAAGAGGCAAAATAAAGAGTTTTCTGAG 13 32 0 GCAAAAAAGA 0.639835 -29 GAGGAAAAGGTTAAGAGGCAAAATA 13 46 0 GAAAAGTAAG 0.914236 -15 TGAGATTAAACAAAAGTTAAAAAACTTCCTGG 14 24 0 CAAAAGAAAA 0.688862 -55 TGTTTAATCTCAAAAGATTTAAACCTCTCCGC 14 44 1 CAAAAGTTAA 0.844889 -35 ****** **** Masking position 5 Map Score: 12.0243 Number of sites scoring better than the average of aligned sites = 628 Number in coding regions = 420 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 235 Fraction of orfs with sites within 600 bp upstream = 0.0377449 Motif number 3 GAAAAAATTTTGCTGAGTAATTAAGT 2 7 0 TGCTGAGTAA 0.950424 -21 CAATCTGTAATGCTGCCCAATCCAAAAAGC 8 137 0 TGCTGCCCAA 0.971677 -164 GCCTATATTTTGCAGCGCAAAGTATAAATC 8 219 1 TGCAGCGCAA 0.973717 -82 TGTTTGGTTGCGCAACGGTGCAACT 9 19 0 GGTTGCGCAA 0.939681 -15 GCTCTATCCATGCTGAGCCACGGGCCCTTA 10 37 0 TGCTGAGCCA 0.990041 -236 TCAGGCAATCTGCTGAGCAATTGTAAAGCT 10 154 0 TGCTGAGCAA 0.993279 -119 TCAGCAGATTGCCTGAGCCATCCACGCCGA 10 168 1 GCCTGAGCCA 0.927882 -105 ********** Masking position 10 Map Score: 7.40335 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 148 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 4 GCACTCAGTTTGTGCAGAGGTTATTAATT 4 53 0 TCTTTGCGAG 0.968219 -19 TTTTTACCTTACGGAGAAGATTGACG 8 2 1 TTCCTACGAG 0.946845 -299 CTTTGTTTATTCAGACCGTACAGAGCACCATAAAC 8 72 0 TCCCTACGAG 0.992771 -229 GCAAGCTCTCTCACCTCTCACAGGGACAGAGAAGA 8 166 1 TCTCCACGGG 0.98095 -135 AGGCCGTCGCTCTATCCATGCTGAGCCACGGGCCC 10 40 0 TCCCTGCGAG 0.996487 -233 GATCGCGGGTTCAAATCCCGCCGGGTCCGCTCCAA 10 86 1 TCTCCGCGGG 0.990685 -187 ACAATCCCGTCATGCGGAGAGGTTTAAAT 14 60 0 TCTCTGCGAG 0.995736 -19 ** ** *** *** Masking position 1 Map Score: 6.88923 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 79 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 5 ATAACCTCTGCACAAACTGAGTGC 4 58 1 CACAAACTGA 0.810717 -14 ATCAGACCAGCCCCACCAGCTAAAAGAATT 7 91 1 CCCCACCAGC 0.979611 -117 GATTGACGTGCCCGAGCAGATAACCACAAA 8 29 1 CCCGAGCAGA 0.95111 -272 TACTGTCTATCCCAACCAGAGGATCGTCAA 8 252 0 CCCAACCAGA 0.994719 -49 TGCACCGTTGCGCAACCAAACA 9 22 1 CGCAACCAAA 0.935866 -12 CCTTAAGTATCCCAACCTGAATCTGGACAC 10 253 1 CCCAACCTGA 0.987942 -20 GGCCACCACCAAAATTGGTGGAA 11 4 1 CACCACCAAA 0.935036 -80 ********** Masking position 5 Map Score: 4.61556 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 215 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 GCTCTGCCATCATCTCCAAAACATAAATA 4 10 1 TCATCTCCAA 0.817885 -62 AGAATTAATAACCTCTGCACAAACTGAGTG 4 51 1 ACCTCTGCAC 0.983808 -21 GCAGCGTTGATGTTCTGCACTCTTTAGTGC 7 145 0 TGTTCTGCAC 0.886863 -63 TAGTTTATGGTGCTCTGTACGGTCTGAATA 8 70 1 TGCTCTGTAC 0.870944 -231 TAGGCGACGGAGAGCTGCACCATTCTTCTC 8 194 0 AGAGCTGCAC 0.90248 -107 ATTTATACTTTGCGCTGCAAAATATAGGCG 8 218 0 TGCGCTGCAA 0.96208 -83 TCCCGCCGGGTCCGCTCCAATCTAAAGATT 10 101 1 TCCGCTCCAA 0.941846 -172 AACCTCTGAAAACCCAGGAAG 14 2 1 ACCTCTGAAA 0.775454 -77 AAAGATTTAAACCTCTCCGCATGACGGGAT 14 56 1 ACCTCTCCGC 0.879748 -23 ********** Masking position 6 Map Score: 3.15454 Number of sites scoring better than the average of aligned sites = 1109 Number in coding regions = 1051 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 7 ACTTAATTACTCAGCAAAATTTTTTCC 2 11 1 TCAGCAAATT 0.961266 -17 TTTTTCCGTGTCGGCAGCGTTGATGTTCTGC 7 157 0 TCGGCAGCTT 0.989653 -51 CTTTTTGGATTGGGCAGCATTACAGATTGCA 8 138 1 TGGGCAGCTT 0.956422 -163 CTACTACCATTCAGCAGCTTTACAATTGCTC 10 139 1 TCAGCAGCTT 0.99127 -134 TTACAATTGCTCAGCAGATTGCCTGAGCCAT 10 158 1 TCAGCAGATG 0.964095 -115 TATTCCTCCGTCAGCTAAATTTGTTTCTTTA 11 51 1 TCAGCTAATT 0.8596 -33 ******** ** Masking position 10 Map Score: 2.95834 Number of sites scoring better than the average of aligned sites = 331 Number in coding regions = 315 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 8 CCTTTTTGAGTGTCGGTGGTACTAATTGC 1 10 0 TGTCGGTGGT 0.778795 -60 GTTTTGGAGATGATGGCAGAGC 4 3 0 TGATGGCAGA 0.948647 -69 AAACTTTCAAAGCTGGCAGATCTTTAATT 7 10 0 AGCTGGCAGA 0.781358 -198 GCTTTTTCCGTGTCGGCAGCGTTGATGTTC 7 160 0 TGTCGGCAGC 0.963098 -48 TTAGTTAGGATGATGGAAGCCCTTGAGCTT 8 111 1 TGATGGAAGC 0.960418 -190 CAGACCGCATTGCTGGAGGCAAGTGTTAAA 10 218 0 TGCTGGAGGC 0.976496 -55 CCACCAATTTTGGTGGTGGCC 11 2 0 TGGTGGTGGC 0.940316 -82 CAAATTTAGCTGACGGAGGAATATTTATAT 11 44 0 TGACGGAGGA 0.948092 -40 ********** Masking position 5 Map Score: 3.37685 Number of sites scoring better than the average of aligned sites = 439 Number in coding regions = 416 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 ********** No masking Map Score: 2.07722e-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: 2.07722e-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 11 ********** No masking Map Score: 2.07722e-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