AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00640_hinf_reg_100.orf -o00640_hinf_100.ace -a/home/amcguire/genomes/ORF_hinf.txt -z/home/amcguire/genomes/hinf.fna -g0.38 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 HI0406 89 acetyl-CoA carboxylase, carboxyl transferase (accA) #2 HI0408 171 ABC transporter, ATP-binding protein (yebM) #3 HI0774 205 acetate CoA-transferase, alpha subunit #4 HI0971 152 acetyl-CoA carboxylase, biotin carboxyl carrier protein (accB) #5 HI0972 174 acetyl-CoA carboxylase, biotin carboxylase (accC) #6 HI1194 300 glycine cleavage system transcriptional activator (gcvA) #7 HI1196 35 succinyl-CoA synthetase, beta subunit (sucC) #8 HI1204 214 acetate kinase (ackA) #9 HI1260 193 acetyl-CoA carboxylase carboxyl transferase subunit beta (accD) Motif number 1 TTGTTATCCTAAAAAGACCGTAAAAATCGACCGC 1 65 0 AAAAAACAAA 0.981413 -25 AGAATTCTATAAAAATGCGTTATTTTCCCCAACC 2 125 1 AAAAAGCATT 0.754569 -47 GATTGATATTAAAAATAGCAAAAAGAATTTCGTA 3 72 0 AAAAAAGAAA 0.95363 -134 GAATTTCGCCAAAAATACTCGATTTTC 4 4 0 AAAAAACATT 0.879651 -149 CGTTCTTCCTAAAAAGATTGAAATTTTAACCGCA 4 128 0 AAAAAATAAT 0.920272 -25 TCCGCCCGACAAAAATATTGGAAA 5 1 0 AAAAAATAAA 0.944538 -174 TTTGTATATGAAATACGGACTAAAGTCCGCCCGA 5 26 0 AAATAGGAAA 0.601453 -149 AATCGGGATGAAAAAAACGCCACTCAATGAGAGC 6 14 1 AAAAAACACT 0.918739 -287 TACCTCAAATAAAAAAACGTCACTTGTCCTTTCC 6 223 0 AAAAAACACT 0.918739 -78 AAAAACACCTCAAAAATTGACCGC 8 1 1 AAAAAACAAA 0.981413 -214 TTTTTACTAAAAATAGACTTAAAATAGCGTATGA 8 40 0 AAATAACAAA 0.901611 -175 TATTTTTAGTAAAAATAGTTTAATTTTTCAAAAA 8 59 1 AAAAAAGAAT 0.93306 -156 TAATTTTTCAAAAAATACGATAAAGTTTGTATTT 8 79 1 AAAAAACAAA 0.981413 -136 TCTGTAAGACAAAAAAATAAAAAAAATGTTCAAT 9 43 1 AAAAAATAAA 0.944538 -151 TCTAGTCAATAAAAAGGTCAAAAA 9 180 1 AAAAAGTAAA 0.878057 -14 ***** ** *** Masking position 5 Map Score: 17.8768 Number of sites scoring better than the average of aligned sites = 483 Number in coding regions = 342 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 2 CGTAAAAATCGACCGCACTTTATCAAGGAA 1 51 0 GACCGCACTT 0.995707 -39 GTTTATTCATAACCGCACTTTTTCCTTTAA 4 95 1 AACCGCACTT 0.996803 -58 TTGAAATTTTAACCGCACTTTTAAAGGAAA 4 115 0 AACCGCACTT 0.996803 -38 TAGTTCGGGAAACCGAACTTGAGTAACAAT 6 99 0 AACCGAACTT 0.9816 -202 CTTACAATACAACCATACTTAATGATTGGT 6 183 0 AACCATACTT 0.892177 -118 CAAATAAAAAAACGTCACTTGTCCTTTCCT 6 222 0 AACGTCACTT 0.911328 -79 CTCAAAAATTGACCGCACTTATCATACGCT 8 19 1 GACCGCACTT 0.995707 -196 ********** Masking position 7 Map Score: 14.2386 Number of sites scoring better than the average of aligned sites = 1471 Number in coding regions = 993 Number in noncoding regions = 478 Number of orfs with sites within 600 bp upstream = 313 Fraction of orfs with sites within 600 bp upstream = 0.050273 Motif number 3 AATTCATTCCTATGGAAAAAGCATTATTCA 2 59 1 TATGGAAAAA 0.793752 -113 TATTTAAGCGTTTGAATAATGCTTTTTCCA 2 71 0 TTTGAATAAT 0.850543 -101 CCCAACCATTGTTGAAAACACGGCGATTTT 2 152 1 GTTGAAAACA 0.856725 -20 AACATATCCATTTGAAATATAAGATACTTA 3 142 1 TTTGAAATAT 0.781963 -64 TTATCGCAAATTTGAAAAAATTAAGGTAAT 4 46 1 TTTGAAAAAA 0.968604 -107 AAAGTGCGGTTATGAATAAACTTACTTTTG 4 86 0 TATGAATAAA 0.888522 -67 TAAAATCGGGATGAAAAAAACGCCACTCA 6 10 1 GATGAAAAAA 0.926106 -291 GAAAAACTAATTTGAAATAAATCTTGTCCA 6 260 1 TTTGAAATAA 0.873654 -41 CCTTTTTGGTTATGAAAACAGTTCAC 7 7 0 TATGAAAACA 0.885969 -29 TATCGTATTTTTTGAAAAATTAAACTATTT 8 71 0 TTTGAAAAAT 0.941199 -144 TACACCTTTTGATGAATAAAATAAATTCAT 8 124 0 GATGAATAAA 0.816711 -91 TCTAAGATGGTTTGAAAAATCAGACATAGA 8 155 0 TTTGAAAAAT 0.941199 -60 ********** Masking position 6 Map Score: 12.6499 Number of sites scoring better than the average of aligned sites = 376 Number in coding regions = 306 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 4 CTGAAAACTTTTTTATTTTAGGG 2 4 0 TTTTATTTTA 0.746303 -168 ATAGGAATGAATTTTCTTTATAATCTGTAG 2 42 0 ATTTTCTTTA 0.844401 -130 GGCGGGTATAAGTTATTTTGATAGTGTTTT 3 22 0 AGTTATTTTG 0.656221 -184 AGAAAGATGTATTTCTTTTACGAAATTCTT 3 54 1 ATTTCTTTTA 0.961497 -152 ATATCAATCTAGTTCCTTTATTGCCTATCA 3 97 1 AGTTCCTTTA 0.883989 -109 TGTTGATATTCTTTCTTTTAATCTCGTTAT 3 174 1 CTTTCTTTTA 0.896422 -32 TAACCGCACTTTTTCCTTTAAAAGTGCGGT 4 104 1 TTTTCCTTTA 0.787683 -49 GGACAAGTGACGTTTTTTTATTTGAGGTAT 6 228 1 CGTTTTTTTA 0.566216 -73 AATGGACAAGATTTATTTCAAATTAGTTTT 6 262 0 ATTTATTTCA 0.656975 -39 TTACCGATGAATTTATTTTATTCATCAAAA 8 118 1 ATTTATTTTA 0.929226 -97 TAGATGATGGATTTCTATTAACCTCAATCA 8 181 1 ATTTCTATTA 0.710797 -34 GTTATCTGAAATTTATTTTGGAGTATTT 9 9 0 ATTTATTTTG 0.805749 -185 CTTATTGAACATTTTTTTTATTTTTTTGTC 9 50 0 ATTTTTTTTA 0.891118 -144 TACTGCTCCGATTTCCTTTTAAACAAGATA 9 92 0 ATTTCCTTTT 0.657286 -102 ********** Masking position 4 Map Score: 8.90708 Number of sites scoring better than the average of aligned sites = 587 Number in coding regions = 451 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 5 AAATCTTGAGAATTCTATAAAAATGCGTTA 2 117 1 AATTCTATAA 0.89763 -55 AAATTCACAGAATTTTATCGCAAATTTGAA 4 32 1 AATTTTATCG 0.960118 -121 AGATTACCTTAATTTTTTCAAATTTGCGAT 4 48 0 AATTTTTTCA 0.759093 -105 GTTCACGCCAAATTTTATAGGGAGAACAAT 5 102 1 AATTTTATAG 0.960878 -73 TATAGACGAAAATTTTATAA 6 291 1 AATTTTATAA 0.939337 -10 AAAAAATACAAACTTTATCGTATTTTTTGA 8 86 0 AACTTTATCG 0.864759 -129 ACAAGTAGCAAATTCTATAAATTTATGTTC 9 135 1 AATTCTATAA 0.89763 -59 TAATACGCGCAATTTTCTAGTCAATAAAAA 9 165 1 AATTTTCTAG 0.883142 -29 ********** Masking position 2 Map Score: 4.74216 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 96 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 6 AACTGTGGCGCAAATGGTTTTCACTGGTTGG 1 17 0 CAAATGTTTT 0.961599 -73 TCTTATATTTCAAATGGATATGTTTCTTGCG 3 135 0 CAAATGATAT 0.885688 -71 AGAATATCAACAAATAAGTATCTTATATTTC 3 155 0 CAAATAGTAT 0.937099 -51 AGCGTTTAACCAAATCGGTTTAATAATATAC 6 48 1 CAAATGGTTT 0.975631 -253 AAATGAGTAACAAATTGTTACTCAAGTTCGG 6 86 1 CAAATGTTAC 0.857603 -215 AGATTTATTTCAAATTAGTTTTTCTAATACC 6 253 0 CAAATAGTTT 0.950354 -48 AAGAGGAGAGCAAATTATCTTGTTTAAAAGG 9 77 1 CAAATATCTT 0.791033 -117 ***** ***** Masking position 4 Map Score: 1.05537 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 116 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 7 GCTTGCCCAACCAGTGAAAACC 1 3 1 TTGCCCAACC 0.970843 -87 ATGCGTTATTTTCCCCAACCATTGTTGAAA 2 139 1 TTCCCCAACC 0.925491 -33 AGTTCCTTTATTGCCTATCAAGGATCATCG 3 107 1 TTGCCTATCA 0.775462 -99 TTCCTACCCTTTTCCTTACAATACAACCAT 6 197 0 TTTCCTTACA 0.911611 -104 TCACTTGTCCTTTCCTACCCTTTTCCTTAC 6 208 0 TTTCCTACCC 0.940947 -93 GTGAACTGTTTTCATAACCAAAAAGGACG 7 10 1 TTTCATAACC 0.854675 -26 GTTTGTATTTTTTCCTTACCGATGAATTTA 8 103 1 TTTCCTTACC 0.969201 -112 TATGTCTGATTTTTCAAACCATCTTAGATG 8 157 1 TTTTCAAACC 0.710351 -58 TTTTATTTTTTTGTCTTACAGACCACGTTA 9 35 0 TTGTCTTACA 0.665622 -159 ********** Masking position 2 Map Score: 2.8498 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 181 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 TTGATAAAGTGCGGTCGATTTTTACGGTCTTTT 1 55 1 GCGTGATTTT 0.965043 -35 TAGTCTGAATGCTGAAAACTTTTTTATTTTAGG 2 12 0 GCGAAATTTT 0.975884 -160 CTTTAAAAGTGCGGTTAAAATTTCAATCTTTTT 4 119 1 GCGTAAATTT 0.949048 -34 TAGTCAGATAGACGTGAATTTTTATGTAGGCTC 5 139 0 GAGTAATTTT 0.962281 -36 GTCCATTATAGACGAAAATTTTATAA 6 285 1 GAGAAATTTA 0.771338 -16 TATGATAAGTGCGGTCAATTTTTGAGGTGTTTT 8 12 0 GCGTAATTTT 0.986928 -203 ** ** ** **** Masking position 8 Map Score: 0.426144 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 195 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 9 ********** No masking Map Score: 4.07441e-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: 4.07441e-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: 4.07441e-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