AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iaraC_ecoli_opreg_100.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 araD 284 L-ribulose-5-phosphate 4-epimerase #2 araB_araC 338 araB: L-ribulokinase, araC: transcriptional regulator for ara operon #3 araJ 125 involved in either transport or processing of arabinose polymers #4 araH_2 23 high-affinity L-arabinose transport system; membrane protein, fragment 2 #5 araG 69 ATP-binding component of high-affinity L-arabinose transport system #6 araF 300 L-arabinose-binding periplasmic protein #7 araE 300 low-affinity L-arabinose transport system proton symport protein Motif number 1 CAGGCGTTACATACCGGATGCGGCTAC 1 6 0 AACCGATGCG 0.988891 -279 CCGGTATGTAACGCCTGATGCGACGCTGACGC 1 21 1 AGCCGATGCG 0.999261 -264 CGCAGCGTGTAGGCCAGATAAGACGCGTCAGC 1 45 0 AGCCGATAAG 0.997449 -240 GCGATTTTGTAGGCCGGATAAGCAAAGCGCAT 1 74 1 AGCCGATAAG 0.997449 -211 CAGGCGTTGAATGCCGGATGCGCTTTGCTTAT 1 91 0 AGCCGATGCG 0.999261 -194 CCGGCATTCAACGCCTGATGCGACGCTGGCGC 1 106 1 AGCCGATGCG 0.999261 -179 CGCAGCGCGTAGGCCTGATAAGACGCGCCAGC 1 130 0 AGCCGATAAG 0.997449 -155 GCGATTTTGTAGGCCGGATAAGCAAAGCGCAT 1 159 1 AGCCGATAAG 0.997449 -126 CAGGCGTTGAATGCCGGATGCGCTTTGCTTAT 1 176 0 AGCCGATGCG 0.999261 -109 CCGGCATTCAACGCCTGATGCGACGCTGGCGC 1 191 1 AGCCGATGCG 0.999261 -94 CGCAGCGTGTAGGCCTGATAAGACGCGCCAGC 1 215 0 AGCCGATAAG 0.997449 -70 GCGATTTTGTAGGCCGGATAAGCAAAGCGCAT 1 244 1 AGCCGATAAG 0.997449 -41 TGACTCCTTCGTGCCGGATGCGCTTTGCTTAT 1 261 0 GGCCGATGCG 0.995331 -24 * *** ****** Masking position 8 Map Score: 61.6717 Number of sites scoring better than the average of aligned sites = 253 Number in coding regions = 61 Number in noncoding regions = 192 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 2 AATCGCAGCGTGTAGGCCAGATAAGACGCG 1 50 0 TGTAGGCCAG 0.993419 -235 GCTGCGATTTTGTAGGCCGGATAAGCAAAG 1 71 1 TGTAGGCCGG 0.998976 -214 CATCAGGCGTTGAATGCCGGATGCGCTTTG 1 96 0 TGAATGCCGG 0.987908 -189 AATCGCAGCGCGTAGGCCTGATAAGACGCG 1 135 0 CGTAGGCCTG 0.986053 -150 GCTGCGATTTTGTAGGCCGGATAAGCAAAG 1 156 1 TGTAGGCCGG 0.998976 -129 CATCAGGCGTTGAATGCCGGATGCGCTTTG 1 181 0 TGAATGCCGG 0.987908 -104 AATCGCAGCGTGTAGGCCTGATAAGACGCG 1 220 0 TGTAGGCCTG 0.996257 -65 GCTGCGATTTTGTAGGCCGGATAAGCAAAG 1 241 1 TGTAGGCCGG 0.998976 -44 ********** Masking position 4 Map Score: 27.6533 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 37 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 3 TATCCGGCCTACAAAATCGCAGCGTGTAGGC 1 63 0 AAAAATCGCA 0.9825 -222 AGGCCGGATAAGCAAAGCGCATCCGGCATTC 1 84 1 ACAAAGCGCA 0.993007 -201 TATCCGGCCTACAAAATCGCAGCGCGTAGGC 1 148 0 AAAAATCGCA 0.9825 -137 AGGCCGGATAAGCAAAGCGCATCCGGCATTC 1 169 1 ACAAAGCGCA 0.993007 -116 TATCCGGCCTACAAAATCGCAGCGTGTAGGC 1 233 0 AAAAATCGCA 0.9825 -52 AGGCCGGATAAGCAAAGCGCATCCGGCACGA 1 254 1 ACAAAGCGCA 0.993007 -31 AGCATTCTGTAACAAAGCGGGACCAAAGCCA 2 132 1 ACAAAGCGGG 0.964334 -207 CAAAGCCATGACAAAAACGCGTAACAAAAGT 2 155 1 AAAAAACGCG 0.955407 -184 CACTCCATCCAAAAAAACGGGTATGGAGAAA 2 313 0 AAAAAACGGG 0.85139 -26 GGAGAGCAATATCACATCGCAGAATTACAGT 6 136 0 ACACATCGCA 0.949166 -165 * ********* Masking position 6 Map Score: 20.2252 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 243 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 4 GCCAGATAAGACGCGTCAGCGTCGCATCAGGCGT 1 31 0 AGCGCAGGCG 0.99893 -254 GCCTGATAAGACGCGCCAGCGTCGCATCAGGCGT 1 116 0 AGCGCAGGCG 0.998919 -169 GCCTGATAAGACGCGCCAGCGTCGCATCAGGCGT 1 201 0 AGCGCAGGCG 0.998919 -84 GAGCCAGTAAAAGACGCAGTGACGGCAATGTCTG 2 62 0 AGACCAGGCG 0.979987 -277 TTGCGATAAAAAGCGTCAGGTAGGATCCGCTAAT 2 269 0 AGCGCAGTGG 0.992439 -70 TCCCCTCTGCATGATGCAGAGGGGGTGTGAACGA 5 25 1 AGATCAGGGG 0.953067 -45 AAACCCTGCCATGCGGCAGGGTCATAAAA 7 6 0 AGCGCAGGCA 0.9905 -295 CAACTCACGCAGGTGTCAGGTCGGAAACAGCATA 7 231 0 AGTGCAGTGG 0.953067 -70 * *** *** * ** Masking position 8 Map Score: 15.7651 Number of sites scoring better than the average of aligned sites = 388 Number in coding regions = 317 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 5 TCTGATGCAATATGGACAATTGGTTTCTTC 2 36 0 TATGGACAAT 0.94794 -303 CCGCTAATCTTATGGATAAAAATGCTATGG 2 247 0 TATGGATAAA 0.980314 -92 AAAAAACGGGTATGGAGAAACAGTAGAGAG 2 303 0 TATGGAGAAA 0.971023 -36 AGGCTAATCTTATGGATTAATCTGCTGTGC 6 38 1 TATGGATTAA 0.980315 -263 ATTGCTCTCCTATGGAGAATTAATTTCTCG 6 157 1 TATGGAGAAT 0.971023 -144 ATAACCATGATATGGATTATGATGATCTAC 7 49 0 TATGGATTAT 0.980315 -252 TGATAATTAATATGGATTATTTCATAACCA 7 72 0 TATGGATTAT 0.980315 -229 ACAGCATAAATATGGATTAAATTGCTGCGA 7 209 0 TATGGATTAA 0.980315 -92 ********** Masking position 6 Map Score: 15.5997 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 44 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 GCGATTTTGTAGGCCGGATAAGCAAAGCGCA 1 74 1 AGCCGGATAA 0.975796 -211 GCGATTTTGTAGGCCGGATAAGCAAAGCGCA 1 159 1 AGCCGGATAA 0.975796 -126 GCGATTTTGTAGGCCGGATAAGCAAAGCGCA 1 244 1 AGCCGGATAA 0.975796 -41 TCTATAATCACGGCAGAAAAGTCCACATTGA 2 187 1 CGCAGAAAAG 0.781714 -152 CTATTCAGCAGGATAATGAATACAGA 3 6 1 CGCAGGATAA 0.988893 -120 AAGTGATAGCTTGCAGGATAACGACCAGCAA 3 58 0 TGCAGGATAA 0.985746 -68 TTTGCCGGAAAAATTCCCCTCT 5 2 1 TGCCGGAAAA 0.979158 -68 GTCGAATGCACAGCAGATTAATCCATAAGAT 6 44 0 CGCAGATTAA 0.865489 -257 TGCATAAATTTAGCGGGAAAAGACATAAGGG 6 98 0 TGCGGGAAAA 0.93028 -203 CAATATCACATCGCAGAATTACAGTGAGAAC 6 130 0 TGCAGAATTA 0.720954 -171 CCTAATTTTACAGCAGATAAAATTCATAAAG 7 111 0 CGCAGATAAA 0.823755 -190 TACTCTCTGCTGGCAGGAAAAA 7 289 1 TGCAGGAAAA 0.980483 -12 * ********* Masking position 4 Map Score: 17.2794 Number of sites scoring better than the average of aligned sites = 965 Number in coding regions = 716 Number in noncoding regions = 249 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987 Motif number 7 GCCTACAAAATCGCAGCGTGTAGGCCAGATA 1 57 0 TCGCAGCGGT 0.996325 -228 GCCTACAAAATCGCAGCGCGTAGGCCTGATA 1 142 0 TCGCAGCGGT 0.996226 -143 GCCTACAAAATCGCAGCGTGTAGGCCTGATA 1 227 0 TCGCAGCGGT 0.996325 -58 TGCTATGGCATAGCAAAGTGTGACGCCGTGC 2 224 0 TAGCAAAGGT 0.944374 -115 TATGGAGAAACAGTAGAGAGTTGCGATAAAA 2 292 0 CAGTAGAGGT 0.933664 -47 TTTTTCCTGCCAGCAGAGAGTAAGACATAGT 7 280 0 CAGCAGAGGT 0.989128 -21 ******** ** Masking position 5 Map Score: 8.13465 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 170 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 GTAGGCCAGATAAGACGCGTCAGCGTCGCAT 1 38 0 TAAGAGCGTC 0.988962 -247 GTAGGCCTGATAAGACGCGCCAGCGTCGCAT 1 123 0 TAAGAGCGCC 0.996244 -162 GTAGGCCTGATAAGACGCGCCAGCGTCGCAT 1 208 0 TAAGAGCGCC 0.996244 -77 TTTTTATCCATAAGATTAGCGGATCCTACCT 2 255 1 TAAGATAGCG 0.874124 -84 AGAGTTGCGATAAAAAGCGTCAGGTAGGATC 2 276 0 TAAAAGCGTC 0.932733 -63 GATTAATCCATAAGATTAGCCTGGAAATCCT 6 29 0 TAAGATAGCC 0.968037 -272 ***** ***** Masking position 5 Map Score: 6.22752 Number of sites scoring better than the average of aligned sites = 247 Number in coding regions = 141 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 9 AGCGTCGCATCAGGCGTTACATACCGGATG 1 18 0 CAGGCGTTAC 0.984824 -267 AGCGTCGCATCAGGCGTTGAATGCCGGATG 1 103 0 CAGGCGTTGA 0.994036 -182 AGCGTCGCATCAGGCGTTGAATGCCGGATG 1 188 0 CAGGCGTTGA 0.994036 -97 CATATTGCATCAGACATTGCCGTCACTGCG 2 52 1 CAGACATTGC 0.942307 -287 ********** Masking position 7 Map Score: 2.66744 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 127 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 CACTGCGTCTTTTACTGGCTCTTCTCGCTAACCCA 2 75 1 TTTGGCTTTT 0.959623 -264 TACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGT 2 143 0 TTTGGCTTGT 0.993533 -196 GGGCGAATTATCTCTTGGCCTTGCTGGTCGTTATC 3 38 1 TTTGGCCTGT 0.982509 -88 AAGCTATCACTTTATTGGCTACGGTGATTGGTAGC 3 77 1 TTTGGCTCGT 0.982509 -49 TGGTAGCCGTTCTGGTGGTTGTGATGGTGGT 3 105 1 TTTGGTTTGT 0.9811 -21 TCATAATCCATATCATGGTTATGAAATAATCCATA 7 57 1 TTTGGTTTGA 0.927571 -244 * * ***** ** * Masking position 6 Map Score: 1.67339 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 52 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 11 TCCCACCATTCAGAGAAGAAACCAATTGTC 2 22 1 CAGAGAAGAA 0.919897 -317 ATAATGAATACAGAGGGGCGAATTATCTCT 3 23 1 CAGAGGGGCG 0.97907 -103 CTGCATCATGCAGAGGGGAATTTTTCCGGC 5 14 0 CAGAGGGGAA 0.993562 -56 CTGCATGATGCAGAGGGGGTGTGAACGACC 5 31 1 CAGAGGGGGT 0.944904 -39 CGGGAAAAGACATAAGGGAAAGCCAATTTG 6 86 0 CATAAGGGAA 0.845211 -215 ATTAATTCTCCATAGGAGAGCAATATCACA 6 151 0 CATAGGAGAG 0.904948 -150 TTCCTGCCAGCAGAGAGTAAGACATAGTGA 7 278 0 CAGAGAGTAA 0.845211 -23 ********** Masking position 4 Map Score: 2.86052 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 209 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 12 AAAGCGCATCCGGCACGAAGGAGTCAAC 1 267 1 CGGACAAGGA 0.927019 -18 TGTAACAAAGCGGGACCAAAGCCATGACAAAA 2 139 1 CGGACAAAGC 0.988407 -200 GACAAAAACGCGTAACAAAAGTGTCTATAATC 2 164 1 CGTACAAAGT 0.816746 -175 TCTATAATCACGGCAGAAAAGTCCACATTGAT 2 187 1 CGGAGAAAGT 0.868519 -152 CTAATCTTATGGATAAAAATGCTATGGCATAG 2 242 0 GGAAAAATGC 0.685875 -97 TGGGTACCAAAGACAACAAGGAT 6 2 1 GGGACAAAGA 0.970869 -299 TAAATTAATCGGAAAACAAAGCATTACCTTTT 6 224 0 GGAAAAAAGC 0.913173 -77 GTTTTGTGTAGGGCAAAAACGAATGACATTCG 6 257 0 GGGAAAACGA 0.800338 -44 CTACACAAAACGACACTAAAGCTGGAGAGAAC 6 278 1 CGAACAAAGC 0.970869 -23 *** ** ***** Masking position 5 Map Score: 1.72558 Number of sites scoring better than the average of aligned sites = 441 Number in coding regions = 403 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 13 ********** No masking Map Score: -8.85746e-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 14 ********** No masking Map Score: -8.85746e-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 15 GTTACCGGTTGGGTTAGCGAGAAGAGCCAGTAA 2 86 0 GGGACGAGAA 0.974804 -253 ATAGCAAAGTGTGACGCCGTGCAAATAATCAAT 2 213 0 GTGGCGTGCA 0.949545 -126 GATAGCTTGCAGGATAACGACCAGCAAGGCCAA 3 52 0 AGGACGACCA 0.887523 -74 TGCAGAGGGGGTGTGAACGACCAGTGATTCACG 5 39 1 GTGACGACCA 0.989051 -31 TTAATCTGCTGTGCATTCGACAATTTGTCTGAC 6 54 1 GTGTCGACAA 0.91525 -247 CAGAATTACAGTGAGAACGTGCATAAATTTAGC 6 115 0 GTGACGTGCA 0.98101 -186 TGTTGACATAGTTTTAGCGAGAAATTAATTCTC 6 171 0 GTTACGAGAA 0.881769 -130 *** * ****** Masking position 13 Map Score: 0.091756 Number of sites scoring better than the average of aligned sites = 436 Number in coding regions = 408 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789