AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i064_Histidine_Biosynthesis_ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 hisL 255 his operon leader peptide #2 hisG 145 ATP phosphoribosyltransferase #3 HI0468 300 ATP phosphoribosyltransferase (hisG) #4 HI0469 92 histidinol dehydrogenase (hisD) #5 HI0470 68 histidinol-phosphate aminotransferase (hisC) #6 HI0471 111 imidazoleglycerol-phosphate dehydratase / histidinol-phosphatase (hisB) #7 HI0472 65 amidotransferase (hisH) #8 HI0473 35 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (hisA) Motif number 1 CAGCACACATCGCCTGAAAGA 2 2 0 CGCCTGAAAG 0.982795 -144 CGTTCATGCACCACTGGAAGATCTGAATGT 2 36 0 CCACTGGAAG 0.974783 -110 CATGAGAAAGCCCCCGGAAGATCACCTTCC 2 66 1 CCCCCGGAAG 0.997684 -80 AATAAAAAAGCCCCCGGAAGGTGATCTTCC 2 81 0 CCCCCGGAAG 0.997684 -65 CATACAATCACGCCTGAAAGATAATCAGGT 3 158 0 CGCCTGAAAG 0.982795 -143 ATTTTTATTACACTCGGAAGATATTTTATT 3 198 0 CACTCGGAAG 0.981231 -103 CAATAAATACCCCTCGGAAGGCAATTTTCG 3 239 1 CCCTCGGAAG 0.996658 -62 AAAAGAAAACCCCTCGAAAATTGCCTTCCG 3 253 0 CCCTCGAAAA 0.937988 -48 ********** Masking position 8 Map Score: 19.1588 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 183 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 2 ATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTT 1 167 1 AAAAAAAAAA 0.823787 -89 TTCAGACAGGTTTAAAGAGGAATAACAAA 2 127 1 TAAAGATAAA 0.863313 -19 TAGTAAAAATGTACTAAAAACACAATTTTT 3 4 1 TAAAATAAAA 0.891817 -297 AAAATACACTTTAAAATTAAAAAAAGCAATTTTTTTG 3 43 0 TAAAAAAAAC 0.953637 -258 AAAGTGTATTTTTAAGGCAATATAAGATCTAATAACA 3 68 1 TAAGAATAAA 0.968014 -233 TGGTGATGATGGTAAGTGCAGATAAAATTCATATTGT 3 120 0 GAAGAATAAA 0.850748 -181 ATTGTATGTTTGGAAGATAATAAAATATCTTCCGAGT 3 180 1 TAAGAAAAAA 0.968019 -121 TAAAAATCAGTGTAAAAGCAATAAATACCCCTCGGAA 3 221 1 TAAAATAAAA 0.891814 -80 TTTTCCTATTTTAAAGTTGAGATAAAAGAAAACCCCT 3 269 0 TAAGAATAAA 0.968018 -32 ATTTTACGGATACAAAGGAAAATAAACA 4 75 1 TAAAAATAAC 0.953637 -18 ATACAAACAGTATAAAACTAAATAATCTCGAATCGCT 6 34 0 TAAAAATAAC 0.953631 -78 TTCGACCGATTGTAAAAGGATAAAAAA 7 49 1 TAAAAAAAAA 0.97354 -17 * *** * **** * Masking position 5 Map Score: 10.3687 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 76 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 3 CGTTAGAAAGCAAGGGCTTTTTTATATATT 1 181 0 CAAGGGCTTT 0.985983 -75 GGTGATCTTCCGGGGGCTTTCTCATGCGTT 2 62 0 CGGGGGCTTT 0.997519 -84 GATCACCTTCCGGGGGCTTTTTTATTGCGC 2 85 1 CGGGGGCTTT 0.997519 -61 AATTGCCTTCCGAGGGGTATTTATTGCTTT 3 235 0 CGAGGGGTAT 0.987298 -66 AGGCAATTTTCGAGGGGTTTTCTTTTATCT 3 257 1 CGAGGGGTTT 0.996105 -44 ********** Masking position 8 Map Score: 10.2628 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 21 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 GCGAGCATATACAATATGAATTTTATCTGC 3 110 1 ACAATATGAA 0.922222 -191 TCTCAACTTTAAAATAGGAAAAACATT 3 284 1 AAAATAGGAA 0.923202 -17 TTGTTGTATGAAAATTTGACTGCTTACGTG 5 37 0 AAAATTTGAC 0.923392 -32 TTTTCATACAACAATACGAAATATGT 5 53 1 ACAATACGAA 0.963919 -16 GAATTTTGCAAAAATACGACAAAAATTAAC 7 22 0 AAAATACGAC 0.980647 -44 GTATTTTTGCAAAATTCGACCGATTGTAAA 7 35 1 AAAATTCGAC 0.964486 -31 ********** Masking position 5 Map Score: 3.97021 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 41 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 5 TCCCCGCTCATTCATTAAACAAATCCATTGC 1 145 1 TTCATAAACA 0.892771 -111 TCTGTGAATGTTTATTCAACTGATGTCTTTT 1 228 0 TTTATCAACT 0.893671 -28 TTCTCATGCGTTCATGCACCACTGGAAGATC 2 43 0 TTCATCACCA 0.944616 -103 AAAACACAATTTTTTTCAAAAAAATTGCTTT 3 27 1 TTTTTCAAAA 0.830262 -274 CAGTCAAATTTTCATACAACAATACGAAATA 5 45 1 TTCATCAACA 0.984664 -24 TATCATTTGCTTTATACAAACAGTATAAAAC 6 53 0 TTTATCAAAC 0.82959 -59 CCTCATACCATTCATATAACATACACGGAGA 6 86 1 TTCATTAACA 0.892809 -26 TTTTGTCGTATTTTTGCAAAATTCGACCGAT 7 28 1 TTTTTCAAAA 0.830262 -38 ***** ***** Masking position 8 Map Score: 2.18079 Number of sites scoring better than the average of aligned sites = 473 Number in coding regions = 407 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 6 ATTCAACTGATGTCTTTTAACCTAAACCACT 1 215 0 TGTTTTTAAC 0.894304 -41 ATATACAATATGAATTTTATCTGCACTTACC 3 116 1 TGATTTTATC 0.981505 -185 GCTTTTACACTGATTTTTATTACACTCGGAA 3 209 0 TGATTTTATT 0.89142 -92 TTCGAGGGGTTTTCTTTTATCTCAACTTTAA 3 265 1 TTTTTTTATC 0.917478 -36 TCGAGATTATTTAGTTTTATACTGTTTGTAT 6 40 1 TTATTTTATA 0.691319 -72 ATGAATGGTATGAGGTTTATCATTTGCTTTA 6 70 0 TGAGTTTATC 0.942294 -42 TGTGTTTGATCCTGTATGACT 8 25 0 TGTTTTGATC 0.926147 -11 *** ******* Masking position 9 Map Score: 1.56092 Number of sites scoring better than the average of aligned sites = 432 Number in coding regions = 368 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 7 TTTGTTATTCCTCTTTAAACCT 2 134 0 TTGTTATCCT 0.869879 -12 CGGAAGATATTTTATTATCTTCCAAACATAC 3 183 0 TTTATTTCTT 0.76306 -118 AATGTTTTTCCTATTTTAAAGT 3 289 0 ATGTTTTCCT 0.961129 -12 TGTTTATTTTCCTTTGTATCCGT 4 80 0 TTTATTTCCT 0.954165 -13 ATTTTTCTCCGTGTATGTTAT 6 101 0 ATTTTTTCCG 0.918753 -11 AGAGCGGTTAATTTTTGTCGTATTTTTGCAA 7 16 1 ATTTTTTCGT 0.893916 -50 TTTTTTATCCTTTTACAATCG 7 55 0 TTTTTTTCCT 0.979531 -11 ****** **** Masking position 5 Map Score: 1.49187 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 183 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 8 ATGAGCGTTAATTAACTATTTATTAATTAGT 1 20 1 ATTAATATTT 0.886429 -236 TTAACTATTTATTAATTAGTTTGTAGATCAA 1 31 1 ATTAATAGTT 0.770435 -225 CAAGGGCTTTTTTATATATTTTATGGCAATG 1 170 0 TTTATTATTT 0.637923 -86 TTGTGTTTTTAGTACATTTTTACTA 3 5 0 AGTACTTTTT 0.746232 -296 TTTGAAAAAAATTGTGTTTTTAGTACATTTT 3 16 0 ATTGTTTTTT 0.941885 -285 TTTCAAAAAAATTGCTTTTTTTAATTTTAAA 3 40 1 ATTGCTTTTT 0.916009 -261 TTAATTTTAAAGTGTATTTTTAAGGCAATAT 3 60 1 AGTGTTTTTT 0.874511 -241 TTCAGGCGTGATTGTATGTTTGGAAGATAAT 3 170 1 ATTGTTGTTT 0.879534 -131 ATTTTGAGATATTGATTATTTAAATGGCGAG 4 29 0 ATTGATATTT 0.925633 -64 GCGATTCGAGATTATTTAGTTTTATACTGTT 6 35 1 ATTATTAGTT 0.843356 -77 ***** ***** Masking position 7 Map Score: 2.32119 Number of sites scoring better than the average of aligned sites = 326 Number in coding regions = 219 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 9 ATTTGTTTAATGAATGAGCGGGGAAAGGAG 1 139 0 TGAATGAGCG 0.97472 -117 CTTCCAGTGGTGCATGAACGCATGAGAAAG 2 46 1 TGCATGAACG 0.885175 -100 AAATGGCGAGTCAAAGCTCGCACTACAT 4 9 0 TCAAAGCTCG 0.937543 -84 TAATTATAGATCTAAGCACGACACGTAAGC 5 16 1 TCTAAGCACG 0.889447 -53 CCTATTTAAGTCACAGAGCGATTCGAGATT 6 18 1 TCACAGAGCG 0.963376 -94 TTGAAAGAGCGGTTAATTTTT 7 2 1 TGAAAGAGCG 0.98629 -64 ********** Masking position 1 Map Score: 0.906817 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 245 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 10 GTCCTCTTAGCCCCCTCCTTTCCCCGCTCA 1 125 1 CCCCCTCCTT 0.969279 -131 CCCTCCTTTCCCCGCTCATTCATTAAACAA 1 137 1 CCCGCTCATT 0.98739 -119 ACCGTTATCAACCGCGCAATAAAAAAGCCC 2 98 0 ACCGCGCAAT 0.959022 -48 ATGGATGATAACCCAGCATTTTGAGATATT 4 47 0 ACCCAGCATT 0.911538 -46 ACAAAAATTAACCGCTCTTTCAA 7 4 0 ACCGCTCTTT 0.966227 -62 ********** Masking position 10 Map Score: 0.35339 Number of sites scoring better than the average of aligned sites = 353 Number in coding regions = 318 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 11 ********** No masking Map Score: -3.1879e-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 12 ********** No masking Map Score: -3.1879e-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 13 ********** No masking Map Score: -3.1879e-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