AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icysB_ecoli_hinf_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 cysB 209 positive transcriptional regulator for cysteine regulon #2 cysK 184 cysteine synthase A, O-acetylserine sulfhydrolase A #3 HI1102 152 cysteine synthetase, putative (cysZ) #4 HI1103 98 cysteine synthetase (cysK) #5 HI1198 120 conserved hypothetical protein #6 HI1199 47 conserved hypothetical protein Motif number 1 GCCGCTTTCGCGACCCTTTGTTTATAAAAAC 1 27 0 CGACCCTTTT 0.9456 -183 GTCGCGAAAGCGGCCCTTTTTTATTGCATAT 1 44 1 CGGCCCTTTT 0.97765 -166 GTTATAGTTAGCACCTTTTTTATTATTAAAT 1 121 1 GCACCTTTTT 0.873633 -89 GCGGCATAAGCCACCCCTGTTTCACACAAAC 2 36 0 CCACCCCTGT 0.830263 -149 GTGGCTTATGCCGCCCCTTATTCCATCTTGC 2 53 1 CCGCCCCTTT 0.988288 -132 ATCCTTACTTCCGCATATTCTCTGAGCGGGT 2 120 1 CCGCATATTT 0.811358 -65 GGTAGCATTAGCACCATTTATAGCACTCTCG 3 38 0 GCACCATTTT 0.796773 -115 CTTTAAAATTCCACACTTTGAAGTATTTTTT 3 84 0 CCACACTTTA 0.894543 -69 TTAAAACAGACCGCACTTTTCCTTTAAAATT 3 105 0 CCGCACTTTC 0.983117 -48 ATTTATAGTACCGCACTTTTGATTAAAAAAA 4 40 0 CCGCACTTTG 0.983117 -59 CCGCACTTTAGTTTTCTAAAG 5 1 1 CCGCACTTTG 0.983117 -120 GCAATTTTGTGCTCACTTTATAATGGCGAGC 5 66 0 GCTCACTTTT 0.893617 -55 GCTATAATCAGCGCACATTTTTTAAGGAAGA 5 95 1 GCGCACATTT 0.95049 -26 GCTTGTGAAAGCGACCTTTCCATTATTCAAG 6 20 1 GCGACCTTTC 0.762608 -28 ********* * Masking position 8 Map Score: 17.2933 Number of sites scoring better than the average of aligned sites = 1532 Number in coding regions = 1315 Number in noncoding regions = 217 Number of orfs with sites within 600 bp upstream = 225 Fraction of orfs with sites within 600 bp upstream = 0.0361388 Motif number 2 GTATAGGTGTGAAGAAAAAATAATATGCAA 1 67 0 GAAGAAAAAA 0.88264 -143 CGCCAGGTGTGACGAAAAAACGATGTTCTG 1 165 1 GACGAAAAAA 0.917673 -45 CTATATACAGAAGGGAAATAATGACATGCA 2 81 0 AAGGGAAATA 0.922064 -104 TATCGCGCGTAAGGAATAAAA 3 2 0 AAGGAATAAA 0.955071 -151 TTTTTATTGAAAGGAAAGAAAA 3 141 1 AAGGAAAGAA 0.964534 -12 AGTCCAACGAAAGGAAAATATT 4 87 1 AAGGAAAATA 0.978043 -12 CACATTTTTTAAGGAAGAAACAC 5 108 1 AAGGAAGAAA 0.969237 -13 TCCATTATTCAAGGAAAACA 6 38 1 AAGGAAAACA 0.973985 -10 ********** Masking position 6 Map Score: 7.74719 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 132 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 3 AATAAAAAAGGGCCGCTTTCGCGACCCTTTGT 1 37 0 GGGCTTTCGC 0.996467 -173 GCGTCTAAGTGGATGGTTTAAC 1 198 1 GGGGTTTAAC 0.948059 -12 TGGAATAAGGGGCGGCATAAGCCACCCCTGTT 2 46 0 GGGCATAAGC 0.989705 -139 GGATACAACAGGTAGCATACCCGCTCAGAGAA 2 137 0 GGGCATACCC 0.982236 -48 ACTGAAATATGGTAGCATTAGCACCATTTATA 3 47 0 GGGCATTAGC 0.994445 -106 ATAATGGAAAGGTCGCTTTCACAAGCGTCTAT 6 14 0 GGGCTTTCAC 0.992074 -34 ** ******** Masking position 8 Map Score: 6.73048 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 186 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 4 CTTTTTTATTGCATATTATTTTTTCTTCACAC 1 59 1 GCATATATTT 0.967418 -151 ATTCCATCTTGCATGTCATTATTTCCCTTCTG 2 72 1 GCATGTATAT 0.977781 -113 TAAGGATTTAGCATATCTATATACAGAAGGGA 2 95 0 GCATATTTAT 0.985522 -90 TCTGTTTTAAGCATATTTTTATTGAAAGGAAA 3 126 1 GCATATTTAT 0.985543 -27 ATAATGGCGAGCATATAAAAATAAAGGCGTAG 5 46 0 GCATATAAAT 0.967417 -75 ****** * *** Masking position 6 Map Score: 2.48541 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 9 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 CGCGACCCTTTGTTTATAAAAACCTGACAGA 1 19 0 TGTTATAAAA 0.952949 -191 TGTATAGGTGTGAAGAAAAAATAATATGCAA 1 67 0 TGAGAAAAAA 0.766145 -143 TCACACAAACGGTTTACAAAATAACCGGTAG 2 15 0 GGTTACAAAA 0.926076 -170 GTATGAAATTGGGATACAACAGGTAGCATAC 2 149 0 GGATACAACA 0.844476 -36 AATAAAAATATGCTTAAAACAGACCGCACTT 3 118 0 TGTTAAAACA 0.835137 -35 ACCGCACTTTTGATTAAAAAAATAGTTATTT 4 31 0 TGTTAAAAAA 0.96333 -68 TATAATGGCGAGCATATAAAAATAAAGGCGT 5 48 0 AGATATAAAA 0.690958 -73 AAATGTGCGCTGATTATAGCAATTTTGTGCT 5 84 0 TGTTATAGCA 0.797433 -37 GTGTTTCTTCCTTAAAAAATGTGCGCTGA 5 102 0 TCTTAAAAAA 0.795072 -19 ** ******** Masking position 6 Map Score: 2.21351 Number of sites scoring better than the average of aligned sites = 315 Number in coding regions = 199 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 6 ********** No masking Map Score: -1.36892e-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 7 ********** No masking Map Score: -1.36892e-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 8 ********** No masking Map Score: -1.36892e-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