AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -icpxR6_rpxx_opreg_100.orf -g0.290 -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 = 0.29 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 RP025 90 unknown #2 RP071 196 TRANSCRIPTIONAL ACTIVATOR PROTEIN CZCR (czcR) #3 RP123 143 HFLC PROTEIN (hflC) #4 RP124 30 PROBABLE PERIPLASMIC SERINE PROTEASE DO-LIKE PRECURSOR (htrA) #5 RP427 121 PETR PROTEIN (ompR) #6 RP822 300 unknown Motif number 1 TAAAAATATATACTTTATAATAGAAGCAAAAT 1 5 0 TATTTATAAA 0.889135 -86 TTATAAAGTATATATTTTTATTGAAATAAAATTGATAC 1 23 1 TAATTATAAA 0.986746 -68 ATAAAATTGATACACTCTTATTGTAGAATGGTTAATAG 1 48 1 TAATTATTAA 0.979657 -43 CAATTAAAGGTAGAATTTAATAGTAAAAATTTTATAAT 2 47 1 TAATTATTAA 0.979657 -150 GTAAAAATTTTATAATTTGATTAAATATTCTTTACTTA 2 69 1 TAATTATAAT 0.979657 -128 ATTCTTTACTTATATTATTAATGAACGTATAAAGCACT 2 95 1 TAATTAAAAT 0.939227 -102 AATTATTAACTAAATTATAATTTTTTATCTAGTGCTTT 2 125 0 TAATTATTTT 0.766063 -72 AATTATTAACTAAATTATTATCAAAATTGAATTTTATG 2 159 1 TAATTATAAT 0.9795 -38 TCCAATGAGATAAAATCTTATCCTAAATGATGTGAACA 3 41 0 TAATTATTAT 0.968525 -103 CTTATTATTTTATAATATCATACTAAAAAAGCCTTGTA 3 107 0 TAATTATTAA 0.979657 -37 GGGATGAGTTTCTAATCTAATATAAATATAACTTA 5 8 0 TCATTATAAA 0.922399 -114 ACATGTTATATACAGTACCAAATAATAAATCATCAT 6 9 0 TAATCAAAAA 0.792368 -292 ACACAATGAGTACATTATAAAGCAAAAAAAACTCTATA 6 186 0 TAATTAAAAA 0.960307 -115 ** * * * ** ** * Masking position 10 Map Score: 16.7165 Number of sites scoring better than the average of aligned sites = 346 Number in coding regions = 189 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 2 TGCTTCTATTATAAAGTATATATTTTTATTGAAA 1 15 1 ATAAATATAT 0.946739 -76 TTTTATTGAAATAAAATTGATACACTCTTATTGT 1 38 1 ATAAATTTAA 0.862451 -53 TAATTATCCAATAATATTGTTGTTTTTCAATTAA 2 20 1 ATAATTTTGT 0.83419 -177 TAATCAAATTATAAAATTTTTACTATTAAATTCT 2 58 0 ATAAATTTAT 0.942649 -139 ACGTTCATTAATAATATAAGTAAAGAATATTTAA 2 89 0 ATAATTATAA 0.959243 -108 ATAAAAAATTATAATTTAGTTAATAATTATTAAC 2 135 1 ATAATTATAT 0.876907 -62 AATTTTGATAATAATTTAGTTAATAATTATTAAC 2 153 0 ATAATTATAT 0.876907 -44 GTACTTTAGCATGATATATCTAATT 3 2 0 ATGATTATAT 0.94232 -142 AGTTTCTAATCTAATATAAATATAACTTA 5 6 0 CTAATTATAA 0.762302 -116 AAAAACAACTATGATATTAATAATTTTGAACCCG 5 66 1 ATGATTTTAT 0.894919 -56 CTATATAAAGATAATATACTTTTTGCACTGTGAT 6 63 0 ATAATTATTT 0.685247 -238 GGTACATTATATAAACTATATAAAGATAATATAC 6 78 0 ATAAATATAA 0.918734 -223 TATAGTTTATATAATGTACCTTATGAGTATCTCC 6 92 1 ATAATTATTT 0.73459 -209 ATTTTTTGTAAAAAAGTTGCTATTACTTCCACGA 6 127 0 AAAAATTTAT 0.600991 -174 TTTTTGCTTTATAATGTACTCATTGTGTATATTA 6 196 1 ATAATTACAT 0.893568 -105 ***** ** ** * Masking position 4 Map Score: 17.5351 Number of sites scoring better than the average of aligned sites = 866 Number in coding regions = 583 Number in noncoding regions = 283 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 3 TAGAAACTCATCCCGTGGTTTGACCACGAA 5 32 1 TCCCGTGGTT 0.995845 -90 TGTTTTTGGCTTTCGTGGTCAAACCACGGG 5 43 0 TTTCGTGGTC 0.952504 -79 ATAATTTTGAACCCGTGGTCAAACCACGAG 5 85 1 ACCCGTGGTC 0.997327 -37 TCATTTTACATCTCGTGGTTTGACCACGGG 5 96 0 TCTCGTGGTT 0.988013 -26 TAGTACTAATACCCGTGGCTTGACCACCGG 6 228 1 ACCCGTGGCT 0.988138 -73 AAGACTGGATACCGGTGGTCAAGCCACGGG 6 239 0 ACCGGTGGTC 0.988757 -62 ********** Masking position 6 Map Score: 10.607 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 2 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 CCTTTAATTGAAAAACAACAATATTATTGG 2 27 0 AAAAACAACA 0.955884 -170 ATATCATACTAAAAAAGCCTTGTAAGAAGA 3 101 0 AAAAAAGCCT 0.936636 -43 TACTCCAAATAAAGACGACAGTAAATATA 4 10 0 AAAGACGACA 0.925693 -21 CACGAAAGCCAAAAACAACTATGATATTAA 5 56 1 AAAAACAACT 0.975861 -66 ATTATAAAGCAAAAAAAACTCTATAGTCAA 6 181 0 AAAAAAAACT 0.962561 -120 GGTTGTCCATAAAAAAGACTGGATACCGGT 6 253 0 AAAAAAGACT 0.975861 -48 ********** Masking position 5 Map Score: 5.08732 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 24 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 AATAAAAATATATACTTTATAATAGAAGCAAA 1 13 0 TATATTTAAA 0.679918 -78 AAGTATATATTTTTATTGAAATAAAATTGATA 1 28 1 TTTTTTGAAT 0.664467 -63 TTGATACACTCTTATTGTAGAATGGTTAATAG 1 54 1 CTTATGTAAA 0.815854 -37 AAACAACAATATTATTGGATAATTAGGTAATT 2 13 0 ATTATGGAAA 0.893684 -184 AAATTCTACCTTTAATTGAAAAACAACAATAT 2 33 0 TTTATTGAAA 0.966657 -164 AAAATTATAATTTAGTTAATAATTATTAACTA 2 139 1 TTTATTAAAA 0.888619 -58 TTGATAATAATTTAGTTAATAATTATTAACTA 2 151 0 TTTATTAAAA 0.888619 -46 CAAAATTGAATTTTATGGAGAAAAATA 2 180 1 TTTTTGGAAA 0.952047 -17 AATATTCCTTATTATTTTATAATATCATACTA 3 120 0 ATTATTTAAA 0.819832 -24 TCTTTTATTATTTTTTGTAAAAAAGTTGCTAT 6 138 0 TTTTTGTAAA 0.921463 -163 TAGAGTTTTTTTTGCTTTATAATGTACTCATT 6 188 1 TTTGTTTAAA 0.829664 -113 ATCCAGTCTTTTTTATGGACAACCTGATCAAT 6 259 1 TTTTTGGAAA 0.952047 -42 **** **** ** Masking position 9 Map Score: 9.74348 Number of sites scoring better than the average of aligned sites = 530 Number in coding regions = 329 Number in noncoding regions = 201 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 6 AATAAAAATATATACTTTATAATAGAAGCAA 1 14 0 TATACTTATA 0.84074 -77 ATTTATTCCTTTTGACTATTAACC 1 77 0 TATTCTTTTG 0.976548 -14 ATTGGATCTTTGCTCTTTTTGAAGTTGATCT 3 73 1 TGCTCTTTTG 0.958528 -71 TTAATATTCCTTATTATTTTATAAT 3 129 0 TATTCTTATT 0.831852 -15 TTATACTCATTTTACATCTCGTGG 5 108 0 TACTCTTTTA 0.917584 -14 ATAAAGATAATATACTTTTTGCACTGTGATA 6 62 0 TATACTTTTG 0.962894 -239 GTTTATATAATGTACCTTATGAGTATCTCCT 6 96 1 TGTACTTATG 0.918617 -205 CTTTATAATGTACTCATTGTGTATATTAGTA 6 202 1 TACTCTTGTG 0.948415 -99 ***** ***** Masking position 7 Map Score: 4.597 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 83 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 7 ********** No masking Map Score: -1.23391e-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: -1.23391e-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 9 ********** No masking Map Score: -1.23391e-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