AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -icpxR9_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 RP785 112 unknown #7 RP822 300 unknown Motif number 1 ATAAAAATATATACTTTATAATAGAAGCAAAA 1 12 0 ATTTTATAAT 0.955061 -79 TTAATAGTAAAAATTTTATAATTTGATTAAAT 2 63 1 AATTTATAAT 0.928103 -134 ATATAAGTAAAGAATATTTAATCAAATTATAA 2 78 0 AGTATTTAAT 0.727719 -119 GCTTTATACGTTCATTAATAATATAAGTAAAG 2 98 0 TTTTAATAAT 0.821434 -99 TAACTAAATTATAATTTTTTATCTAGTGCTTT 2 125 0 ATTTTTTTAT 0.860534 -72 AAATTATAATTTAGTTAATAATTATTAACTAA 2 140 1 TTTTAATAAT 0.823579 -57 ATATTCCTTATTATTTTATAATATCATACTAA 3 119 0 TTTTTATAAT 0.952841 -25 AACCACGGGATGAGTTTCTAATCTAATATAAA 5 20 0 TGTTTCTAAT 0.74491 -102 CCACGGGTTCAAAATTATTAATATCATAGTTG 5 71 0 AATTATTAAT 0.511549 -51 CGGGATGACGATAGTTTATTATGAATTATAAA 6 65 1 ATTTTATTAT 0.935298 -48 TGATGCTCGTTGTTTTTATAATTCATAATAAA 6 79 0 TGTTTATAAT 0.948745 -34 ATGATGATTTATTATTTGGTACTGT 7 4 1 ATTTTATTAT 0.907213 -297 CACAGTGCAAAAAGTATATTATCTTTATATAG 7 65 1 AATATATTAT 0.625086 -236 ATCTTTATATAGTTTATATAATGTACCTTATG 7 85 1 AGTATATAAT 0.882358 -216 ACTATATAGGATCTTTTATTATTTTTTGTAAA 7 149 0 ATTTTATTAT 0.952263 -152 AGAGTTTTTTTTGCTTTATAATGTACTCATTG 7 189 1 TTTTTATAAT 0.953158 -112 ACCGGTATCCAGTCTTTTTTATGGACAACCTG 7 253 1 AGTTTTTTAT 0.866342 -48 ** ******** Masking position 5 Map Score: 19.0008 Number of sites scoring better than the average of aligned sites = 1236 Number in coding regions = 778 Number in noncoding regions = 458 Number of orfs with sites within 600 bp upstream = 226 Fraction of orfs with sites within 600 bp upstream = 0.0362994 Motif number 2 AAAATTACCTAATTATCCAATAATA 2 2 1 AATACAATTA 0.889341 -195 ATGAACGTATAAAGCACTAGATAAAAAATTATAA 2 115 1 AACACGATAA 0.973231 -82 AAAAAATTATAATTTAGTTAATAATTATTAACTA 2 137 1 AATAGAATAA 0.880218 -60 TTTTGATAATAATTTAGTTAATAATTATTAACTA 2 151 0 AATAGAATAA 0.880218 -46 TTTCGTGGTCAAACCACGGGATGAGTTTCTAATC 5 29 0 AACACGATGA 0.985726 -93 ACCCGTGGTCAAACCACGAGATGTAAAATGAGTA 5 95 1 AACACGATGT 0.888319 -27 TTACGTGAATAAGTTACGAGATAAAAGAGT 6 7 0 AATACGATAA 0.984856 -106 AACTTCTACAAATTTACGGGATGACGATAGTTTA 6 49 1 AATACGATGA 0.991979 -64 CATGTTATATACAGTACCAAATAATAAATCATCA 7 12 0 ACTACAATAA 0.854434 -289 TAGTTTATATAATGTACCTTATGAGTATCTCCTT 7 94 1 AATACTATGA 0.941328 -207 TATTAGTACTAATATACACAATGAGTACATTATA 7 205 0 AATACAATGA 0.984856 -96 CAACCTGATCAATCTACGTGGTGACACAAAATT 7 278 1 AATACGGTGA 0.955014 -23 ** *** ***** Masking position 6 Map Score: 14.648 Number of sites scoring better than the average of aligned sites = 209 Number in coding regions = 140 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 3 TAAAAATATATACTTTATAATAGAAGCAAAAT 1 7 0 TATTTATAAG 0.712484 -84 TTATAAAGTATATATTTTTATTGAAATAAAATTGAT 1 23 1 TAATTATAAA 0.971558 -68 ATAAAATTGATACACTCTTATTGTAGAATGGTTAAT 1 48 1 TAATTATTAG 0.967162 -43 CAATTAAAGGTAGAATTTAATAGTAAAAATTTTATA 2 47 1 TAATTATTAA 0.979177 -150 GTAAAAATTTTATAATTTGATTAAATATTCTTTACT 2 69 1 TAATTATAAT 0.84338 -128 TCCATAAAATTCAATTTTGATAATAATTTAGTTAAT 2 163 0 TCATTATTAA 0.963355 -34 TCCAATGAGATAAAATCTTATCCTAAATGATGTGAA 3 43 0 TAATTATTAA 0.979177 -101 CTTATTATTTTATAATATCATACTAAAAAAGCCTTG 3 109 0 TAATTATTAA 0.979177 -35 GGGATGAGTTTCTAATCTAATATAAATATAACTTA 5 10 0 TCATTATAAA 0.950238 -112 AAAGCCAAAAACAACTATGATATTAATAATTTTGAA 5 60 1 ACATTATTAA 0.752781 -62 AAAGATCCTATATAGTTTGACTATAGAGTTTTTTTT 7 165 1 TAATTACTAG 0.847248 -136 ACACAATGAGTACATTATAAAGCAAAAAAAACTCTA 7 188 0 TAATTAAAAA 0.812744 -113 ** * * * ** *** Masking position 10 Map Score: 11.2879 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 121 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 4 TCATCCCGTGGTTTGACCACGAAAGCCAAAA 5 39 1 GTTGACCACG 0.998356 -83 ACATCTCGTGGTTTGACCACGGGTTCAAAAT 5 88 0 GTTGACCACG 0.998356 -34 AATACCCGTGGCTTGACCACCGGTATCCAGT 7 235 1 GTTGACCACC 0.988224 -66 TCACCACGTAGATTGATCAGGTTGTCCATAA 7 271 0 GTTGATCAGG 0.971268 -30 AATTTTGTGTCACCACGTAGATTGATC 7 284 0 GGTCACCACG 0.987574 -17 * ********* Masking position 6 Map Score: 6.43504 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 2 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 ATTTTGCTTCTATTATAAAG 1 1 1 ATTTTGCTTC 0.921056 -90 GAGTGTATCAATTTTATTTCAATAAAAATA 1 35 0 ATTTTATTTC 0.921143 -56 TTACTATTAAATTCTACCTTTAATTGAAAA 2 43 0 ATTCTACCTT 0.843836 -154 TTAGGATAAGATTTTATCTCATTGGATCTT 3 53 1 ATTTTATCTC 0.972709 -91 TTATACTCATTTTACATCTCGTGGTTTG 5 104 0 ATTTTACATC 0.88056 -18 ACTCTTTTATCTCGTAACTTATT 6 4 1 CTTTTATCTC 0.931876 -109 CACGTAAAAAATTTTAACTTCTACAAATTT 6 34 1 ATTTTAACTT 0.685337 -79 TTGCACTGTGATACTGCCTCAGCTTTATAC 7 45 0 ATACTGCCTC 0.844771 -256 TGCAAAAAGTATATTATCTTTATATAGTTT 7 70 1 ATATTATCTT 0.778593 -231 AAAAAAGTTGCTATTACTTCCACGAAGGAG 7 122 0 CTATTACTTC 0.740106 -179 AATTTTGTGTCACCACGTAGA 7 290 0 ATTTTGTGTC 0.811018 -11 ********** Masking position 5 Map Score: 4.52723 Number of sites scoring better than the average of aligned sites = 468 Number in coding regions = 359 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 6 ACCTTTAATTGAAAAACAACAATATTATTG 2 28 0 GAAAAACAAC 0.964578 -169 AGATCAACTTCAAAAAGAGCAAAGATCCAA 3 74 0 CAAAAAGAGC 0.967377 -70 TAATATCATACTAAAAAAGCCTTGTAAGAA 3 103 0 CTAAAAAAGC 0.896946 -41 CCACGAAAGCCAAAAACAACTATGATATTA 5 55 1 CAAAAACAAC 0.989678 -67 TTATGAATTATAAAAACAACGAGCATCAAG 6 83 1 TAAAAACAAC 0.948382 -30 CATTATAAAGCAAAAAAAACTCTATAGTCA 7 182 0 CAAAAAAAAC 0.97704 -119 ********** Masking position 5 Map Score: 4.97209 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 65 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 ATTAGAAACTCATCCCGTGGTTTGACCACG 5 30 1 CATCCCGTGG 0.982084 -92 TAATAATTTTGAACCCGTGGTCAAACCACG 5 83 1 GAACCCGTGG 0.992582 -39 ATTAGTACTAATACCCGTGGCTTGACCACC 7 226 1 ATACCCGTGG 0.993649 -75 AAAAGACTGGATACCGGTGGTCAAGCCACG 7 241 0 ATACCGGTGG 0.970443 -60 ********** Masking position 8 Map Score: 2.75407 Number of sites scoring better than the average of aligned sites = 3 Number in coding regions = 0 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 ATTATAAAGTATATATTTTTATTGAAATAA 1 22 1 ATATATTTTT 0.666191 -69 AAAAACAACAATATTATTGGATAATTAGGT 2 17 0 ATATTATTGG 0.850632 -180 AGTAAAAATTTTATAATTTGATTAAATATT 2 68 1 TTATAATTTG 0.936861 -129 AGATAAAAAATTATAATTTAGTTAATAATT 2 133 1 TTATAATTTA 0.745016 -64 TTAATATTCCTTATTATTTTATAATATCAT 3 124 0 TTATTATTTT 0.776389 -20 AATATCATAGTTGTTTTTGGCTTTCGTGGT 5 54 0 TTGTTTTTGG 0.50846 -68 ATGATGATTTATTATTTGGTACTGTATA 7 9 1 TTATTATTTG 0.94633 -292 TAAAGATAATATACTTTTTGCACTGTGATA 7 62 0 ATACTTTTTG 0.694011 -239 TATTATCTTTATATAGTTTATATAATGTAC 7 81 1 ATATAGTTTA 0.623287 -220 GGATCTTTTATTATTTTTTGTAAAAAAGTT 7 143 0 TTATTTTTTG 0.934691 -158 AAAAGATCCTATATAGTTTGACTATAGAGT 7 164 1 ATATAGTTTG 0.893644 -137 ********** Masking position 7 Map Score: 3.38118 Number of sites scoring better than the average of aligned sites = 682 Number in coding regions = 481 Number in noncoding regions = 201 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 9 ********** No masking Map Score: -3.19501e-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 10 ********** No masking Map Score: -3.19501e-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 11 ********** No masking Map Score: -3.19501e-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