AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -irpoN_ctra_opreg_300.orf -g0.413 -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 = 0.413 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 glnP 206 ABC Amino Acid Transporter Permease #2 CT465 92 hypothetical protein #3 CT466 293 hypothetical protein #4 atoC 42 2-component regulatory system-ATPase #5 CT663 300 hypothetical protein #6 CT665 43 hypothetical protein #7 CT666 26 hypothetical protein Motif number 1 GAGGCCATATAAAATGTACACGAGTTTTTATTT 1 52 1 AAAGTAACGA 0.98586 -155 TTTATCGAAAAAATTTTATACGACTTCTGTTTC 1 91 0 AAATTAACGA 0.858987 -116 TTCGTTAGAGAAAAAGTACAAGATCTAGTACTT 2 36 0 AAAGTAAAGA 0.97764 -57 GTTTCCCGCTGAATGGAAAAAGACTTATATATT 2 67 0 GAAGAAAAGA 0.932492 -26 TTAAGAGGACAAAGTATAGGGGAGAGAAGGTTT 3 44 0 AAAATAGGGA 0.826864 -250 CTAGGTCTGAAAACAGAAGAAGAAATAGAGTTT 3 99 0 AAAGAAAAGA 0.97764 -195 CGGCGTGGCGGAATGGTAGACGCGGTAGACTCA 3 142 1 GAAGTAACGC 0.874359 -152 CCTTTTCTTGAAAGAGAACGCGAACAGGCAACT 3 266 1 AAAGAAGCGA 0.972374 -28 CTTTCAATTTAAAGTACAAAAGAATTTTAGAAA 5 109 0 AAAACAAAGA 0.748098 -192 TTTGTACTTTAAATTGAAAGGGATGAAAGAGAA 5 122 1 AAAGAAGGGA 0.955819 -179 ATGAAAGAGAAAACAGAAAAGGCTCCTCTATCG 5 144 1 AAAGAAAGGC 0.93122 -157 ACCTACTTTAAAAAGAAAAACGATTTCTCATCT 5 177 0 AAAAAAACGA 0.938993 -124 TGTAAACGGTAAAAGAGAGGGTATCT 7 4 1 AAAGTAAAGA 0.97764 -23 *** *** **** Masking position 8 Map Score: 15.6767 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 172 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 2 GAGTTTTTATTTTTTTTCGAAACAGAAGTCG 1 73 1 TTTTTTTGAA 0.960065 -134 CGTATAAAATTTTTTCGATAAAAGATTTTAA 1 102 1 TTTTTCGTAA 0.959282 -105 TAGGAAAGGCTTTTTTTATAAGAACCTTTCG 1 134 1 TTTTTTTTAA 0.976979 -73 GATCTTGTACTTTTTCTCTAACGAATATATA 2 44 1 TTTTTCTTAA 0.976533 -49 GAGAGAAGGTTTTTTTGTTAAGGAAAATACG 3 25 0 TTTTTTGTAA 0.960065 -269 TCGTAGGACCCTTTTCTTGAAAGAGAACGCG 3 257 1 CTTTTCTGAA 0.862236 -37 TCGTGCCCGATTTTTTTCTAAAATTCTTTTG 5 95 1 TTTTTTTTAA 0.976987 -206 AGAAATCGTTTTTCTTTTTAAAGTAGGTATT 5 182 1 TTTCTTTTAA 0.918541 -119 ******* *** Masking position 10 Map Score: 9.34025 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 124 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 3 TGGCCTCCAAAAGTATTGTCGGCTTACAAGATA 1 26 0 ATATTGTCGC 0.887426 -181 AGCTTCTCTCTCCTATCATGGAT 2 1 1 ATTCTCTCCC 0.987005 -92 TTGTTAAGGAAAATACGCTCAGCAGAGGTAT 3 9 0 ATACGCTCGC 0.970028 -285 TAACAAAAAAACCTTCTCTCCCCTATACTTTGT 3 36 1 ATTCTCTCCC 0.987005 -258 TAGACTCAAAATCTACTCTTAGCAGTAAGGTGT 3 167 1 ATACTCTTGC 0.965362 -127 CTCCCAAAACACATTTTCCCGGCACAAATCAAC 5 32 0 ATTTTCCCGC 0.966779 -269 TCTGGGTCCGAAATACTCCCTCCCTAGCTATTG 5 248 0 ATACTCCCCC 0.991697 -53 AGATTTATTCCTACCTGGAAGAATT 6 29 0 ATATTCCTCC 0.91437 -15 * ******* ** Masking position 1 Map Score: 5.89354 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 51 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 4 TCTTGTGATACTAATGACAGGATAGGGGATA 1 186 1 CTAATGAGGA 0.856807 -21 AGTACTTTCATCCATGATAGGAGAGAGAAGCT 2 11 0 TCCATGAGGA 0.823379 -82 AAAGTTTCCCGCTGAATGGAAAAAGACTTA 2 73 0 CCGCTGAGGA 0.997246 -20 ATACCTCTGCTGAGCGTATTTTCCTTAA 3 7 1 CTGCTGAGTA 0.982276 -287 AGAGTTTTTTCCCCTGACAGGAAATATCCTTA 3 74 0 CCCCTGAGGA 0.993508 -220 CAACACCTTACTGCTAAGAGTAGATTTTGAGT 3 170 0 CTGCTAAGTA 0.860897 -124 GTGATTAATGCCGGCGATTGGACTCGAACCAA 3 199 0 CCGGCGAGGA 0.956691 -95 GGAATGGGCCCCGCTGACCTTATGCTGAGTTA 5 217 0 CCGCTGATTA 0.940593 -84 ******* *** Masking position 7 Map Score: 4.01765 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 65 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 5 CCTCCAAAAGTATTGTCGGCTTACAAGATA 1 26 0 TATTGTCGGC 0.976608 -181 CCGACAATACTTTTGGAGGCCATATAAAAT 1 37 1 TTTTGGAGGC 0.944415 -170 ACCTAGATGGTTATGCCGGCGTGGCGGAAT 3 126 1 TTATGCCGGC 0.994007 -168 GAAATGTGATTAATGCCGGCGATTGGACTC 3 206 0 TAATGCCGGC 0.991436 -88 CCAAAACACATTTTCCCGGCACAAATCAAC 5 32 0 TTTTCCCGGC 0.985402 -269 ********** Masking position 4 Map Score: 4.32678 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 23 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 6 TATCCCCTATCCTGTCATTAGT 1 195 0 ATCCCTATCC 0.973193 -12 AGCTTCTCTCTCCTATCATGGAT 2 3 1 CTCTCTCTCC 0.995117 -90 ACAAAAAAACCTTCTCTCCCCTATACTTTGT 3 38 1 CTCTCTCCCC 0.986757 -256 ACAGAAAAGGCTCCTCTATCGAGATGAGAAA 5 156 1 CTCTCTATCG 0.951353 -145 TGGGTCCGAAATACTCCCTCCCTAGCTATTG 5 248 0 ATCTCCCTCC 0.979333 -53 AGATACCCTCTCTTTTACCGTTT 7 14 0 ATCCCTCTCT 0.953678 -13 ** ******** Masking position 2 Map Score: 3.5942 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 93 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 ATAGTTACATACATTTCTTGTGATACTAAT 1 171 1 ACATTTCTTG 0.948302 -36 TATCCCCTATCCTGTCATTAGTAT 1 193 0 CCCTATCCTG 0.947589 -14 AGCTTCTCTCTCCTATCATGGATGAAAGTA 2 11 1 TCCTATCATG 0.762435 -82 CCTCTTAAGGATATTTCCTGTCAGGGGAAA 3 69 1 ATATTTCCTG 0.885585 -225 GGAAAAAACTCTATTTCTTCTTCTGTTTTC 3 94 1 CTATTTCTTC 0.839725 -200 GGCATTAATCACATTTCATGATTTATATTG 3 219 1 ACATTTCATG 0.948302 -75 TTCGTAGGACCCTTTTCTTGAAAGAGAACG 3 256 1 CCTTTTCTTG 0.920095 -38 TTTCTGTTTTCTCTTTCATCCCTTTCAATT 5 133 0 CTCTTTCATC 0.863517 -168 ********** Masking position 6 Map Score: 0.669821 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 198 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 AAATGTACACGAGTTTTTATTTTTTTTCGA 1 63 1 GAGTTTTTAT 0.874011 -144 AATTAGGAAAGGCTTTTTTTATAAGAACCT 1 131 1 GGCTTTTTTT 0.837547 -76 TAGGGGAGAGAAGGTTTTTTTGTTAAGGAA 3 31 0 AAGGTTTTTT 0.83959 -263 AGAAGAAATAGAGTTTTTTCCCCTGACAGG 3 85 0 GAGTTTTTTC 0.975817 -209 GGGGTTTTTCAGAGGTGAGT 4 33 0 GGGGTTTTTC 0.970406 -10 GTTCGTGCCCGATTTTTTTCTAAAATTCTT 5 93 1 GATTTTTTTC 0.861925 -208 GCAGTTCGAGGTTTATTTAATTCTTCC 6 8 1 GAGGTTTATT 0.89336 -36 ********** Masking position 5 Map Score: 1.62186 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 285 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: -1.04149e-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 10 ********** No masking Map Score: -1.04149e-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 11 ********** No masking Map Score: -1.04149e-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