AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -irpoN_ctra_opreg_100.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 CT466 293 hypothetical protein #3 atoC 42 2-component regulatory system-ATPase #4 CT663 300 hypothetical protein #5 CT665 43 hypothetical protein #6 CT666 26 hypothetical protein Motif number 1 CTTTCCTAATTAAAATCTTTTATCGAAAAAATT 1 109 0 TAATCTTTTT 0.850401 -98 TTCTTATAAAAAAAGCCTTTCCTAATTAAAATC 1 125 0 AAACCTTTCT 0.982081 -82 CTTTTTTTATAAGAACCTTTCGTTCAATATAGT 1 143 1 AGACCTTTCT 0.960865 -64 TCCTTAACAAAAAAACCTTCTCTCCCCTATACT 2 32 1 AAACCTTCTT 0.942235 -262 AATAATTCGTAGGACCCTTTTCTTGAAAGAGAA 2 251 1 AGACCTTTTT 0.988449 -43 TCGGGCACGAACGACTCGTTCTTTTGATTTCTA 4 72 0 AGATCGTTCT 0.947232 -229 ATTTTTTTCTAAAATTCTTTTGTACTTTAAATT 4 104 1 AAATCTTTTT 0.972956 -197 ATCTCGATAGAGGAGCCTTTTCTGTTTTCTCTT 4 148 0 AGACCTTTTT 0.988449 -153 TATCGAGATGAGAAATCGTTTTTCTTTTTAAAG 4 172 1 AAATCGTTTT 0.894191 -129 * ** ****** * Masking position 9 Map Score: 10.7906 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 99 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 GAGTTTTTATTTTTTTTCGAAACAGAAGTCGT 1 73 1 TTTTTTTGAA 0.97117 -134 GTCGTATAAAATTTTTTCGATAAAAGATTTTA 1 100 1 ATTTTTTGAA 0.827046 -107 TAGGAAAGGCTTTTTTTATAAGAACCTTTCGT 1 134 1 TTTTTTTTAG 0.881471 -73 GTTACATACATTTCTTGTGATACTAATGACAG 1 174 1 TTTCTTGGAA 0.975485 -33 GAGAGAAGGTTTTTTTGTTAAGGAAAATACGC 2 24 0 TTTTTTGTAG 0.889599 -270 GTAGGACCCTTTTCTTGAAAGAGAACGCGAAC 2 259 1 TTTCTTGAAA 0.858945 -35 CGGGAAAATGTGTTTTGGGAGATGTCTTTAGA 4 44 1 TGTTTTGGAA 0.940579 -257 TTTTGGGAGATGTCTTTAGAAATCAAAAGAAC 4 56 1 TGTCTTTGAA 0.894592 -245 TCGTGCCCGATTTTTTTCTAAAATTCTTTTGT 4 95 1 TTTTTTTTAA 0.945336 -206 AGAAATCGTTTTTCTTTTTAAAGTAGGTATTG 4 182 1 TTTCTTTTAA 0.949271 -119 ******* ** * Masking position 6 Map Score: 8.481 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 228 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 TATCTTGTAAGCCGACAATACTTTTGGAGG 1 26 1 GCCGACAATA 0.979325 -181 ATTTTATATGGCCTCCAAAAGTATTGTCGG 1 37 0 GCCTCCAAAA 0.950681 -170 ATTCCGCCACGCCGGCATAACCATCTAGGT 2 126 0 GCCGGCATAA 0.994714 -168 GAGTCCAATCGCCGGCATTAATCACATTTC 2 206 1 GCCGGCATTA 0.992443 -88 GTTGATTTGTGCCGGGAAAATGTGTTTTGG 4 32 1 GCCGGGAAAA 0.987111 -269 ********** Masking position 7 Map Score: 4.79399 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 4 TTTTATACGACTTCTGTTTCGAAAAAAAAT 1 81 0 CTTCTGTTTC 0.967191 -126 TCTATTTCTTCTTCTGTTTTCAGACCTAGA 2 103 1 CTTCTGTTTT 0.906204 -191 GCCTGTTCGCGTTCTCTTTCAAGAAAAGGG 2 265 0 GTTCTCTTTC 0.93361 -29 CGCGAACAGGCAACTCTTTT 2 284 1 CAACTCTTTT 0.920711 -10 CGGCACAAATCAACTCATTCAGAGCAGCTC 4 16 0 CAACTCATTC 0.848148 -285 TTTTCTCTTTCATCCCTTTCAATTTAAAGT 4 127 0 CATCCCTTTC 0.957649 -174 ACAGAAAAGGCTCCTCTATCGAGATGAGAA 4 156 1 CTCCTCTATC 0.903944 -145 TTCACGTGCTCATCTCTAACTGAGAGCTCT 4 278 0 CATCTCTAAC 0.828217 -23 AGATACCCTCTCTTTTACCGTTTACA 6 11 0 CCTCTCTTTT 0.934594 -16 ********** Masking position 4 Map Score: 4.13918 Number of sites scoring better than the average of aligned sites = 386 Number in coding regions = 385 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 5 AGTTTTTTCCCCTGACAGGAAATATCCTTAA 2 73 0 CCGACAGGAA 0.958675 -221 GCATAACCATCTAGGTCTGAAAACAGAAGAA 2 111 0 CTGGTCTGAA 0.907331 -183 AACACATTTTCCCGGCACAAATCAACTCATT 4 27 0 CCGGCACAAA 0.971209 -274 TAGAAAAAAATCGGGCACGAACGACTCGTTC 4 84 0 TCGGCACGAA 0.971221 -217 ACTGAGAGCTCTGGGTCCGAAATACTCCCTC 4 259 0 CTGGTCCGAA 0.97396 -42 TTTAATTCTTCCAGGTAGGAATAAATCT 5 26 1 CCGGTAGGAA 0.989623 -18 ** ******** Masking position 10 Map Score: 1.13562 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 36 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 ********** No masking Map Score: 6.2771e-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 7 ********** No masking Map Score: 6.2771e-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 8 ********** No masking Map Score: 6.2771e-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