AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -iflhCD_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 fliA 107 Sigma-28/WhiG Family #2 yscU 256 YopS Translocation Protein U #3 CT102 134 hypothetical protein #4 yscL 275 Yop Translocation L #5 CT663 300 hypothetical protein #6 CT665 43 hypothetical protein #7 CT666 26 hypothetical protein #8 CT670 22 hypothetical protein Motif number 1 TAAGGGTAGATATTGTTTAAAAATTTTATTTGA 1 46 1 TATTGTTAAA 0.84616 -62 TAGCCTTATTTTTTAGTTTGTAAAAGAAATTTT 1 81 1 TTTTATTTAA 0.801111 -27 TAACACAGCCTTTTTATTATTAAGGAAAAAGAA 2 44 1 TTTTTTTAAA 0.959881 -213 CTAATCTTGCTTTTTCTTTAGAATTTCTTTTTC 2 68 0 TTTTTTTTAA 0.969386 -189 GAGAACGGAATATTTTTTTTAAAGAGCGTTTTT 2 110 0 TATTTTTTAA 0.934872 -147 AACCCCTTACTCTTTGTTTATAAATGGGATGAG 2 148 1 TCTTTTTTAA 0.967362 -109 TATATAAATGTTTTTCTCAAGAAAGAAGGTGGC 2 186 0 TTTTTTCAAA 0.874555 -71 CCTAAAGTATTTTTTAGAAAAGAGGGAGTA 3 8 1 TATTTTTAAA 0.91594 -127 GAACAAGGGCTCTTGATTAATAAGCTTTGGCTT 3 60 1 TCTTGTTAAA 0.919114 -75 ATTTGGTGCTTCTTTTTTTTGTATATATGGGAG 4 40 0 TCTTTTTTTA 0.759333 -236 AGGATCGCATTCTTTTTTACACAGAGATCGAGG 4 136 0 TCTTTTTACA 0.780258 -140 CGACTCGTTCTTTTGATTTCTAAAGACATCTCC 5 61 0 TTTTGTTTAA 0.94119 -240 TCGTGCCCGATTTTTTTCTAAAATTCTTTTGTA 5 95 1 TTTTTTCTAA 0.900482 -206 TGAGAAATCGTTTTTCTTTTTAAAGTAGGTATT 5 180 1 TTTTTTTTAA 0.969421 -121 ***** *** ** Masking position 13 Map Score: 16.5378 Number of sites scoring better than the average of aligned sites = 243 Number in coding regions = 243 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 AAGAGTTATTGATTAGGAGTTAT 1 3 1 GAGTATTGAT 0.755248 -105 TATTGATTAGGAGTTATGTGTTAGTTGTGTA 1 17 1 GAGTATGTGT 0.816036 -91 GGGTTCTTTAGAGAACGGAATATTTTTTTTA 2 122 0 GAGACGGAAT 0.860812 -135 TATAAACAAAGAGTAAGGGGTTCTTTAGAGA 2 139 0 GAGAAGGGGT 0.986442 -118 AGGATCCGGCGAGGAAGAGGTCTTTT 3 119 1 GAGAAGAGGT 0.968799 -16 TTTTTACACAGAGATCGAGGTTTTCCTGACC 4 125 0 GAGTCGAGGT 0.986469 -151 CCTTCTGACGAGGTAGGGATCCTTTGGCAA 4 256 0 GAGTAGGGAT 0.989695 -20 CTCTAACTGAGAGCTCTGGGTCCGAAATACT 5 264 0 GAGTCTGGGT 0.976914 -37 CCAGAGCTCTCAGTTAGAGATGAGCACGTGA 5 276 1 CAGTAGAGAT 0.941052 -25 GCAGTTCGAGGTTTATTTAATT 6 2 1 CAGTCGAGGT 0.965981 -42 TTAATTCTTCCAGGTAGGAATAAATCT 6 27 1 CAGTAGGAAT 0.866072 -17 *** ******* Masking position 2 Map Score: 12.3273 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 130 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 3 CACATAACTCCTAATCAATAACTCTT 1 7 0 CTAATCAATA 0.967181 -101 AATAAAATTTTTAAACAATATCTACCCTTA 1 46 0 TTAAACAATA 0.933952 -62 CTTTTACAAACTAAAAAATAAGGCTAAATC 1 77 0 CTAAAAAATA 0.956446 -31 AAAAGAAATTCTAAAGAAAAAGCAAGATTA 2 70 1 CTAAAGAAAA 0.811449 -187 AAAACGCTCTTTAAAAAAAATATTCCGTTC 2 111 1 TTAAAAAAAA 0.757928 -146 TCCCTCTTTTCTAAAAAATACTTTAGG 3 8 0 CTAAAAAATA 0.956446 -127 AGCCCTTGTTCTAATCAATAAGCTTTGGCA 3 41 0 CTAATCAATA 0.967181 -94 CCAAAGCTTATTAATCAAGAGCCCTTGTTC 3 60 0 TTAATCAAGA 0.904463 -75 TCGCCGGATCCTAATCAAGATATGTCCCTC 3 101 0 CTAATCAAGA 0.96654 -34 CGATCTCTGTGTAAAAAAGAATGCGATCCT 4 139 1 GTAAAAAAGA 0.805374 -137 ********** Masking position 4 Map Score: 10.1034 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 132 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 TTTTAGAAAAGAGGGAGTATGCCAAAGCTT 3 22 1 GAGGGAGTAT 0.957383 -113 TTTTGTATATATGGGAGTGTAATAGCAGTG 4 27 0 ATGGGAGTGT 0.809096 -249 AAACGAGAGCGATCGAGGGTCAGGAAAACC 4 108 1 GATCGAGGGT 0.985181 -168 TTTACACAGAGATCGAGGTTTTCCTGACCC 4 124 0 GATCGAGGTT 0.976894 -152 ACGAGCAAAGGAGCGAGGTTCCCTGCCTGT 4 221 1 GAGCGAGGTT 0.990839 -55 AATAGCTAGGGAGGGAGTATTTCGGACCCA 5 249 1 GAGGGAGTAT 0.957383 -52 GCAGTTCGAGGTTTATTTAATTC 6 4 1 GTTCGAGGTT 0.939314 -40 TAAACGGTAAAAGAGAGGGTATCT 7 13 1 AAGAGAGGGT 0.881721 -14 ********** Masking position 6 Map Score: 7.03099 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 100 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 TATTTGATTTAGCCTTATTTTTTAGTTTGT 1 72 1 AGCCTTATTT 0.767719 -36 GAAGTTGTACAGCTTTTTCTTAAGGCTAAC 2 18 1 AGCTTTTTCT 0.947066 -239 AGGCTAACACAGCCTTTTTATTATTAAGGA 2 40 1 AGCCTTTTTA 0.836433 -217 TCTTTAGAATTTCTTTTTCCTTAATAATAA 2 57 0 TTCTTTTTCC 0.803586 -200 GCACTAATCTTGCTTTTTCTTTAGAATTTC 2 74 0 TGCTTTTTCT 0.882066 -183 TTTTTTAAAGAGCGTTTTTCATGAAGCACT 2 99 0 AGCGTTTTTC 0.907389 -158 AGAGAACGGAATATTTTTTTTAAAGAGCGT 2 114 0 ATATTTTTTT 0.627424 -143 TATTTGGTGCTTCTTTTTTTTGTATATATG 4 44 0 TTCTTTTTTT 0.795211 -232 ATAGCATTGTAGATTTTTTCTCCGATGGCT 4 71 1 AGATTTTTTC 0.805111 -205 AAGGATCGCATTCTTTTTTACACAGAGATC 4 140 0 TTCTTTTTTA 0.55098 -136 AAAGAATGCGATCCTTGTCTGGCTATCCCT 4 154 1 ATCCTTGTCT 0.544035 -122 TCGATAGAGGAGCCTTTTCTGTTTTCTCTT 5 148 0 AGCCTTTTCT 0.936381 -153 GAGATGAGAAATCGTTTTTCTTTTTAAAGT 5 176 1 ATCGTTTTTC 0.822274 -125 AGATTTATTCCTACCTGGAA 6 34 0 AGATTTATTC 0.457629 -10 ********** Masking position 5 Map Score: 7.50234 Number of sites scoring better than the average of aligned sites = 953 Number in coding regions = 953 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 GTACAGCTTTTTCTTAAGGCTAACACAGCCTT 2 24 1 TTCTAAGCTA 0.91385 -233 AAAAAAAATATTCCGTTCTCTAAAGAACCCCT 2 123 1 TTCCTTTCTA 0.824371 -134 CAGGGAGATCTTCTCACTGCTATTACACTCCC 4 13 1 TTCTACGCTA 0.899152 -263 TAGATTTTTTCTCCGATGGCTATGTTAAAAAC 4 80 1 CTCCATGCTA 0.93182 -196 GATCCTTGTCTGGCTATCCCTAGTAAATGACA 4 163 1 TGGCATCCTA 0.712704 -113 CGTTACTTTATTCCCAACGCGATGAGGCATGT 4 192 0 TTCCAAGCGA 0.885605 -84 CGACTCGTTCTTTTGATTTCTAAAGACATCTC 5 62 0 TTTTATTCTA 0.629206 -239 GAAAAACGATTTCTCATCTCGATAGAGGAGCC 5 164 0 TTCTATTCGA 0.881719 -137 TGCTGAGTTATGCCAATACCTACTTTAAAAAG 5 195 0 TGCCATCCTA 0.950445 -106 GCGGGGCCCATTCCAATAGCTAGGGAGGGAGT 5 235 1 TTCCATGCTA 0.986214 -66 GTATTCACGTGCTCATCTCTAACTGAGAGCT 5 280 0 TGCTATTCTA 0.924041 -21 **** ** **** Masking position 12 Map Score: 4.25473 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 155 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 TAAACAAAGAGTAAGGGGTTCTTTAGAGAAC 2 137 0 GTAGGGGTTC 0.909866 -120 GAAAGAAGGTGGCAGATGCTCATCCCATTTA 2 168 0 GGAGATGCTC 0.937463 -89 GATCCGGCGAGGAAGAGGTCTTTT 3 121 1 GGAGAGGTCT 0.970886 -14 ATCAGGGAGATCTTCTCACTGCTAT 4 5 1 GGAGATCTTC 0.836277 -271 AAAGCCAACAGGCAGGGAACCTCGCTCCTTT 4 227 0 GGAGGGAACC 0.939626 -49 CTTCTGACGAGGTAGGGATCCTTTGGCAAAG 4 254 0 GGAGGGATCC 0.984393 -22 AATGTGTTTTGGGAGATGTCTTTAGAAATCA 5 50 1 GGAGATGTCT 0.928751 -251 CCTAGCTATTGGAATGGGCCCCGCTGACCTT 5 228 0 GGATGGGCCC 0.945573 -73 ** ******** Masking position 4 Map Score: 2.33562 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 134 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 8 GTTTATAAATGGGATGAGCATCTGCCACCT 2 163 1 GGGATGAGCA 0.988978 -94 TTGGCTTCGTAGGATGAGGGACATATCTTG 3 86 1 AGGATGAGGG 0.937439 -49 TATTCCCAACGCGATGAGGCATGTCATTTA 4 186 0 GCGATGAGGC 0.951536 -90 TAAATTGAAAGGGATGAAAGAGAAAACAGA 5 131 1 GGGATGAAAG 0.90643 -170 CTCCTCTATCGAGATGAGAAATCGTTTTTC 5 166 1 GAGATGAGAA 0.96261 -135 CTCTCAGTTAGAGATGAGCACGTGAATAC 5 282 1 GAGATGAGCA 0.975504 -19 ********** Masking position 5 Map Score: 2.49834 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 57 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 TTATTTTTTAGTTTGTAAAAGAAATTTTTT 1 86 1 GTTTGTAAAA 0.79883 -22 GCGATCGAGGGTCAGGAAAACCTCGATCTC 4 116 1 GTCAGGAAAA 0.975828 -160 GCCTCATCGCGTTGGGAATAAAGTAACGAG 4 196 1 GTTGGGAATA 0.955126 -80 GTTGATTTGTGCCGGGAAAATGTGTTTTGG 5 32 1 GCCGGGAAAA 0.965672 -269 AATTCTTCCAGGTAGGAATAAATCT 6 29 1 GGTAGGAATA 0.861086 -15 GTCTGGAAAATAGTAGGATT 8 1 1 GTCTGGAAAA 0.975826 -22 ********** Masking position 7 Map Score: 1.71222 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 74 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 AGATGGCCAGTTGCTTAAGCGCTATAAGGA 2 237 0 TTGCTTAAGC 0.721455 -20 AAGAGGGAGTATGCCAAAGCTTATTGATTA 3 30 1 ATGCCAAAGC 0.98971 -105 TCATCCTACGAAGCCAAAGCTTATTAATCA 3 73 0 AAGCCAAAGC 0.952309 -62 CGTTACTTTATTCCCAACGCGATGAGGCAT 4 194 0 TTCCCAACGC 0.936869 -82 TAGGGATCCTTTGGCAAAGCCAACAGGCAG 4 243 0 TTGGCAAAGC 0.948694 -33 CTAAAGACATCTCCCAAAACACATTTTCCC 5 45 0 CTCCCAAAAC 0.866567 -256 ATGCTGAGTTATGCCAATACCTACTTTAAA 5 198 0 ATGCCAATAC 0.866187 -103 ********** Masking position 7 Map Score: 0.779835 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 176 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: -9.71011e-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 12 ********** No masking Map Score: -9.71011e-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 13 ********** No masking Map Score: -9.71011e-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