AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -icpxR_hinf_opreg_100.orf -g0.38 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HI0079 102 peptidyl-prolyl cis-trans isomerase B (ppiB) #2 HI0269 125 RNA polymerase sigma-32 factor (rpoH) #3 HI0837 53 response regulator (cpxR) #4 HI0839 116 conserved hypothetical protein #5 HI0845 86 conserved hypothetical protein #6 HI1004 272 peptidyl-prolyl cis-trans isomerse, putative #7 HI1157 71 ATP-binding protein protein (cydD) #8 HI1158 73 thioredoxin reductase (trxB) #9 HI1159 284 conserved hypothetical protein #10 HI1259 193 periplasmic serine protease Motif number 1 CGGTTTGTTTTTATTTCATTTTACGAGCTTAAAA 1 11 0 TTATCTTTAC 0.803973 -92 AACCGCACTTTTATAGCACTTTTACCTCGATTGT 1 40 1 TTATCCTTTA 0.855825 -63 TTTTATAATAATTGAACTTTCAATTG 2 3 1 TTATTATTAA 0.643245 -123 ATAAGACAGATTTTATCAATTGAAAGTTCAATTA 2 19 0 TTTTCATTAA 0.947001 -107 CCCTTCTTTATTTTGGCTTTTGCCAATCAATGTA 2 97 0 TTTTCTTTCC 0.70117 -29 CTTTTACCAATTATTCTTATTGTAGTGTGGTGAA 3 21 0 TTATTATTTA 0.666318 -33 TAAGCCAAATTTTTTTTATTTTTAACATT 4 6 0 TTTTTTTTTA 0.881734 -111 ATAATTTCTTTTTTCTTGCTGAAAAAGTGCGGTT 4 68 1 TTTTTCTGAA 0.652982 -49 ATTTGCCTATTTTTTACGATTAAAAAGGAAATAG 5 39 1 TTTTCATTAA 0.946951 -48 TATTTCCTTTTTATTTCATTGCTATTTCCTTTTT 5 60 0 TTATCTTGTA 0.819556 -27 GAGGATGGAGTTTTCACTTTTTAAGATGCTAATT 6 109 1 TTTTCTTTAA 0.960518 -164 AGATGCTAATTTTTTACGTTTAGATTATAATCGG 6 132 1 TTTTCTTTGA 0.931508 -141 AAATATAAAATTTTCCCGATTATAATCTAAACGT 6 147 0 TTTTCATTTA 0.951911 -126 AAATTGTGCATTTTTTCAATTAACATTCTATAAC 6 190 0 TTTTCATTAC 0.892087 -83 AATTCCCCTCTTTTAACTCTTTTAAAGAGGGGAA 7 22 1 TTTTCCTTTA 0.942145 -50 ATAAGTTGCATTTTACTGATTATAAACTTTTTGC 8 11 0 TTTTTATTTA 0.845628 -63 TTTAGAAACGTTTTACCATTTCTATTA 9 4 0 TTTTCTTTTA 0.96421 -281 ATCAGCCATGTTTTATCCTTGTGAAAAAAATAAT 9 65 0 TTTTCTTGGA 0.862824 -220 CTGATTTTCCTTTTATCGTTGAGATCAACGAACA 9 94 1 TTTTCTTGGA 0.862778 -191 TCGCTCTTTTTCACAATTTACTTTTCCAAGA 9 264 0 TTTTCATTAC 0.892087 -21 TTTTTGACCTTTTTATTGACTAGAA 10 2 1 TTTTCTTTTA 0.96421 -192 TGTAAGACCGTTTTTGTACTGCTCCGATTTCCTT 10 77 1 TTTTTCTGTC 0.490798 -117 GGAGAGCAAATTATCTTGTTTAAAAGGAAATCGG 10 100 0 TTATTTTTAA 0.710456 -94 **** * *** ** Masking position 10 Map Score: 28.5087 Number of sites scoring better than the average of aligned sites = 940 Number in coding regions = 704 Number in noncoding regions = 236 Number of orfs with sites within 600 bp upstream = 214 Fraction of orfs with sites within 600 bp upstream = 0.034372 Motif number 2 TTGTTAATAAGACAGATTTTATCAATTGAA 2 29 0 GACAGATTTT 0.774313 -97 GGTATCATAAGCCAAATTTTTTTTATTTTT 4 17 0 GCCAAATTTT 0.871357 -100 AAATTATAACCGCACTTTTTCAGCAAGAAA 4 79 0 CGCACTTTTT 0.895647 -38 TATAATTTGCGGCAAATTTTTCAAAG 4 101 1 GGCAAATTTT 0.980421 -16 AGTATCATTTGCCTATTTTTTACGATTAAA 5 33 1 GCCTATTTTT 0.58074 -54 GTCATTTTTTGGCAAAATTTAAATCAAAAG 6 26 1 GGCAAAATTT 0.94893 -247 AATCAAAAGCGGCAATATTTGGTGGTGTTT 6 47 1 GGCAATATTT 0.898051 -226 CTTTTTAAGATGCTAATTTTTTACGTTTAG 6 125 1 TGCTAATTTT 0.823967 -148 ATTATAATCGGGAAAATTTTATATTTATAA 6 155 1 GGAAAATTTT 0.896994 -118 ATTGAAAAAATGCACAATTTAACAAACTCA 6 204 1 TGCACAATTT 0.847632 -69 TTTAAAGAGGGGAACTTTTTCTATAATCAC 7 42 1 GGAACTTTTT 0.850829 -30 AGCAAAGTGCGGAAGATTTTAGAAACGTTT 9 25 0 GGAAGATTTT 0.923261 -260 AAAAAATAATGGCTGATTTTAGCAAAGTGC 9 45 0 GGCTGATTTT 0.967577 -240 GATAAAACATGGCTGATTTTCCTTTTATCG 9 82 1 GGCTGATTTT 0.967577 -203 TAAGGATTGTTGCAGTATTTCAGTAAGATT 9 129 0 TGCAGTATTT 0.725074 -156 ATAAAGAATCGGCGGATTTTTTGGCACTAC 9 197 1 GGCGGATTTT 0.952564 -88 TCGCTCTTTTTCACAATTTAC 9 274 0 CGCTCTTTTT 0.787337 -11 TGTTCTAATACGCGCAATTTTCTAGTCAAT 10 25 0 CGCGCAATTT 0.661015 -169 CTCCTCTTATTGAACATTTTTTTTATTTTT 10 130 1 TGAACATTTT 0.722775 -64 ********** Masking position 8 Map Score: 22.2033 Number of sites scoring better than the average of aligned sites = 1428 Number in coding regions = 1140 Number in noncoding regions = 288 Number of orfs with sites within 600 bp upstream = 210 Fraction of orfs with sites within 600 bp upstream = 0.0337295 Motif number 3 TTTGTTTTTATTTCATTTTACGAGCTTAAA 1 12 0 TTTCATTTTA 0.855857 -91 TTTGTTTTCCCTCTAAAAAATTAAG 1 88 0 TTTCCCTCTA 0.963077 -15 CGTTTCCCTTCTTTATTTTGGCT 2 113 0 TTCCCTTCTT 0.960632 -13 TGGAGATTCCTTTTACCAATTATTC 3 39 0 ATTCCTTTTA 0.816985 -15 ACCTAAATAATTTCTTTTTTCTTGCTGAAA 4 62 1 TTTCTTTTTT 0.822551 -55 TTCATTGCTATTTCCTTTTTAATCGTAAAA 5 50 0 TTTCCTTTTT 0.981501 -37 TGCTATTTCCTTTTTATTTCATTGC 5 72 0 TTTCCTTTTT 0.981501 -15 AGGATGGAGTTTTCACTTTTTAAGATGCTA 6 110 1 TTTCACTTTT 0.870539 -163 TTCTAACCAATTCCCCTCTTTTAACTCTTT 7 14 1 TTCCCCTCTT 0.952548 -58 ATAGAAAAAGTTCCCCTCTTTAAAAGAGTT 7 36 0 TTCCCCTCTT 0.952548 -36 CATGGCTGATTTTCCTTTTATCGTTGAGAT 9 89 1 TTTCCTTTTA 0.97471 -196 ACTGCTCCGATTTCCTTTTAAACAAGATAA 10 94 1 TTTCCTTTTA 0.97471 -100 ********** Masking position 7 Map Score: 21.2631 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 117 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 4 AGCTCGTAAAATGAAATAAAAACAAACCGC 1 16 1 ATGAAATAAA 0.785832 -87 CGAGGTAAAAGTGCTATAAAAGTGCGGTTT 1 39 0 GTGCTATAAA 0.940102 -64 TAACAAATTGGTTCAATAAGATAGCTTATT 2 53 1 GTTCAATAAG 0.933882 -73 ATAGCTTATTGTGCTATAACTAGGTACATT 2 73 1 GTGCTATAAC 0.912623 -53 GGAAATAGCAATGAAATAAAAAGGAAATAG 5 65 1 ATGAAATAAA 0.785832 -22 TTCAATTAACATTCTATAACCCTTGTTATA 6 180 0 ATTCTATAAC 0.856953 -93 TAATAATATAATGCAATAAGTTGCATTTTA 8 30 0 ATGCAATAAG 0.954139 -44 GCAATTTTCTAGTCAATAAAAAGGTCAAAA 10 12 0 AGTCAATAAA 0.735155 -182 CAAGTAGCAAATTCTATAAATTTATGTTCT 10 49 0 ATTCTATAAA 0.900784 -145 TAAAAAAAATGTTCAATAAGAGGAGAGCAA 10 125 0 GTTCAATAAG 0.933882 -69 ********** Masking position 6 Map Score: 7.4215 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 167 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 5 AGTGCTATAAAAGTGCGGTTTGTTTTTATT 1 30 0 AAGTGCGGTT 0.984392 -73 ATCGAGGTAAAAGTGCTATAAAAGTGCGGT 1 41 0 AAGTGCTATA 0.665715 -62 CTTGCTGAAAAAGTGCGGTTATAATTTGCG 4 82 1 AAGTGCGGTT 0.984392 -35 GAAGCGTAAAGTGCGGTCATTTTTTGGC 6 9 1 AAGTGCGGTC 0.981589 -264 AAAGAGTTAAAAGAGGGGAATTGGTTAGAA 7 14 0 AAGAGGGGAA 0.943465 -58 AACTCTTTTAAAGAGGGGAACTTTTTCTAT 7 36 1 AAGAGGGGAA 0.943465 -36 GATTTTAGCAAAGTGCGGAAGATTTTAGAA 9 31 0 AAGTGCGGAA 0.98912 -254 ********** Masking position 2 Map Score: 7.76649 Number of sites scoring better than the average of aligned sites = 1753 Number in coding regions = 1207 Number in noncoding regions = 546 Number of orfs with sites within 600 bp upstream = 337 Fraction of orfs with sites within 600 bp upstream = 0.0541279 Motif number 6 TTGGCAAAAGCCAAAATAAAGAAGGGAAAC 2 105 1 CCAAAATAAA 0.963079 -21 AATGTTAAAAATAAAAAAAATTTGG 4 6 1 TAAAAATAAA 0.6846 -111 TTTAGGTTCTACCAAATAATCGGGTATCAT 4 39 0 ACCAAATAAT 0.483485 -78 TTTGGTAGAACCTAAATAATTTCTTTTTTC 4 53 1 CCTAAATAAT 0.632218 -64 GCAATCAAACCTAAGATAAATTTAGAAATC 6 236 0 CTAAGATAAA 0.768505 -37 ATCCTTGTGAAAAAAATAATGGCTGATTTT 9 55 0 AAAAAATAAT 0.78741 -230 ATTTTTTTCACAAGGATAAAACATGGCTGA 9 68 1 CAAGGATAAA 0.859887 -217 TCGTTGATCTCAACGATAAAAGGAAAATCA 9 95 0 CAACGATAAA 0.769308 -190 TTTACTTTTCCAAGAATAAATTGTCCTTGA 9 249 0 CAAGAATAAA 0.881798 -36 TTCCTTTTAAACAAGATAATTTGCTCTCCT 10 105 1 ACAAGATAAT 0.803501 -89 CTGTAAGACAAAAAAATAAAAAAAATGTTC 10 141 0 AAAAAATAAA 0.877171 -53 AAATACTCCAAAATAAATTTCAGATAA 10 177 0 CCAAAATAAA 0.963079 -17 ********** Masking position 6 Map Score: 4.67971 Number of sites scoring better than the average of aligned sites = 649 Number in coding regions = 501 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 7 GCTATAAAAGTGCGGTTTGTTTTTATTTCATTTT 1 23 0 TGCGTTTTTT 0.988166 -80 GCTGAAAAAGTGCGGTTATAATTTGCGGCAAATT 4 85 1 TGCGTAATTT 0.937361 -32 TTTATTTCATTGCTATTTCCTTTTTAATCGTAAA 5 51 0 TGCATTTTTT 0.970274 -36 TGCTATTTCCTTTTTATTTCATTG 5 73 0 TGCATTTTTT 0.970274 -14 AAGCGTAAAGTGCGGTCATTTTTTGGCAAAATTT 6 12 1 TGCGTATTTT 0.988166 -261 TAGGTTTGATTGCTGTATCGTTTTTAGTTG 6 253 1 TGCGTTTTTT 0.988166 -20 TGCTAAAATCAGCCATTATTTTTTTCACAAGGAT 9 51 1 AGCATATTTT 0.854002 -234 GTTGCAGTATTTCAGTAAGATTTTGTTCGTTGAT 9 117 0 TTCGTATTTT 0.903146 -168 *** ** * **** Masking position 6 Map Score: 9.43414 Number of sites scoring better than the average of aligned sites = 317 Number in coding regions = 179 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 8 ********** No masking Map Score: 1.43773e-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: 1.43773e-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 CTTATTGAACCAATTTGTTAATAAGACAGA 2 43 0 CAATTTGTTA 0.938155 -83 AGAAATCTTTGAGTTTGTTAAATTGTGCAT 6 213 0 GAGTTTGTTA 0.808615 -60 TAAAAGAGGGGAATTGGTTAGAAGAT 7 7 0 GAATTGGTTA 0.756388 -65 TTAAAGAGGGGAACTTTTTCTATAATCACG 7 43 1 GAACTTTTTC 0.629541 -29 AAATCTTCCGCACTTTGCTAAAATCAGCCA 9 36 1 CACTTTGCTA 0.804144 -249 ATTTCAGTAAGATTTTGTTCGTTGATCTCA 9 113 0 GATTTTGTTC 0.889476 -172 TATTGTTCTGCAACTTGCTCAAGTAGTGCC 9 219 0 CAACTTGCTC 0.915167 -66 AATTGTCCTTGATATTGTTCTGCAACTTGC 9 231 0 GATATTGTTC 0.531082 -54 ATATCAAGGACAATTTATTCTTGGAAAAGT 9 246 1 CAATTTATTC 0.679585 -39 CTAATACGCGCAATTTTCTAGTCAATAAAA 10 21 0 CAATTTTCTA 0.73026 -173 TAAATTTATAGAATTTGCTACTTGTAAGAC 10 55 1 GAATTTGCTA 0.954441 -139 TTAAACAAGATAATTTGCTCTCCTCTTATT 10 111 1 TAATTTGCTC 0.813046 -83 ********** Masking position 2 Map Score: 2.5064 Number of sites scoring better than the average of aligned sites = 773 Number in coding regions = 701 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 11 ********** No masking Map Score: 1.43773e-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 12 ********** No masking Map Score: 1.43773e-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 13 ********** No masking Map Score: 1.43773e-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