AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -iphoB_hinf_opreg_300.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 HI0362 300 iron (chelated) ABC transporter, periplasmic-binding protein (yfeA) #2 HI1379 300 phosphate regulon transcriptional regulatory protein (phoB) #3 HI1382 90 phosphate ABC transporter, permease protein (pstC) #4 HI1383 300 phosphate ABC transporter, periplasmic-binding protein (pstS) Motif number 1 TTTCTTGGTCAGTTGTTTTGGTTTGTTCTG 1 31 1 AGTTGTTTTG 0.867715 -270 TAAGTTCAGCAATAGTCTTGGCTGCTTGTG 1 79 0 AATAGTCTTG 0.895751 -222 ATACTAACCAAAATGTTTTGTTCTTTTTTC 1 109 1 AAATGTTTTG 0.7063 -192 ATTTATTTATAATTATTTCGTACAAAATGT 1 150 0 AATTATTTCG 0.908193 -151 TAAATAAATCTATTATTTTGATAATCATTC 1 171 1 TATTATTTTG 0.962795 -130 CTACTTTTTATATTGTTTTGGAATGGGAAT 1 197 0 TATTGTTTTG 0.944932 -104 AAAGTAGTACTATTATCTCCGATGAATAAT 1 220 1 TATTATCTCC 0.737484 -81 ATAACCACAGTATAATCGTTTTAACTCC 2 33 0 TATAATCG 0.00533927 -268 TTACCGCGAATATAATCTTCTGTACGTTGT 2 177 0 TATAATCTTC 0.80182 -124 AAAATGGGGTAGTTATTTTGAGTTCTCTTA 2 205 1 AGTTATTTTG 0.908193 -96 GGTTATCTTAAATAATTTTGGAAAATACTT 3 71 1 AATAATTTTG 0.934393 -20 AAGTATTTTCCAAAATTATT 3 81 0 AAGTATTTTC 0.6885 -10 CACAATTATTTTCTACACTTCGC 4 4 1 AATTATTTTC 0.933393 -297 CCAGTGATGCTATTAGCTTGAGCAAAAGGT 4 124 0 TATTAGCTTG 0.774446 -177 ********** Masking position 8 Map Score: 10.7113 Number of sites scoring better than the average of aligned sites = 1246 Number in coding regions = 1034 Number in noncoding regions = 212 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 2 GAAAAAAGAACAAAACATTTTGGTTAGTATT 1 108 0 CAAACATTTT 0.814086 -193 TTCATACATTCAATACATTTTGTACGAAATA 1 136 1 CAATCATTTT 0.922857 -165 GAGATAATAGTACTACTTTTTATATTGTTTT 1 208 0 TACTCTTTTT 0.577639 -93 TGGTCAAACACAACAAATTTTTGATAGACCC 2 141 1 CAACAATTTT 0.900414 -160 TCAAAATAACTACCCCATTTTACCGCGAATA 2 195 0 TACCCATTTT 0.956972 -106 AATACATTCTCACCAAACTTTTACTTTTTAA 2 235 0 CACCAACTTT 0.946336 -66 AAGTGAGAAATAATACATTCTCACCAAACTT 2 246 0 TAATCATTCT 0.715372 -55 TATTATTTCTCACTTCACTTTTATGCCATAA 2 262 1 CACTCACTTT 0.958902 -39 CTTTATTTTATACCGCACTTTATACAAAACC 3 16 1 TACCCACTTT 0.964324 -75 CAAAACCTAGCACTTAACATTAATAAAGTGC 3 40 1 CACTAACATT 0.520245 -51 TATTTAAGATAACCGCACTTTATTAATGTTA 3 54 0 AACCCACTTT 0.828883 -37 GCGGTTATCTTAAATAATTTTGGAAAATACT 3 69 1 TAAAAATTTT 0.599325 -22 TGCATAAACATAACAAATTCTCCTTGAGTGT 4 49 0 TAACAATTCT 0.655124 -252 GATGGATTGATAATTAACTTTATTCCCAGTT 4 214 0 TAATAACTTT 0.832475 -87 **** ****** Masking position 2 Map Score: 9.77149 Number of sites scoring better than the average of aligned sites = 1816 Number in coding regions = 1286 Number in noncoding regions = 530 Number of orfs with sites within 600 bp upstream = 353 Fraction of orfs with sites within 600 bp upstream = 0.0566977 Motif number 3 GATAATAGTACTACTTTTTATATTGTTTTGG 1 206 0 CTCTTTTTAT 0.92346 -95 GTGTAGCTTGTTGCATATTATGAGTTACTAT 2 61 0 TTCATATTAT 0.734015 -240 AAAATAACTACCCCATTTTACCGCGAATATA 2 193 0 CCCATTTTAC 0.946026 -108 AATACTCCTTCATTTGATTTATGGCATA 2 283 0 CTCATTTGAT 0.94704 -18 AATCTCTTTATTTTATACCGCACTTT 3 6 1 CTTATTTTAT 0.882604 -85 TTATTTTATACCGCACTTTATACAAAACCTA 3 18 1 CCCACTTTAT 0.973937 -73 TTTAAGATAACCGCACTTTATTAATGTTAAG 3 52 0 CCCACTTTAT 0.973937 -39 TAAGATTTTTTTTCATTTTATGCATAAACAT 4 69 0 TTCATTTTAT 0.939021 -232 ** ******** Masking position 10 Map Score: 4.20195 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 149 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 4 TTATAAATAAATCTATTATTTTGATAATCA 1 168 1 ATCTATTATT 0.786496 -133 TCAATAGCTCAACAATTATTCATCGGAGAT 1 234 0 AACAATTATT 0.890611 -67 TGAGCTATTGAACAATTATTCAGGCATTCA 1 253 1 AACAATTATT 0.890611 -48 AAGTATTTTCCAAAATTATTTAAGATAACC 3 71 0 CAAAATTATT 0.886602 -20 CACAATTATTTTCTACACTT 4 1 1 CACAATTATT 0.971375 -300 ********** Masking position 5 Map Score: 3.22466 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 36 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 GTTGTTTTGGTTTGTTCTGTCATTTTAGGTTTA 1 42 1 TTTTCTTCAT 0.916604 -259 TTCTGTCATTTTAGGTTTATCATCACAAGCAGC 1 56 1 TTATTTTCAT 0.881174 -245 AAAATGTTTTGTTCTTTTTTCATACATTCAATA 1 118 1 GTTTTTTCAT 0.980381 -183 AAAATAATAGATTTATTTATAATTATTTCGTAC 1 157 0 ATTTTTTAAT 0.742048 -144 TCACCAAACTTTTACTTTTTAATAAGAGAACTC 2 224 0 TTTTTTTAAT 0.904435 -77 GGTGAGAATGTATTATTTCTCACTTCACTTTTA 2 252 1 TATTTTTCAC 0.80094 -49 AACGTAATAAGATTTTTTTTCATTTTATGCATA 4 74 0 GATTTTTCAT 0.94817 -227 TTTATTCCCAGTTTCTTTCTCATATAAAGATGC 4 194 0 GTTTTTTCAT 0.980381 -107 *** *** **** Masking position 12 Map Score: 1.97614 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 132 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 6 ********** No masking Map Score: -3.30159e-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 7 ********** No masking Map Score: -3.30159e-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 8 ********** No masking Map Score: -3.30159e-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