AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i117_Oligopeptide_Transport_hinf_reg_100.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -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 HI0853 140 heme-binding lipoprotein (dppA) #2 HI1123 80 oligopeptide ABC transporter, permease protein (oppB) #3 HI1124 295 oligopeptide ABC transporter, periplasmic-binding protein (oppA) #4 HI1187 89 dipeptide ABC transporter, permease protein (dppB) #5 HI1188 300 DNA helicase II (uvrD) Motif number 1 TCCACCAACAAGAAATATCAATAAGATATAAGCAAAT 1 58 0 AAATTAAGAT 0.820164 -83 TTACTCGTATTTAAGTGCGGTTAAAAATCGTCGTATT 2 15 1 TAATCAAAAA 0.772456 -66 AAAATGGGCGAAAAGTGCGGTCAAAAAATACGACGAT 2 41 0 AAATCAAAAA 0.947618 -40 AACAACTCCAACCAAAATGGGCGAAAAG 2 63 0 AAATCAAAAT 0.977414 -18 TTACGATAGCACAATTAGCATTAAAAGGGTAATTTAT 3 50 1 AAATGAAAAG 0.92331 -246 GTTGTGTCTAATAAATCGCTAAAAAAATTGCTAAAAG 3 151 0 AAATGAAAAA 0.963933 -145 TTGTCAGGAAATTATTTGAAGAAAAATTGAGTTTTGT 3 190 0 ATATGAAAAT 0.963267 -106 TAATTTCCTGACAAATCTTTACAAAAATGAATTTTTG 3 213 1 AAATTAAAAA 0.933562 -83 AAGTCTTCTATTTATTAGCTCAAAAATTCATTTTTGT 3 233 0 TTATGAAAAT 0.860541 -63 AATAAATAGAAGACTTTTTATAAAAATATCGCCTAAT 3 254 1 AACTTAAAAT 0.820161 -42 CTTCAAAGAAATTAATCGGTAAAAAATATAATACTCT 4 17 0 ATATGAAAAT 0.970516 -73 CGTAGATAATAAAAGTGCGGTAAAAATTCACCGCACT 4 54 0 AAATCAAAAT 0.977414 -36 TGTCATCATGGGTATTTTTGGAAAAATGAGAAACCTT 5 46 1 GTATTAAAAT 0.731935 -255 AAGTTTGTTTATAAATAGTATAAAAATAGCTTTCAAA 5 114 1 AAATGAAAAT 0.984596 -187 AATCCCGCTTAATATTATTCTTAAAATGTTCTACCCT 5 188 1 ATATTAAAAT 0.945385 -113 * ** * * ***** Masking position 13 Map Score: 17.09 Number of sites scoring better than the average of aligned sites = 761 Number in coding regions = 526 Number in noncoding regions = 235 Number of orfs with sites within 600 bp upstream = 201 Fraction of orfs with sites within 600 bp upstream = 0.032284 Motif number 2 ACGATTTTTAACCGCACTTAAATACGAGTA 2 16 0 ACCGCACTTA 0.99297 -65 GTATTTTTTGACCGCACTTTTCGCCCATTT 2 47 1 ACCGCACTTT 0.997824 -34 GTAAAAATTCACCGCACTCTTCAAAGAAAT 4 42 0 ACCGCACTCT 0.995218 -48 GTGAATTTTTACCGCACTTTTATTATCTAC 4 60 1 ACCGCACTTT 0.997824 -30 AAAATGTTCTACCCTACTTTTGATATACTC 5 210 1 ACCCTACTTT 0.961956 -91 ********** Masking position 6 Map Score: 10.8007 Number of sites scoring better than the average of aligned sites = 1251 Number in coding regions = 808 Number in noncoding regions = 443 Number of orfs with sites within 600 bp upstream = 298 Fraction of orfs with sites within 600 bp upstream = 0.0478638 Motif number 3 ATTAATTTGTTATAATCCATAGAA 1 1 1 ATAATTTTAA 0.949367 -140 GTTATAATCCATAGAATTTTTTTATTTAAAAAAA 1 19 1 ATGATTTTTA 0.982668 -122 TTCTCCTTGAATGGACTTGTTTAAATCTAATCAG 3 15 1 ATGATTTTTA 0.982668 -281 CAATTTTTTTAGCGATTTATTAGACACAACTCAC 3 158 1 AGGATTTTAA 0.93564 -138 TTGAAGAAAAATTGAGTTTTGTGAGTTGTGTCTA 3 178 0 ATGATTTGTA 0.965173 -118 AAGATTTGTCAGGAAATTATTTGAAGAAAAATTG 3 198 0 AGAATTTTTA 0.945865 -98 TAGCTCAAAAATTCATTTTTGTAAAGATTTGTCA 3 221 0 ATCATTTGTA 0.887267 -75 TTTTTTACCGATTAATTTCTTTGAAGAGTGCGGT 4 28 1 ATAATTTTTA 0.972784 -62 GATTAAGTCATTAAACAACATTCCT 5 2 1 ATAATCTTAA 0.814137 -299 ** ** ** *** * Masking position 7 Map Score: 6.00674 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 144 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 4 TAGCTCCATCGTTTAACCATAAATGGTAGGG 1 97 1 GTTTAACATA 0.934626 -44 ATTTAAGTGCGGTTAAAAATCGTCGTATTTT 2 23 1 GGTTAAAATC 0.832062 -58 GAAAAGTGCGGTCAAAAAATACGACGATTTT 2 38 0 GTCAAAAATA 0.759976 -43 GAATGGACTTGTTTAAATCTAATCAGGTTAC 3 23 1 GTTTAAACTA 0.927331 -273 GAAATTAATCGGTAAAAAATATAATACTCTT 4 16 0 GGTAAAAATA 0.867165 -74 TTAAAAGTTTGTTTATAAATAGTATAAAAAT 5 110 1 GTTTATAATA 0.886034 -191 TTTATAAATAGTATAAAAATAGCTTTCAAAG 5 121 1 GTATAAAATA 0.895941 -180 TTGATGTTGAGTTTAAGGATATAGGAGAATC 5 161 1 GTTTAAGATA 0.963384 -140 GGGTAGAACATTTTAAGAATAATATTAAGCG 5 193 0 TTTTAAGATA 0.674592 -108 TCTTTAATCTGTTTAAATTTACAGTTATTAT 5 274 0 GTTTAAATTA 0.895941 -27 AATTTAAACAGATTAAAGATAGTTT 5 286 1 GATTAAAATA 0.906067 -15 ******* *** Masking position 5 Map Score: 6.98081 Number of sites scoring better than the average of aligned sites = 241 Number in coding regions = 175 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 5 GCTAAAAGTGATGATATGAGAGGCGGGGGATC 3 127 0 AGATATGGAG 0.976277 -169 AATTTTTTTAGCGATTTATTAGACACAACTCA 3 159 1 GGATTTATAG 0.826638 -137 AAGAAAAATTGAGTTTTGTGAGTTGTGTCTAA 3 177 0 GGTTTTGGAG 0.929657 -119 CATTTTTGTAAAGATTTGTCAGGAAATTATTT 3 210 0 AGATTTGCAG 0.96963 -86 TGAGAGGTAAACGAATTAAAAGTTTGTTTATA 5 95 1 AGAATTAAAG 0.726845 -206 TCAAAACCATATGCTTTGAAAGCTATTTTTAT 5 133 0 AGCTTTGAAG 0.921187 -168 GTTGAGTTTAAGGATATAGGAGAATCCCGCTT 5 166 1 AGATATAGAG 0.941474 -135 GTGAAACAATAAGATTTGTGAGTATATCAAAA 5 227 0 AGATTTGGAG 0.991183 -74 * ****** *** Masking position 11 Map Score: 3.37584 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 59 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 AGATATAAGCAAATTTCCCTTTTTTTAAAT 1 42 0 AAATTTCCCT 0.958439 -99 TTTCCTACATAAATTACCCTTTTAATGCTA 3 65 0 AAATTACCCT 0.967768 -231 CCTATTGTAAATATTTTCCTACATAAATTA 3 79 0 ATATTTTCCT 0.935644 -217 TTTTCTTCAAATAATTTCCTGACAAATCTT 3 202 1 ATAATTTCCT 0.917788 -94 GGTAAAAAATATAATACTCTTGAATT 4 7 0 ATAATACTCT 0.890575 -83 CATTTTTCCAAAAATACCCATGATGACAAT 5 44 0 AAAATACCCA 0.827216 -257 ATCCCGCTTAATATTATTCTTAAAATGTTC 5 189 1 ATATTATTCT 0.837187 -112 ********** Masking position 3 Map Score: 3.75875 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 135 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 7 AGGGAATGCCCTACCATTTATGGTTAAACGAT 1 104 0 CTACATTATG 0.961902 -37 CATTCCCTGCCTAACATTGAGGT 1 128 1 CTAAATGAGG 0.960684 -13 AAAAAAATTGCTAAAAGTGATGATATGAGAGG 3 136 0 CTAAATGATG 0.97733 -160 CTCGTAGATAATAAAAGTGCGGTAAAAATTCA 4 61 0 ATAAATGCGG 0.717281 -29 CTTTTATTATCTACGAGTGATGGA 4 76 1 CTACATGATG 0.99102 -14 TTTTCCAAAAATACCCATGATGACAATAATAG 5 39 0 ATACCTGATG 0.929965 -262 AGCTATTTTTATACTATTTATAAACAAACTTT 5 113 0 ATACATTATA 0.693027 -188 ATGTTCTACCCTACTTTTGATATACTCACAAA 5 213 1 CTACTTGATA 0.839803 -88 **** * ***** Masking position 3 Map Score: 1.85848 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 156 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 ********** No masking Map Score: -6.44162e-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 9 ********** No masking Map Score: -6.44162e-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: -6.44162e-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