AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i030_Glycerol_Uptake_hinf_reg_300.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 HI0686 292 glycerol-3-phosphatase transporter (glpT) #2 HI0687 99 conserved hypothetical protein #3 HI0688 94 H. influenzae predicted coding region HI0688 #4 HI0690 229 glycerol uptake facilitator protein (glpF) #5 HI1010 158 3-hydroxyisobutyrate dehydrogenase, putative #6 HI1014 55 conserved hypothetical protein #7 HI1017 237 glycerol uptake facilitator protein (glpF) Motif number 1 AATGTAAGAAAAAATAATATAAAAAGTGTAATCA 1 31 1 AAAATTAAAA 0.965796 -262 TAAGAAAGTAAAAAAAATCAAAAATGTGAAGTGT 1 178 0 AAAATAAAAA 0.984217 -115 CGAATCATAAAAGAAAATAAAAAATAAGAAAGTA 1 202 0 AAAATAAAAA 0.984217 -91 ATTTAGATGACACATAATTAAAAAGTTGGAGAAA 1 264 1 CAAATAAAAA 0.964045 -29 TAACTATCATAAGAATAATAAAAAGATAAGTATC 2 57 1 AAAAAAAAAA 0.965796 -43 GTTTCTATATCGTAGAAACTAAAAATCTACTCTA 4 53 1 CGAAATAAAA 0.70272 -177 TTTTATCACTAAAATTAACAAAAAATAACATTTT 5 45 1 AAAAAAAAAA 0.965796 -114 TCTAGATCACAGAATGATAAAAAATGTTATTTTT 5 65 0 AGAATAAAAA 0.964045 -94 GATAGGAGTGAAGATTATGTAAAATATCAACCTT 7 161 1 AAAATTAAAA 0.965796 -77 GCCAAGTCCTAACACCATAAAAAATGCTGTTCCC 7 212 0 AAAATAAAAA 0.984217 -26 ** * ** ***** Masking position 7 Map Score: 13.9314 Number of sites scoring better than the average of aligned sites = 362 Number in coding regions = 253 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 2 ACCCCCGATTCCCAAAATGTAAGAAAAAATAA 1 16 1 CCCAAAATGA 0.771419 -277 AAAAATAATATAAAAAGTGTAATCATTGTAGG 1 40 1 TAAAAAGTGA 0.959831 -253 GTAAAAAAAATCAAAAATGTGAAGTGTTTCAC 1 173 0 TCAAAAATGA 0.972286 -120 TAAAAGAAAATAAAAAATAAGAAAGTAAAAAA 1 197 0 TAAAAAATAA 0.868165 -96 CCTTACTGTTTCAAAAGGGTAAATTTAGATGA 1 242 1 TCAAAAGGGA 0.941768 -51 GACACATAATTAAAAAGTTGGAGAAAAAATT 1 272 1 TAAAAAGTTA 0.675845 -21 TTAGCTTAAAAAAGGCGGTGGGCAAATT 2 7 1 TAAAAAAGGG 0.924169 -93 ATGATAGTTACAAAAAAGGCGACTAAGCAATT 2 35 0 CAAAAAAGGA 0.951595 -65 TTTACTTTTCCCAAAAATGATACTTATCTTTT 2 77 0 CCAAAAATGA 0.951594 -23 GAGAATTTATTAAAAAAGAATACGGAGTGTTT 4 151 0 TAAAAAAGAA 0.844176 -79 CACAGAATGATAAAAAATGTTATTTTTTGTTA 5 60 0 TAAAAAATGA 0.977063 -99 CCTAACACCATAAAAAATGCTGTTCCCACAAG 7 207 0 TAAAAAATGG 0.936765 -31 ********* * Masking position 6 Map Score: 11.4305 Number of sites scoring better than the average of aligned sites = 383 Number in coding regions = 300 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 3 AATGTTGTTAATTTTGGCCGCACTTCCCTACAATG 1 63 0 ATTTGCCCTT 0.950747 -230 TGTGATCAATATCACAAAATCGCTTTCTTTTACAC 1 102 0 ATCCAACCTT 0.984215 -191 CGGTGTAAAGATTTGTGAAACACTTCACATTTTTG 1 159 1 ATTGGACCTT 0.949541 -134 TTCTTTTATGATTCGCAAATCCCTTACTGTTTCAA 1 221 1 ATTGAACCTT 0.9708 -72 TAAATGGAGAATTGCTAACGCCCTTAATAAAACCA 3 65 0 ATTCACCCTT 0.990186 -30 AACACTCTTCATTTCAACCGCACTTCTAAGGAGTG 4 201 1 ATTCACCCTT 0.990186 -29 GTGCATTGATAACCTAAGATCGCTTGGTGGCAATT 7 27 0 AACTAACCTT 0.790598 -211 TGCTAGGGTTATCTCTAGCACTCTTTTTATATCTA 7 126 1 ATCCACCCTT 0.989989 -112 *** * * * * *** Masking position 1 Map Score: 5.46479 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 175 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 4 TCAAAAGGGTAAATTTAGATGACACATAATTA 1 252 1 AATTTAGATA 0.92912 -41 GTATAGTTAAATATCTGGTTCAATTGGTTTTA 3 41 1 AATCTGGTTA 0.84907 -54 AAACTTAAATGGAGAATTGCTA 3 83 0 AACTTAAATG 0.669104 -12 TACGATATAGAAACCTAGTTAACCGTGGGTAT 4 35 0 AACCTAGTTA 0.951953 -195 CTAGGTTAGAACACCTAGATTGATTATGATGT 4 95 0 AACCTAGATG 0.950129 -135 ATTAAATCTGAGATCTAGATCACAGAATGATA 5 80 0 AATCTAGATA 0.924657 -79 TCTAGATCTCAGATTTAATTTATTGTATCGGC 5 93 1 AATTTAATTA 0.706959 -66 ATATACAGATAAATTTAGTTAAGATCTATTAG 5 127 1 AATTTAGTTA 0.92416 -32 CACTCTTTTTATATCTAGATAGGAGTGAAGAT 7 144 1 AATCTAGATG 0.918314 -94 * ******** * Masking position 6 Map Score: 5.2079 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 76 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 TGTTTACCCCCGATTCCCAAAATGT 1 5 1 TACCCCGATT 0.991965 -288 TGGGTATGTTTACCCACGGTTGTGAGGGATA 4 11 0 TACCCCGGTT 0.99095 -219 TGGGTAAACATACCCACGGTTAACTAGGTTT 4 26 1 TACCCCGGTT 0.99095 -204 TTCTTAAATTTAACTGCGGTTTTAAAAACAC 6 14 1 TAACTCGGTT 0.970024 -42 ***** ***** Masking position 2 Map Score: 3.93587 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 2 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 AATCAAAAATGTGAAGTGTTTCACAAATCT 1 167 0 GTGAAGTGTT 0.897889 -126 AACTTAAATGGAGAATTGCTAACGCCCTTA 3 74 0 GAGAATTGCT 0.769916 -21 AAAAAAGAATACGGAGTGTTTTGAAATAGC 4 142 0 ACGGAGTGTT 0.95733 -88 CGGTTGAAATGAAGAGTGTTTTCCCTAAGT 4 191 0 GAAGAGTGTT 0.942551 -39 CCGCACTTCTAAGGAGTGATCT 4 218 1 AAGGAGTGAT 0.951715 -12 TGAATAAATGATGGAGTGCTAGGGTTATCT 7 110 1 ATGGAGTGCT 0.976729 -128 CTAGATATAAAAAGAGTGCTAGAGATAACC 7 132 0 AAAGAGTGCT 0.955284 -106 ********** Masking position 5 Map Score: 2.5835 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 27 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 TGAGTGTAAAAGAAAGCGATTTTGTGATATTG 1 99 1 AGAAGCATTT 0.988616 -194 CTTTTGAAACAGTAAGGGATTTGCGAATCATA 1 227 0 AGAAGGATTT 0.963018 -66 AAAAAAGGCGACTAAGCAATTTGCCCACCGCC 2 24 0 ACAAGCATTT 0.984357 -76 AATTCAAATAAGGAGGCTATTTCAAAACACTC 4 127 1 AGAGGCATTT 0.975885 -103 AAAAATTGCCACCAAGCGATCTTAGGTTATCA 7 24 1 ACAAGCATCT 0.965846 -214 ** **** **** Masking position 4 Map Score: 1.33315 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 39 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 TGTTTACCCCCGATTCCCAAAATGTAAGAA 1 11 1 CGATTCCCAA 0.813114 -282 AAAATGTGAAGTGTTTCACAAATCTTTACA 1 162 0 GTGTTTCACA 0.849511 -131 AAATCCCTTACTGTTTCAAAAGGGTAAATT 1 237 1 CTGTTTCAAA 0.947006 -56 TTTTACTTTTCCCAAAAATGATACT 2 85 0 CTTTTCCCAA 0.800187 -15 TTAACTATACCTATTCCACCAACATCATCT 3 21 0 CTATTCCACC 0.878116 -74 ATCAATCTAGGTGTTCTAACCTAGAATTCA 4 103 1 GTGTTCTAAC 0.794448 -127 AATAAGGAGGCTATTTCAAAACACTCCGTA 4 133 1 CTATTTCAAA 0.854157 -97 GAAATGAAGAGTGTTTTCCCTAAGTAAAGG 4 186 0 GTGTTTTCCC 0.651512 -44 AATTTAACTGCGGTTTTAAAAACACATATT 6 20 1 CGGTTTTAAA 0.684346 -36 ATAAAAAATGCTGTTCCCACAAGTTCACCA 7 200 0 CTGTTCCCAC 0.970971 -38 ********** Masking position 5 Map Score: 1.10549 Number of sites scoring better than the average of aligned sites = 554 Number in coding regions = 494 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 9 CTTTTTATATTATTTTTTCTTACATTTTGG 1 27 0 TATTTTTTCT 0.897493 -266 GCGAATGCGAAAATTATTGTGATCAATATC 1 124 0 AAATTATTGT 0.594905 -169 TCACATTTTTGATTTTTTTTACTTTCTTAT 1 183 1 GATTTTTTTT 0.794927 -110 TTTACTTTCTTATTTTTTATTTTCTTTTAT 1 200 1 TATTTTTTAT 0.762467 -93 AATTTTTTCTCCAACTTTTT 1 283 0 AATTTTTTCT 0.870533 -10 TGTTAGAGTAGATTTTTAGTTTCTACGATA 4 60 0 GATTTTTAGT 0.892557 -170 TATTTTTTGTTAATTTTAGTGATAAAACGT 5 42 0 TAATTTTAGT 0.656623 -117 TAAAAAATGTTATTTTTTGTTAATTTTAGT 5 52 0 TATTTTTTGT 0.961161 -107 TCTCAGATTTAATTTATTGTATCGGCTAAT 5 99 1 AATTTATTGT 0.84084 -60 CAATTTTTCGGATTTTCTGTA 7 2 0 GATTTTCTGT 0.861732 -236 ********** Masking position 5 Map Score: 3.81235 Number of sites scoring better than the average of aligned sites = 512 Number in coding regions = 416 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 10 ********** No masking Map Score: 2.13406e-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 11 ********** No masking Map Score: 2.13406e-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: 2.13406e-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