AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -itorR_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 HI0643 32 biotin sulfoxide reductase (bisC) #2 HI0644 148 cytochrome C-type protein (yecK) #3 HI0645 54 lysophospholipase L2 (pldB) #4 HI0646 158 aspartate-semialdehyde dehydrogenase (asd) #5 HI0647 277 transport protein, putative #6 HI0648 241 modulator of drug activity B (mdaB) #7 HI0652 62 3-deoxy-d-manno-octulosonic-acid transferase (kdtA) Motif number 1 AACACTATATAAATCAATAAATAACGATTAGTA 2 10 0 AAAAAAATAA 0.870418 -139 AAAATGTTATAAGCTGAAGAAAAACACTATATAA 2 32 0 AAGAGAAAAA 0.919729 -117 TCCAATAAAATAATAAAAAACAACCCTAAC 2 129 0 AAAAAAAAAA 0.961511 -20 AAGTGTGGTTAATTTAAAAGAAAATTTAATTTAA 4 22 0 AAAAAGAAAA 0.953527 -137 TCGCGAAAGAAATTAAATAAAAAAGTGTGGTTAA 4 44 0 AAAAAAAAAA 0.961511 -115 AAGCACAACAAACTAAGGAAACAACA 4 143 1 AAAGAAACAA 0.891899 -16 AATCTTAACGAAATAAACAAAAAATCCATCTTCG 5 32 0 AAAAAAAAAA 0.961511 -246 CTTGGGGTTGAATTTTGCATAAAATAACCATTCT 5 117 1 AATGATAAAA 0.61243 -161 CAATTTTCGCAAGAAAGGTGATAAATTAAAGACT 5 186 1 AAAGTGATAA 0.540856 -92 AATGATAAAAATAAGTCCGACATA 5 264 0 AATAAAATAA 0.624998 -14 TAAAAATCGGCAAGAAATTTTCTGCCG 6 4 1 AAGGAAGAAA 0.785897 -238 TTAAAATAAAAAATCGGCAGAAAATTTCTTGCCG 6 18 0 AAGGAGAAAA 0.962014 -224 AATTGGTGGAAATCGAACGAAAAATGACCGCACT 6 53 0 AAAAGAAAAA 0.913511 -189 TGGAATTGAAAATTCGGTAAAAAATTGGTGGAAA 6 75 0 AAGGAAAAAA 0.968588 -167 GTCTAGAAATAACGTGGCAGACAAATATACTTTT 6 195 1 AAGGAGACAA 0.880255 -47 ATACTTTTAAAAATTAACGTAAAAAGGCATA 6 221 1 AAAAGTAAAA 0.702956 -21 GTATAGCAAAAAAAGGATTGAAAAT 7 2 0 AAGATGAAAA 0.806827 -61 ** ** ****** Masking position 2 Map Score: 16.1605 Number of sites scoring better than the average of aligned sites = 1108 Number in coding regions = 808 Number in noncoding regions = 300 Number of orfs with sites within 600 bp upstream = 231 Fraction of orfs with sites within 600 bp upstream = 0.0371025 Motif number 2 ATTTTACTTTCACTACAAAGGG 3 2 1 TTTTATTTCA 0.868693 -53 TACTACGCCCTTTTCATTAAAAAATT 3 39 1 TTTTCTTAAA 0.914014 -16 TTAAATTAAATTTTCTTTTAAATTAACCACA 4 22 1 TTTTCTTTAA 0.958408 -137 TAACCACACTTTTTTATTTAATTTCTTTCGC 4 45 1 TTTTTTTTAA 0.912006 -114 GAAAGATCAATTTTCATTAAAAATACTTGAT 4 76 1 TTTTCTTAAA 0.914014 -83 CGAAGATGGATTTTTTGTTTATTTCGTTAAG 5 32 1 TTTTTGTTTA 0.794544 -246 AGAATGGTTATTTTATGCAAAATTCAACCCC 5 120 0 TTTTAGCAAA 0.884859 -158 AAGGTAAAGATTTTAAGCTAAGTGATGTAGA 5 224 1 TTTTAGCTAA 0.935514 -54 TCTGCCGATTTTTTATTTTAAAAGTGCGGTC 6 31 1 TTTTATTTAA 0.965488 -211 TATGCCTTTTTACGTTAATTTTTAAAAG 6 224 0 TTTTAGTTAA 0.974025 -18 GCCGAAATTTTTTTAAGTATAACCGAATTTC 7 38 1 TTTTAGTATA 0.86136 -25 ***** ***** Masking position 11 Map Score: 10.5925 Number of sites scoring better than the average of aligned sites = 380 Number in coding regions = 268 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 3 TGAATGAATTAACTATCTAAAACGAG 1 7 1 AATTAACTAT 0.810884 -26 ATAAATCAATAAATAACGATTAGTA 2 6 0 AAATAACGAT 0.886743 -143 AAACCTCTACAATCAACCCTAACTATAAGT 2 98 1 AATCAACCCT 0.963312 -51 AAATAATAAAAAACAACCCTAACTACTTAT 2 122 0 AAACAACCCT 0.970014 -27 TTTTCTTTTAAATTAACCACACTTTTTTAT 4 32 1 AATTAACCAC 0.899711 -127 TAAAAAAATCCATCTTCAATACG 5 4 1 AAAAATCCAT 0.919875 -274 GAAATAAACAAAAAATCCATCTTCGTATTG 5 27 0 AAAAATCCAT 0.919875 -251 ATTTTGCATAAAATAACCATTCTTTCGCTC 5 128 1 AAATAACCAT 0.979299 -150 GTAGGGTGGGAATAAACCCTAGTTAAACGC 6 145 0 AATAAACCCT 0.96051 -97 ********** Masking position 5 Map Score: 8.09225 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 165 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 4 AATCGTTATTTATTGATTTATATAGTGTTT 2 15 1 TATTGATTTA 0.716248 -134 ATATCATAGTTTTTGATTTACAAAACCTCT 2 76 1 TTTTGATTTA 0.952075 -73 GTAGTTAGGGTTGTTTTTTATTATTTTATT 2 126 1 TTGTTTTTTA 0.7618 -23 TACTACGCCCTTTTCATTAAAAAATT 3 39 1 TTTTCATTAA 0.920166 -16 TTAAATTAAATTTTCTTTTAAATTAACCAC 4 22 1 TTTTCTTTTA 0.929093 -137 TAACCACACTTTTTTATTTAATTTCTTTCG 4 45 1 TTTTTATTTA 0.948461 -114 GAAAGATCAATTTTCATTAAAAATACTTGA 4 76 1 TTTTCATTAA 0.920166 -83 TAACGCTATCTTGTAATTAATAATGCTATT 4 112 1 TTGTAATTAA 0.737759 -47 GAAGATGGATTTTTTGTTTATTTCGTTAAG 5 33 1 TTTTTGTTTA 0.83016 -245 CTTTCCAAGTCTTTAATTTATCACCTTTCT 5 197 0 CTTTAATTTA 0.776068 -81 TCTGCCGATTTTTTATTTTAAAAGTGCGGT 6 31 1 TTTTATTTTA 0.892852 -211 ********** Masking position 10 Map Score: 7.51307 Number of sites scoring better than the average of aligned sites = 637 Number in coding regions = 419 Number in noncoding regions = 218 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 5 GTATTTTTAATGAAAATTGATCTTTCGCGA 4 72 0 TGAAAATTGA 0.969312 -87 ATCTTCGTATTGAAGATGGATTTTTTTA 5 9 0 TGAAGATGGA 0.973733 -269 ATCTTCAATACGAAGATGGATTTTTTGTTT 5 22 1 CGAAGATGGA 0.988175 -256 ACCTTTCTTGCGAAAATTGAGTAGAATCTT 5 175 0 CGAAAATTGA 0.986234 -103 GGAAATCGAACGAAAAATGACCGCACTTTT 6 50 0 CGAAAAATGA 0.956133 -192 ********** Masking position 6 Map Score: 5.04273 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 25 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 6 CTACAATCAACCCTAACTATAAGTAGTTAG 2 104 1 CCCTAACTAT 0.879822 -45 TAAAAAACAACCCTAACTACTTATAGTTAG 2 116 0 CCCTAACTAC 0.979306 -33 GCTATTCAAGCACAACAAACTAAGGAAACA 4 136 1 CACAACAAAC 0.795494 -23 GCCTTGGTTGCCCAAAAAACTTGGTAGATT 5 73 0 CCCAAAAAAC 0.941144 -205 TGGGCTTAAGCCCACCCTACATTGGCTACA 6 114 0 CCCACCCTAC 0.991387 -128 AGGGTTTATTCCCACCCTACGGGCTGTAAT 6 155 1 CCCACCCTAC 0.991387 -87 ********** Masking position 9 Map Score: 3.34693 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 48 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 TGCAAAATTCAACCCCAAGCATTGGCTTTG 5 106 0 AACCCCAAGC 0.974077 -172 GCGTGGGCTTAAGCCCACCCTACATTGGCT 6 117 0 AAGCCCACCC 0.996373 -125 GGGTGGGCTTAAGCCCACGCGTTTAACTAG 6 127 1 AAGCCCACGC 0.996373 -115 ACTAGGGTTTATTCCCACCCTACGGGCTGT 6 152 1 ATTCCCACCC 0.975529 -90 ********** Masking position 7 Map Score: 2.74006 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 14 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 AATGTTATAAGCTGAAGAAAAACACTATATA 2 33 0 GCTGAGAAAA 0.91212 -116 CTATGATATTTCTCAAGAAAAAATGTTATAA 2 54 0 TCTCAGAAAA 0.963371 -95 AATTGATCTTTCGCGAAAGAAATTAAATAAA 4 57 0 TCGCAAAGAA 0.922004 -102 CCATTCTTTCGCTCTATAAAATTTCAAACGC 5 144 1 GCTCATAAAA 0.71128 -134 TACTCAATTTTCGCAAGAAAGGTGATAAATT 5 182 1 TCGCAGAAAG 0.949368 -96 TAAAAATCGGCAAGAAATTTTCTGCCG 6 7 1 TCGGAAGAAA 0.905154 -235 AAATAAAAAATCGGCAGAAAATTTCTTGCCG 6 18 0 TCGGAGAAAA 0.9848 -224 AATTGAAAATTCGGTAAAAAATTGGTGGAAA 6 75 0 TCGGAAAAAA 0.976103 -167 TCGGCTAGTATAGCAAAAAAAGGATTGAAAA 7 12 0 TAGCAAAAAA 0.832216 -51 **** ****** Masking position 6 Map Score: 6.00854 Number of sites scoring better than the average of aligned sites = 414 Number in coding regions = 347 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 9 GCGTAGTAAATACGCCCTTTGTAGTGAAAG 3 17 0 TACGCCCTTT 0.993284 -38 GCGTATTTACTACGCCCTTTTCATTAAAAA 3 32 1 TACGCCCTTT 0.993284 -23 GTCTTTAATTTATCACCTTTCTTGCGAAAA 5 189 0 TATCACCTTT 0.899947 -89 TATGCCTTTTTACGTTAATT 6 232 0 TATGCCTTTT 0.960178 -10 ********** Masking position 8 Map Score: 1.77401 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 13 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 10 TTCAGCTTATAACATTTTTTCTTGAGAAATA 2 48 1 ACATTTTTTC 0.740909 -101 CTTGAGAAATATCATAGTTTTTGATTTACAA 2 68 1 ACATAGTTTT 0.79641 -81 ATTTTACTTTCACTACAAAGG 3 1 1 ATTTACTTTC 0.811939 -54 ATTTAATTTAATCACTCTTTTT 4 2 0 ACACTCTTTT 0.950417 -157 GATTAAATTAAATTTTCTTTTAAATTAACCA 4 20 1 ATTTTCTTTT 0.799399 -139 TTTTAAATTAACCACACTTTTTTATTTAATT 4 37 1 ACACACTTTT 0.950395 -122 GCATAAAATAACCATTCTTTCGCTCTATAAA 5 133 1 ACATTCTTTC 0.966854 -145 TTAATTTATCACCTTTCTTGCGAAAATTGAG 5 184 0 ACTTTCTTGC 0.761398 -94 ACGAAAAATGACCGCACTTTTAAAATAAAAA 6 40 0 ACGCACTTTT 0.855042 -202 GTGGCAGACAAATATACTTTTAAAAATTAAC 6 208 1 ATATACTTTT 0.883659 -34 * ********* Masking position 8 Map Score: 3.53901 Number of sites scoring better than the average of aligned sites = 1186 Number in coding regions = 809 Number in noncoding regions = 377 Number of orfs with sites within 600 bp upstream = 284 Fraction of orfs with sites within 600 bp upstream = 0.0456152 Motif number 11 ********** No masking Map Score: 3.16435e-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: 3.16435e-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 AGTTTGTTGTGCTTGAATAGCATTATTAATT 4 126 0 GCTTGATAGC 0.789218 -33 GGCAACCAAGGCTTACAAAGCCAATGCTTGG 5 91 1 GCTTAAAAGC 0.769597 -187 TTCAATTCCAGCTAATGTAGCCAATGTAGGG 6 99 1 GCTAAGTAGC 0.668573 -143 AAAAATTTCGGCTAGTATAGCAAAAAAAGGA 7 19 0 GCTAGATAGC 0.677198 -44 ***** ***** Masking position 3 Map Score: 0.398639 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 25 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 14 ********** No masking Map Score: 3.16435e-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 15 ********** No masking Map Score: 3.16435e-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