AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00440_bsub_reg_100.orf -o00440_bsub_100.ace -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -g0.44 -x5 -e 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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 yabF 144 similar to hypothetical proteins #2 yclB 89 similar to phenylacrylic acid decarboxylase #3 yefA 255 alternate gene name: yerS; similar to RNA methyltransferase #4 patA 300 aminotransferase #5 gerCA 162 heptaprenyl diphosphate synthase component I #6 yqeT 24 similar to ribosomal protein L11 methyltransferase #7 dnaJ 199 heat-shock protein #8 patB 80 aminotransferase #9 ywnE 242 similar to cardiolipin synthase Motif number 1 GGGCGCAAAACCCTCTGAATACATAAGTAT 1 14 0 CCCTCTGAAT 0.96031 -131 GGGTTTTGCGCCCTCTGTTTTTTTCGTTAT 1 31 1 CCCTCTGTTT 0.974884 -114 GGTTTTCAATCACGCTGAAAAGATGACAAA 3 76 0 CACGCTGAAA 0.937819 -180 GGTTTGCCTACACGCTGAAACTTGGCTTGA 3 192 1 CACGCTGAAA 0.937819 -64 GCTGGCTGTCCCCGCTGTTAAAAGCAAATG 5 11 1 CCCGCTGTTA 0.990635 -152 GCTGTATCCTCCCGCTGTTTGCGAGCATTT 5 36 0 CCCGCTGTTT 0.994142 -127 AATCTGGATCGCCGCTCTTTATTCTTTTAA 9 124 1 GCCGCTCTTT 0.908567 -119 TTTGTAACCCCGCTCATTCATATTTATC 9 225 0 CCCGCTCATT 0.983617 -18 ********** Masking position 6 Map Score: 9.60629 Number of sites scoring better than the average of aligned sites = 519 Number in coding regions = 479 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 2 TTTAGGATTTTGTCATCTTTTCAGCGTGATT 3 68 1 TGTATCTTTT 0.958655 -188 AATCGCTGGTTGTCTTCTTTTTTTCTGAAAA 4 162 1 TGTTTCTTTT 0.964978 -139 GCTGATCATTTGTCACCTTTTTAACTGATAT 4 232 0 TGTACCTTTT 0.968863 -69 ATATAATGAGTTTATCCTATTTTACCACTAG 4 262 0 TTTTCCTATT 0.777825 -39 TATGTATGAGTTTTATCTTTTCATTCGCTTA 5 100 0 TTTATCTTTT 0.945289 -63 GATTATGAAATGTGTTCTTTTCGGTCAGCTC 7 39 0 TGTTTCTTTT 0.964978 -161 GATGCCTGACTTTGACTTTCTAATCATTGAA 7 73 0 TTTACTTTCT 0.606046 -127 ATCTCTTGGCTTTGACTTTTTTTCTTGCCCG 7 101 1 TTTACTTTTT 0.800331 -99 TAAATTAGATTGTATCATTTTGAATTATGAT 7 151 0 TGTTCATTTT 0.78378 -49 CTCATGTATGTTTATTCTTCTAAGCTTCACT 8 49 0 TTTTTCTTCT 0.887388 -32 ATCGCCGCTCTTTATTCTTTTAAAATGTGAG 9 131 1 TTTTTCTTTT 0.953557 -112 *** ******* Masking position 8 Map Score: 9.41816 Number of sites scoring better than the average of aligned sites = 775 Number in coding regions = 623 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 3 TTGGCTTACCAAGCCAAGTT 3 1 0 AAGCCAAGTT 0.994308 -255 TTGGCTTGGTAAGCCAAGCTCAGAATGTTG 3 14 1 AAGCCAAGCT 0.990337 -242 TGGCCTATTCAAGCCAAGTTTCAGCGTGTA 3 200 0 AAGCCAAGTT 0.994308 -56 TGGCTTGAATAGGCCAAGTTTTTCTTTCGC 3 214 1 AGGCCAAGTT 0.987454 -42 AAAAAAGTCAAAGCCAAGAGATGCCTGACT 7 93 0 AAGCCAAGAG 0.968898 -107 ********** Masking position 6 Map Score: 7.73189 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 28 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 4 CTTTATTGTATCATGTTCTATTATTGTTTATATG 4 121 0 TCATCATTAT 0.935228 -180 CTGTTTGCGAGCATTTGCTTTTAACAGCGGGGAC 5 18 0 GCATCTTTAA 0.919778 -145 ATTCGCTTACGCAGGTATCATTATAGCATAAAAA 5 75 0 GCATTATTAT 0.947047 -88 GTCCCCAAATTCACATTTATTTCTTAATCTATGT 5 126 0 TCATTTTTCT 0.83634 -37 TTATGATTTTTCAATTCCTTTTATCCCGGGCAAG 7 124 0 TCATCTTTAT 0.965324 -76 TTAGATTGTATCATTTTGAATTATGATTTTTCAA 7 144 0 TCATGATTAT 0.80395 -56 AGATAGAACTGCAAATTTTATTATAAGCGGTG 8 9 0 GCATTATTAT 0.947047 -72 TGTTACCCCCTCATGTATGTTTATTCTTCTAAGC 8 55 0 TCATTTTTAT 0.967499 -26 ACGAACGTTATCATATGTGTTTATTTTAACGCAG 9 46 1 TCATTTTTAT 0.967498 -197 AAACCAGCTTGCACCTGCGTTAAAATAAACACAT 9 60 0 GCATCTTAAA 0.570447 -183 AAAAATACGGGCAGATTTCTTTAAAACCAGCTTG 9 83 0 GCATTTTTAA 0.924584 -160 GTAACCCCGCTCATTCATATTTATCAAGAAGATT 9 216 0 TCACTTTTAT 0.836338 -27 *** * * ***** Masking position 3 Map Score: 8.9252 Number of sites scoring better than the average of aligned sites = 286 Number in coding regions = 228 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 5 CCTCTGTTTTTTTCGTTATAATAGACAAAGT 1 42 1 TTTCTTATAA 0.897471 -103 TAAGAAAAAGTTTCATGAATATACAAAAGTT 1 101 1 TTTCTGAATA 0.953283 -44 ACTTACCTGAATATGAAGAAAGA 4 3 1 TTACTGAATA 0.763149 -298 TATGTGCCAATTTCATTAATAGCCATAATCA 4 94 0 TTTCTTAATA 0.927313 -207 TGTCTTCTTTTTTTCTGAAAAGAAAGGTATG 4 172 1 TTTTTGAAAA 0.762623 -129 GAACTGCAAATTTTATTATAAGCGGTG 8 7 0 TTTTTTATAA 0.645541 -74 CAGCTTGCACCTGCGTTAAAATAAACACATA 9 59 0 CTGCTTAAAA 0.762848 -184 TACGGGCAGATTTCTTTAAAACCAGCTTGCA 9 81 0 TTTCTTAAAA 0.960816 -162 GATCCAGATTCTTCGTGAAAAATACGGGCAG 9 103 0 CTTCTGAAAA 0.956585 -140 CCGCTCTTTATTCTTTTAAAATGTGAGTGTT 9 135 1 TTCTTTAAAA 0.700224 -108 GCCATTAGTATTCCATGAATAACAGTGATCT 9 185 0 TTCCTGAATA 0.897856 -58 TAATGGCAATCTTCTTGATAAATATGAATGA 9 209 1 CTTCTGATAA 0.886806 -34 **** ****** Masking position 8 Map Score: 6.96669 Number of sites scoring better than the average of aligned sites = 1215 Number in coding regions = 993 Number in noncoding regions = 222 Number of orfs with sites within 600 bp upstream = 245 Fraction of orfs with sites within 600 bp upstream = 0.0393511 Motif number 6 CGAGCGTCTAATAAGCAGAAAATGCACTTT 1 68 0 ATAAGCAGAA 0.935876 -77 GACGCTCGATATAAGAAAAAGTTTCATGAA 1 90 1 ATAAGAAAAA 0.920818 -55 AGTTTCATGAATATACAAAAGTTTTTATTT 1 109 1 ATATACAAAA 0.799937 -36 TGATATATCCATATGAAAAATATCTATTAA 2 56 0 ATATGAAAAA 0.822445 -34 ACTTACCTGAATATGAAGAAAGAATCAGCT 4 11 1 ATATGAAGAA 0.861422 -290 ATTAATAGCCATAATCAAAATGAAGGTCTT 4 81 0 ATAATCAAAA 0.675749 -220 ATTGGCACATATAAACAATAATAGAACATG 4 114 1 ATAAACAATA 0.560533 -187 TTCTTTTCAGAAAAAAAGAAGACAACCAGC 4 166 0 AAAAAAAGAA 0.646677 -135 TCATTATAGCATAAAAAAAAGAATTGGCTG 5 62 0 ATAAAAAAAA 0.914777 -101 GGGGCTGACACTAAAAAGAAC 7 2 0 CTAAAAAGAA 0.730653 -198 CTTGCCCGGGATAAAAGGAATTGAAAAATC 7 124 1 ATAAAAGGAA 0.730653 -76 ********** Masking position 3 Map Score: 3.52853 Number of sites scoring better than the average of aligned sites = 673 Number in coding regions = 484 Number in noncoding regions = 189 Number of orfs with sites within 600 bp upstream = 187 Fraction of orfs with sites within 600 bp upstream = 0.0300353 Motif number 7 TGTTGAATTCGTGAGCACCGAAGCACAGGC 3 145 1 GTGAGCACCG 0.980403 -111 CGCATTCGTTGTCAGGCCTGTGCTTCGGTG 3 160 0 GTCAGGCCTG 0.971752 -96 TCTTTTTAGTGTCAGCCCCGCTTCCGGAGC 7 13 1 GTCAGCCCCG 0.997277 -187 GTTCTTTTCGGTCAGCTCCGGAAGCGGGGC 7 27 0 GTCAGCTCCG 0.992591 -173 ********** Masking position 4 Map Score: 2.3989 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 46 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 8 TCGTTATAATAGACAAAGTGCATTTTCTGC 1 54 1 AGACAAAGTG 0.95964 -91 ATTTCCTCCAAGACAAAATAAAAACTTTTG 1 124 0 AGACAAAATA 0.859266 -21 CTCAGAATGTTGACAAAATCCTAAAACAGT 3 32 1 TGACAAAATC 0.921038 -224 GCTGAAAAGATGACAAAATCCTAAAACGAA 3 63 0 TGACAAAATC 0.921038 -193 TAATAGCCATAATCAAAATGAAGGTCTTCG 4 79 0 AATCAAAATG 0.758832 -222 ATGATTAGAAAGTCAAAGTCAGGCATCTCT 7 77 1 AGTCAAAGTC 0.968974 -123 CAAGAAAAAAAGTCAAAGCCAAGAGATGCC 7 98 0 AGTCAAAGCC 0.892416 -102 AAAAATCATAATTCAAAATGATACAATCTA 7 147 1 ATTCAAAATG 0.758832 -53 ********** Masking position 5 Map Score: 2.55878 Number of sites scoring better than the average of aligned sites = 355 Number in coding regions = 289 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 9 CCTAGACTTCAAAGGTTTTCAATCACGCTG 3 89 0 AAAGGTTTTC 0.923533 -167 CAACGAATGCGAAGGTTTGCCTACACGCTG 3 179 1 GAAGGTTTGC 0.98518 -77 TGCTCTTCTTGAAGGTCAGCTGATTCTTTC 4 28 0 GAAGGTCAGC 0.980436 -273 TAATCAAAATGAAGGTCTTCGTGCCAAATC 4 70 0 GAAGGTCTTC 0.874446 -231 CAAGCTTCACGAACGTTATCATATGTGTTT 9 38 1 GAACGTTATC 0.926071 -205 ********** Masking position 6 Map Score: 1.91934 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 84 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 10 ACGAATTCAACATTCGCTGTGCTCCGATGC 3 127 0 CATTCGCTGT 0.987139 -129 CAAACCTTCGCATTCGTTGTCAGGCCTGTG 3 168 0 CATTCGTTGT 0.93634 -88 CCAAGTTTTTCTTTCGCTTAAAACTAGAGG 3 227 1 CTTTCGCTTA 0.937821 -29 TGTTTGCGAGCATTTGCTTTTAACAGCGGG 5 21 0 CATTTGCTTT 0.931625 -142 TTTATCTTTTCATTCGCTTACGCAGGTATC 5 90 0 CATTCGCTTA 0.980244 -73 ********** Masking position 4 Map Score: 2.45278 Number of sites scoring better than the average of aligned sites = 200 Number in coding regions = 182 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 11 TATGAAGAAAGAATCAGCTGACCTTCAAGA 4 22 1 GAATCAGCTG 0.923472 -279 TCTTCGTGCCAAATCAGATACGGAGGATGC 4 55 0 AAATCAGATA 0.854189 -246 TCTAATCATTGAATCAGATTATGAAATGTG 7 56 0 GAATCAGATT 0.975485 -144 TTTCTCACATAAATTAGATTGTATCATTTT 7 161 0 AAATTAGATT 0.713905 -39 GATTTCTTTAAAACCAGCTTGCACCTGCGT 9 74 0 AAACCAGCTT 0.897015 -169 AAAGAGCGGCGATCCAGATTCTTCGTGAAA 9 114 0 GATCCAGATT 0.842015 -129 TTTGTAATGGGAATCAGATCACTGTTATTC 9 170 1 GAATCAGATC 0.947161 -73 ********** Masking position 6 Map Score: 0.692453 Number of sites scoring better than the average of aligned sites = 459 Number in coding regions = 416 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 12 ********** No masking Map Score: -5.87318e-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 13 ********** No masking Map Score: -5.87318e-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 14 TTCAATCATACTCCTGATATATCC 2 76 0 AATCATACCC 0.946441 -14 ATGTTGACAAAATCCTAAAACAGTTTTCGTT 3 38 1 AATCCTAAAC 0.971825 -218 AAGATGACAAAATCCTAAAACGAAAACTGTT 3 56 0 AATCCTAAAC 0.971825 -200 AACTACCAACTCCTCATCCAATAA 6 6 0 ACTCCTCACC 0.918234 -19 GGAATTGAAAAATCATAATTCAAAATGATAC 7 140 1 AATCATAATC 0.868587 -60 ATAATCCTCCCCCTTTATTTGAT 9 3 1 AATCCTCCCC 0.960875 -240 TCCCATTACAAATTATAACACTCACATTTTA 9 151 0 AATTATAAAC 0.684166 -92 ******** ** Masking position 1 Map Score: 0.451392 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 151 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 15 ********** No masking Map Score: -5.87318e-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