AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -imalT_bsub_opreg_100.orf -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 glgD 23 ADP-glucose pyrophosphorylase #2 glgB 300 1,4-alpha-glucan branching enzyme #3 yurJ 181 similar to multiple sugar ABC transporter (ATP-binding protein) #4 yurN 57 similar to sugar permease #5 yurO 80 similar to multiple sugar-binding protein #6 yurP 215 similar to opine catabolism #7 yvfL 39 similar to maltodextrin transport system permease #8 yvfK 140 similar to maltose/maltodextrin-binding protein #9 yvdH 39 similar to maltodextrin transport system permease #10 yvdG 95 similar to maltose/maltodextrin-binding protein #11 yvdF 112 similar to glucan 1,4-alpha-maltohydrolase #12 msmX 120 multiple sugar-binding transport ATP-binding protein Motif number 1 GTTACCGCCGTGAAAGGGCGGTGTCTTAAC 2 24 0 TGAAAGGGCG 0.98724 -277 AGCCCTTTCCTGAAAGCGCTTATACTTATA 2 219 0 TGAAAGCGCT 0.926699 -82 AGCGCTTTCAGGAAAGGGCTTTTTTTTATT 2 229 1 GGAAAGGGCT 0.932662 -72 CTATGATGTCAGAAAGGATGATTAC 2 286 1 AGAAAGGATG 0.89341 -15 ACGGGTCAAAAGATAGGGGGACTTTTCTG 3 163 1 AGATAGGGGG 0.936235 -19 ATCAAAGAAAAGGTGAAGCTTCGCA 4 6 1 AGAAAAGGTG 0.941151 -52 CTTTATAAAAAGAAAAGGTGCGAAGCTTCA 4 24 0 AGAAAAGGTG 0.941151 -34 CGGATGACAGACAAAGGGTCTATATGCGAA 6 82 0 ACAAAGGGTC 0.850824 -134 TCGGTAGGAATGAAAGCGCTTTAAAGATAA 8 107 0 TGAAAGCGCT 0.926699 -34 TCATTCCTACCGAAAGGGTGACAATCA 8 124 1 CGAAAGGGTG 0.969854 -17 ATTGTCCTATAGAAAGCGGTTACAACAACT 10 37 0 AGAAAGCGGT 0.960592 -59 AAAACGGAAATCAAAGGGGGAAAC 11 99 1 TCAAAGGGGG 0.956629 -14 ACTCAATATAAGAAAGCGTTTACAATAACA 12 87 1 AGAAAGCGTT 0.957445 -34 GTTTACAATAACAAAGGGGGATGTTAG 12 104 1 ACAAAGGGGG 0.977026 -17 ********** Masking position 5 Map Score: 19.3488 Number of sites scoring better than the average of aligned sites = 730 Number in coding regions = 543 Number in noncoding regions = 187 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 2 ATGATTTATAAAAACAAAAAAACCTTGCAG 2 98 0 AAAACAAAAA 0.680927 -203 TTTAAAATAAAGAACAAAATCTAAGACATA 2 130 0 AGAACAAAAT 0.795881 -171 TTTCTGAAGAAAAACGAAATATATGGAGAT 2 174 0 AAAACGAAAT 0.829834 -127 AATTTGTATTATAACGTCATAATACATTAT 3 44 0 ATAACGTCAT 0.674866 -138 TACTCTAAAAATAACAGAAAGACCAAGTTG 3 116 1 ATAACAGAAA 0.904949 -66 ATAATGTTATATAACATTATAGTCTAATGC 5 33 0 ATAACATTAT 0.821218 -48 ATAATGTTATATAACATTATAGTCTAATGT 5 43 1 ATAACATTAT 0.821218 -38 GGACTTTAATATAACAATATATAATGTTAT 6 161 1 ATAACAATAT 0.927612 -55 ATAACGTTATATAACATTATATATTGTTAT 6 171 0 ATAACATTAT 0.821218 -45 ATAATGTTATATAACGTTATATAATAAAAA 6 181 1 ATAACGTTAT 0.497168 -35 TTTGTTACCGATAACAGAATG 10 2 0 ATAACAGAAT 0.967287 -94 CCTGTTACCGATAACAGAATAAGGCGC 11 8 0 ATAACAGAAT 0.967287 -105 CGGCTTCAATAAAACGGAAATCAAAGGGGG 11 89 1 AAAACGGAAA 0.713101 -24 ********** Masking position 4 Map Score: 14.2528 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 193 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 3 CAAGGTTTTTTTGTTTTTATAAATCATGATA 2 101 1 TTGTTTTTTA 0.841401 -200 TAGATTTTGTTCTTTATTTTAAAAACAGACT 2 137 1 TCTTTATTTA 0.905058 -164 TAACCTATTATTTATATTATAATGTATTATG 3 26 1 TTTATATTTA 0.894407 -156 AAAATGTAAATTTGTATTATAACGTCATAAT 3 51 0 TTTGTATTTA 0.958513 -131 AAATTTACATTTTTTATTTTAGAAATATAGC 3 69 1 TTTTTATTTA 0.976077 -113 ACATTATATATTGTTATATTAAAGTCCGCGG 6 157 0 TTGTTATATA 0.841402 -59 TCACTCCTCGTTTTTATTATATAACGTTATA 6 190 0 TTTTTATTTA 0.976077 -26 GAAAGCTAGATTTGTATTGTAAGAGAGGTGA 7 14 1 TTTGTATTTA 0.958513 -26 ACATCCCCCTTTGTTATTGTAAACGCTTTCT 12 97 0 TTGTTATTTA 0.971143 -24 ******** ** Masking position 5 Map Score: 9.86046 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 64 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 4 ATTCGAACCCGTGTTACCGCCGTGAAAGGG 2 36 0 GTGTTACCGC 0.986003 -265 TTGTCTATAAGTATAAGCGCTTTCAGGAAA 2 214 1 GTATAAGCGC 0.845345 -87 TAGATTTGTATTGTAAGAGAGGTGAAAACG 7 20 1 TTGTAAGAGA 0.783734 -20 AACTTTCGATTTGTTACCGATAACAGAATG 10 11 0 TTGTTACCGA 0.958914 -85 TCGAAAGTTGTTGTAACCGCTTTCTATAGG 10 32 1 TTGTAACCGC 0.989692 -64 CCTTTTCACCCTGTTACCGATAACAGAATA 11 17 0 CTGTTACCGA 0.913364 -96 CTTATATTGAGTGTAACAGCAATTCCCTCT 12 69 0 GTGTAACAGC 0.963679 -52 CCCTTTGTTATTGTAAACGCTTTCTTATAT 12 92 0 TTGTAAACGC 0.936818 -29 ********** Masking position 6 Map Score: 6.59297 Number of sites scoring better than the average of aligned sites = 330 Number in coding regions = 288 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 5 CTATAAATGAAAACTATGATGTCAGAAAGGA 2 273 1 AAACTATATG 0.976061 -28 TTTATATTATAATGTATTATGACGTTATAAT 3 36 1 AATGTATATG 0.97606 -146 ATTATAGTCTAATGCATAATGGTTCTTCATT 5 17 0 AATGCATATG 0.915464 -64 ATTATGCATTAGACTATAATGTTATATAACA 5 28 1 AGACTATATG 0.958486 -53 TCTGGACATTAGACTATAATGTTATATAACA 5 47 0 AGACTATATG 0.958486 -34 TTAATATAACAATATATAATGTTATATAACG 6 166 1 AATATATATG 0.947633 -50 CTTTAAAGATAATATAGCATGCCTGAGAAAA 8 88 0 AATATAGATG 0.827764 -53 TCATAGTTTGAAAGTATCATGATGAAATTGT 11 56 0 AAAGTATATG 0.976061 -57 ******* *** Masking position 6 Map Score: 5.70923 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 65 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 ACTGAAGAGGGGGCAGAGTCA 1 13 1 GGGCAGAGTC 0.983103 -11 CGCCGTGAAAGGGCGGTGTCTTAACCGCTT 2 19 0 GGGCGGTGTC 0.97969 -282 AGGGTAGCCTCCTTTTAACCT 3 2 1 GGGTAGCCTC 0.990183 -180 AGGGTTGGCCTCCTCTGGACAT 5 69 0 GGTTGGCCTC 0.941292 -12 AACGGCGGGATAGCGTCCGGAAGAATA 9 8 1 GGATAGCGTC 0.973686 -32 TCGCTAAAATGGGCAGCGTTCATAAAATCA 12 40 0 GGGCAGCGTT 0.979155 -81 ********** Masking position 9 Map Score: 4.59859 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 158 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 CGAAATATATGGAGATTTTTGTAGTCTGTT 2 160 0 GGAGATTTTT 0.928975 -141 TTTCAGGAAAGGGCTTTTTTTTATTTCTTC 2 234 1 GGGCTTTTTT 0.881044 -67 CAAAAGATAGGGGGACTTTTCTG 3 169 1 GGGGACTTTT 0.982726 -13 CTTTTGATTTGGGCATTTTTTCGCATATAG 6 63 1 GGGCATTTTT 0.972734 -153 AATCCTACCCGCGGACTTTAATATAACAAT 6 149 1 GCGGACTTTA 0.893613 -67 AAAATGGCTGGGTGATTTTATGAACGCTGC 12 28 1 GGTGATTTTA 0.90946 -93 AATAACAAAGGGGGATGTTAG 12 110 1 GGGGATGTTA 0.952333 -11 ********** Masking position 8 Map Score: 3.14648 Number of sites scoring better than the average of aligned sites = 315 Number in coding regions = 205 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 8 AGGGTAGCCTCCTTTTAACCTATTATTTATA 3 11 1 CCTTTTACCT 0.989104 -171 AGTCCCCCTATCTTTTGACCCGTTATTTCGT 3 155 0 TCTTTTACCC 0.977525 -27 CGTTTTCACCTCTCTTACAAT 7 29 0 CGTTTTACCT 0.971317 -11 ATAGAGTAAATTTTTTTACCTAAATAAAAAA 8 34 0 TTTTTTACCT 0.910242 -107 TGGGAACAATCCTTTTCACCCTGTTACCGAT 11 26 0 CCTTTTACCC 0.989899 -87 ****** **** Masking position 6 Map Score: 2.74351 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 19 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 TCGTTTTTCTTCAGAAAATGAAGTTAATTG 2 187 1 TCAGAAAATG 0.983914 -114 AATCGATTACTCTAAAAATAACAGAAAGAC 3 109 1 TCTAAAAATA 0.875697 -73 AAATAACGGGTCAAAAGATAGGGGGACTTT 3 158 1 TCAAAAGATA 0.82777 -24 TCTGAAAATGAAGAACCATT 5 1 1 TCTGAAAATG 0.9704 -80 TTGAGAAATTTCAGAAAATAATATTGACAA 6 121 1 TCAGAAAATA 0.974937 -95 ATAGCATGCCTGAGAAAATGTGTAAACAAA 8 76 0 TGAGAAAATG 0.933444 -65 ********** Masking position 5 Map Score: 2.72117 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 197 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 10 ********** No masking Map Score: 2.65986e-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: 2.65986e-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: 2.65986e-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