AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i127_bsub_mtub_300.orf -o127_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 yurN 57 similar to sugar permease #2 yurO 80 similar to multiple sugar-binding protein #3 yurP 215 similar to opine catabolism #4 yurQ 102 yurQ #5 yurR 300 similar to opine catabolism #6 msmX 120 multiple sugar-binding transport ATP-binding protein #7 yxkF 183 similar to hypothetical proteins #8 Rv1234 149 hypothetical protein Rv1234 Motif number 1 ATCAAAGAAAAGGTGAAGCTTCGCA 1 4 1 AAGAAAAGGG 0.962362 -54 TCCTTTATAAAAAGAAAAGGTGCGAAGCTTCA 1 24 0 AAGAAAAGGG 0.962362 -34 TCTGAAAATGAAGAACCATTATG 2 2 1 CGAAAATGAG 0.839597 -79 ATTCGGATGACAGACAAAGGGTCTATATGCGA 3 83 0 CGACAAAGGT 0.711749 -133 ACGTTATATAATAAAAACGAGGAGTGAAGGAT 3 194 1 AAAAAACGAG 0.865512 -22 GCTAACACATACAGAAAAGAAAAGCTAGAACA 4 45 0 AAGAAAAGAA 0.527468 -58 TTTATCTTTAATGAAAAAGAGGACGTGAACTG 4 78 1 AGAAAAAGAG 0.945413 -25 AGATCAGGATCAGGCACAGGCGCAGTCACAAG 5 20 0 CGGCACAGGG 0.83934 -281 ATGAAAATGAAGAAAACAGACGCGATGCGGCA 5 105 0 AAAAACAGAG 0.780338 -196 CACTATCAATAGAGAAAGGATGATACCATGAG 5 148 0 AAGAAAGGAG 0.756785 -153 AGACATTATAATAGAAAAGGTGTTTGCAT 5 282 1 AAGAAAAGGG 0.962362 -19 GAAATATGCACGAAAAATGGCTGGGTGATTTT 6 15 1 CAAAAATGGT 0.460163 -106 AGCGTTTACAATAACAAAGGGGGATGTTAG 6 101 1 AAACAAAGGG 0.904074 -20 TTGGCTTCAGCGGAAATAGAAGAAGACATGCA 7 32 0 CGAAATAGAG 0.704728 -152 ATGTTCTCCACTAAAAAAGAGTATATCCGGTA 7 108 0 CAAAAAAGAT 0.778014 -76 TCAACCTATCCCGGCAACGATGCTCGCCGTTC 8 16 1 CGGCAACGAG 0.879551 -134 CCTGACTGGACATGAAACGATGGCGCTGAAAA 8 102 1 CTGAAACGAG 0.630575 -48 AACGATGGCGCTGAAAAAGGGGGGCGGAGGAG 8 117 1 CGAAAAAGGG 0.973084 -33 * ******** * Masking position 6 Map Score: 14.7563 Number of sites scoring better than the average of aligned sites = 3513 Number in coding regions = 2946 Number in noncoding regions = 567 Number of orfs with sites within 600 bp upstream = 582 Fraction of orfs with sites within 600 bp upstream = 0.093479 Motif number 2 GCATTAGACTATAATGTTATATAACATTAT 2 33 1 ATAATGTTAT 0.627308 -48 ACATTAGACTATAATGTTATATAACATTAT 2 43 0 ATAATGTTAT 0.627308 -38 ATAACATTATATATTGTTATATTAAAGTCC 3 161 0 ATATTGTTAT 0.895648 -55 ATAACAATATATAATGTTATATAACGTTAT 3 171 1 ATAATGTTAT 0.627308 -45 ATAATGTTATATAACGTTATATAATAAAAA 3 181 1 ATAACGTTAT 0.499664 -35 ********** Masking position 7 Map Score: 8.61223 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 6 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 3 TCTGAAAATGAAGAACCATTA 2 2 1 CTGAAAATGA 0.887738 -79 TTGGCCTCCTCTGGACATTAGACTATAATG 2 57 0 CTGGACATTA 0.952569 -24 AATCAAAAGCCAGAACTTGACTTAAGCTCT 3 42 0 CAGAACTTGA 0.913016 -174 GCGCCTGTGCCTGATCCTGATCTGTGTTCA 5 29 1 CTGATCCTGA 0.976582 -272 ACTGAATATACAGATCCTTACATAAGAGAG 7 156 1 CAGATCCTTA 0.831906 -28 CCGGGAGTAGCTGGACCTGACTGGACATGA 8 87 1 CTGGACCTGA 0.991436 -63 CTGGACCTGACTGGACATGAAACGATGGCG 8 97 1 CTGGACATGA 0.986599 -53 ********** Masking position 10 Map Score: 5.94429 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 278 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 4 ATAGTCTAATGTCCAGAGGAGGCCAACCCT 2 61 1 GCCAGAGGCA 0.995301 -20 TCTGCGGATTGAACAGCGAAGCCAGAGCTTAAGTCA 3 19 1 GACAGAGCCA 0.954377 -197 AGTGGCAAAAGTCCAAAACAGCGGTAATGCAAAAGT 5 70 0 GCCAAAGCGA 0.986523 -231 TTCGCGGTTTTTCCACATTAGGGCAAAAGGTCGAAG 5 219 1 TCCATAGGGA 0.956496 -82 TATGAACGCTGCCCATTTTAGCGAGAGGGAATTGCT 6 46 1 GCCATAGCGA 0.992315 -75 AGACATGCAGGACCAAAGGAGGGTCATCTT 7 5 0 GCCAGAGGGA 0.998012 -179 AGCGACCGAGGCCCACCGAACGGCGAGCATCGTTGC 8 29 0 GCCAGACGGA 0.989742 -121 * *** * **** * Masking position 10 Map Score: 5.26927 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 42 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 5 AAGGTGAAGCTTCGCACCTTTTCTTTTTATA 1 20 1 TTCGACCTTT 0.871506 -38 TGCATAATGGTTCTTCATTTTCAGA 2 5 0 TTCTCATTTT 0.902889 -76 TTAAGTCAAGTTCTGGCTTTTGATTTGGGCA 3 47 1 TTCTGCTTTT 0.976086 -169 TGGCTTTTGATTTGGGCATTTTTTCGCATAT 3 60 1 TTTGGCATTT 0.842561 -156 CAATATTATTTTCTGAAATTTCTCAATAATT 3 116 0 TTCTAAATTT 0.726342 -100 AATAAAGCTGTTCTAGCTTTTCTTTTCTGTA 4 37 1 TTCTGCTTTT 0.976086 -66 TTACCGCTGTTTTGGACTTTTGCCACTGCCG 5 79 1 TTTGACTTTT 0.780122 -222 CGCGTCTGTTTTCTTCATTTTCATGACGATT 5 113 1 TTCTCATTTT 0.902889 -188 TTGGACGAACTTCGCGGTTTTTCCACATTAG 5 209 1 TTCGGGTTTT 0.915342 -92 AATGCTTTCCTTCGACCTTTTGCCCTAATGT 5 233 0 TTCGCCTTTT 0.981392 -68 CCAGCCATTTTTCGTGCATATTTCCAAT 6 8 0 TTCGGCATAT 0.816895 -113 CCTGCATGTCTTCTTCTATTTCCGCTGAAGC 7 30 1 TTCTCTATTT 0.684498 -154 **** ****** Masking position 9 Map Score: 8.65585 Number of sites scoring better than the average of aligned sites = 1302 Number in coding regions = 1120 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 206 Fraction of orfs with sites within 600 bp upstream = 0.0330871 Motif number 6 CAGCGGTAATGCAAAAGTCGTGGTCAGCGTG 5 57 0 GCAAAGTCGT 0.980995 -244 TGCGGCAGTGGCAAAAGTCCAAAACAGCGGT 5 81 0 GCAAAGTCCA 0.870658 -220 GATACCATGAGCGAAAATCGTCATGAAAATG 5 128 0 GCGAAATCGT 0.986141 -173 TACTCTCCTATCGAATATCCTGTCACTATCA 5 172 0 TCGAAATCCT 0.919632 -129 TGGAAAAACCGCGAAGTTCGTCCAATCTCTT 5 203 0 GCGAATTCGT 0.887034 -98 CCACCGAACGGCGAGCATCGTTGCCGGGATA 8 22 0 GCGAGATCGT 0.979617 -128 ***** ***** Masking position 4 Map Score: 2.1707 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 170 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 AAAAGGTGAAGCTTCGCACCTTTTCTTTTTA 1 18 1 GCTTCGCCCT 0.960509 -40 GGGTATCTCATCTCCTTTATAAA 1 45 0 GTATCTCTCT 0.980779 -13 TGCCACTGCCGCATCGCGTCTGTTTTCTTCA 5 99 1 GCATCGCTCT 0.989617 -202 CTTTGGTCCTGCATGTCTTCTTCTATTTCCG 7 23 1 GCATGTCTCT 0.963452 -161 TTCCCTTTCAGTTTCTCGTCTATCTATACCG 7 82 1 GTTTCTCTCT 0.972686 -102 AGAGTCTCCTCTCTTATGTAAG 7 172 0 GAGTCTCTCT 0.944364 -12 ******* *** Masking position 4 Map Score: 2.72525 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 118 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 8 TGTTATATAACATTATAGTCTAATGCATAA 2 29 0 CATTATAGTC 0.977089 -52 TGTTATATAACATTATAGTCTAATGTCCAG 2 47 1 CATTATAGTC 0.977089 -34 TATATTGTTATATTAAAGTCCGCGGGTAGG 3 152 0 TATTAAAGTC 0.886506 -64 CGTTATATAACATTATATATTGTTATATTA 3 167 0 CATTATATAT 0.832431 -49 AGAACAGCTTTATTATATTTGTTTGTCATG 4 21 0 TATTATATTT 0.757798 -82 TCCTCTTTTTCATTAAAGATAAATGCTAAC 4 71 0 CATTAAAGAT 0.887388 -32 ********** Masking position 5 Map Score: 0.671023 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 101 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 9 TAAAAACGAGGAGTGAAGGAT 3 205 1 GAGTGAAGGA 0.974115 -11 AGAGTAAAGAGATTGGACGAACTTCGCGGT 5 197 1 GATTGGACGA 0.925252 -104 TAGGGCAAAAGGTCGAAGGAAAGCATTTGA 5 237 1 GGTCGAAGGA 0.975976 -64 CTCAACCCGCGAGCGACCGAGGCCCACCGA 8 46 0 GAGCGACCGA 0.963267 -104 TGAAAAAGGGGGGCGGAGGAGAATGAGAAC 8 128 1 GGGCGGAGGA 0.989981 -22 ********** Masking position 10 Map Score: 0.60581 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 162 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 10 ********** No masking Map Score: 9.40348e-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 11 ********** No masking Map Score: 9.40348e-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 12 ********** No masking Map Score: 9.40348e-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