AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00471_bsub_reg_300.orf -o00471_bsub_300.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 ylbQ 159 similar to pyrimidine-thiamine biosynthesis #2 yllA 70 yllA #3 yllB 125 similar to hypothetical proteins #4 ylxA 69 alternate gene name: yllC; similar to hypothetical proteins #5 ftsL 39 cell-division protein #6 spoVD 116 penicillin-binding protein #7 murE 175 UDP-N-acetylmuramoylananine-D-glutamate-2,6- diaminopimelate ligase #8 mraY 112 phospho-N-acetylmuramoyl-pentapeptide transferase #9 yrpC 300 similar to glutamate racemase #10 ysmB 243 similar to transcriptional regulator (MarR family) #11 gerE 115 transcriptional regulator #12 ysmA 62 ysmA #13 sdhA 33 succinate dehydrogenase (flavoprotein subunit) #14 sdhC 292 succinate dehydrogenase (cytochrome b558 subunit) #15 murC 249 UDP-N-acetyl muramate-alanine ligase #16 ytpS 159 ytpS #17 ytpP 234 similar to thioredoxin H1 Motif number 1 GTTTACCCATAAAAAGAAACCCTGAACTAGT 3 33 0 AAAAAGAACC 0.945329 -93 GAAGGCATAAAAAAAGAAAGCCTGCATAACG 6 23 0 AAAAAGAAGC 0.962507 -94 ATTCAGGCATAAAATGAAACAAGCCTAAATA 6 80 1 AAAATGAACA 0.948131 -37 CTTCAATGATAAAAAGAACGAATTAGAATGT 7 139 1 AAAAAGAAGA 0.976996 -37 TCATATGGAAAAAAATCATGAATATGATAAC 8 52 1 AAAAATCAGA 0.590207 -61 ATTAGCTTTGAAAATGTAGGAGTATTTAGAT 9 45 0 AAAATGTAGA 0.847162 -256 GAATCAAACGAAAAAGAACCATTTTACTATT 9 225 0 AAAAAGAACA 0.966224 -76 CATATGATAAAAAAAGAATGAGACAGAAAGC 9 270 1 AAAAAGAAGA 0.976996 -31 CGGCTCCTTCCAAAAGAAGGAATACCGGCAA 10 14 0 CAAAAGAAGA 0.852124 -230 AATGCTGTGCAAAACGTAGGCAAGTCATAAA 10 85 1 AAAACGTAGC 0.692734 -159 TTTTTTGAAGAAAATGCAAGACTCGCAGGAG 10 162 0 AAAATGCAGA 0.895548 -82 ATTTTCTTCAAAAAAGAAGGAAAATAGACAC 10 178 1 AAAAAGAAGA 0.976996 -66 ATTCTTATGAAAAATTAAGCAAGAAATATAT 14 80 1 AAAATTAACA 0.6624 -213 GTTTGGTGTGAAAATGAACCCATA 15 4 0 AAAATGAACC 0.917005 -246 TCCGCCAAAAAAAACGAATCATGTGAAAAGC 16 22 1 AAAACGAACA 0.924814 -138 ******** ** Masking position 4 Map Score: 17.8474 Number of sites scoring better than the average of aligned sites = 932 Number in coding regions = 751 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 184 Fraction of orfs with sites within 600 bp upstream = 0.0295535 Motif number 2 ACAAATCTCCCCCTTTGTTGTTTCTA 1 6 1 TCTCCCCCTT 0.889191 -154 TGCCCCACTTTCTCTCCTTAACTCACCACTA 3 98 0 TCTCTCCTTA 0.839266 -28 ATTGTGTTGGTCCCACCTTTTATCAGGATGA 4 49 0 TCCCACCTTT 0.934463 -21 GAGACCGTTCACTCCTTATTTAGGCTTGT 6 98 0 TCACTCCTTT 0.876642 -19 TGTCCTTTTCTCCTCCTGTTTCTTTCAAAC 8 93 0 CTCCTCCTGT 0.745749 -20 TTCGATCTTATCTCCCCTTCTCAAGTTTTGC 9 155 1 TCTCCCCTTT 0.967629 -146 GTCCTCTATTTCTCTCCTGCGAGTCTTGCAT 10 149 1 TCTCTCCTGG 0.971699 -95 TTGTAAACGTCACCTCCTGCGCCCTTCTTAC 11 21 1 CACCTCCTGG 0.817507 -95 TCTGATTCGCTCTCACCTTAGCAAGGAGGGT 11 87 1 TCTCACCTTG 0.859257 -29 CTTTTTTCATCTCCTTATTGTTTAAAAA 12 45 0 CATCTCCTTT 0.806442 -18 GATAGCCCCTCTCCCTCTAGTAATCTAG 13 16 0 CCTCTCCCTT 0.87048 -18 CTGTCTCCCCTCTCTCCTGCGTATATTATAG 14 13 1 TCTCTCCTGG 0.971699 -280 TCTGTAATCCTCCCCCCTGTTTGAGCTATAA 14 38 0 TCCCCCCTGT 0.98154 -255 TACTTTACCCCCTGTTTGATAAGTGC 14 277 0 TACCCCCTGT 0.898465 -16 AATAAAAATCCCTCCTTATGTATATCCAT 17 9 1 TCCCTCCTTT 0.984529 -226 TTCATATCCCTCCAGTTGTTTATGTTC 17 218 0 TCCCTCCAGT 0.887542 -17 ********* * Masking position 6 Map Score: 17.4673 Number of sites scoring better than the average of aligned sites = 566 Number in coding regions = 322 Number in noncoding regions = 244 Number of orfs with sites within 600 bp upstream = 282 Fraction of orfs with sites within 600 bp upstream = 0.0452939 Motif number 3 GAGAGAAAGTGGGGCAAGAGATC 3 113 1 GGGGAGAGAT 0.991885 -13 AACGCTTTTGTGCGTAAGAGATCCTTGAGTGA 10 211 1 TGCGAGAGAT 0.979323 -33 AAGAGATCCTTGAGTGAGGGATGGACAA 10 226 1 TGAGAGGGAT 0.830833 -18 ATGTAAGAAGGGCGCAGGAGGTGACGTTTACA 11 22 0 GGCGGGAGGT 0.913995 -94 ACCTCTCCCATGCGGAAGAGGTTTTTTCTTAC 12 12 0 TGCGAGAGGT 0.958594 -51 GCAGGAGAGAGGGGAGACAGAT 14 1 0 GGGGACAGAT 0.973841 -292 TGAAAGAAGTGGGGGAAGAGATTTAGCACATT 14 243 1 GGGGAGAGAT 0.991885 -50 CGTCATATACTGGGGAACAGATAGACGTTTGT 15 215 1 TGGGACAGAT 0.94987 -35 AAACTATAAGGGAGTTAGAGATAAATT 16 143 1 GGAGAGAGAT 0.976359 -17 **** ****** Masking position 12 Map Score: 10.4666 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 60 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 CCATGTGCTTAAAATTAAAGTTTAAATATTTGGA 1 66 0 AAATTATTTA 0.958862 -94 ACTTCGCTCCACAACTTCATTTTACACTGTTTAC 3 58 0 AAACTATTTA 0.919711 -68 CACTCTAAAAACAATTTCAATTCATCCTGATAAA 4 28 1 AAATTATTCA 0.906633 -42 GAACCATTTTACTATTCAAATTTAATATGGGAGC 9 207 0 ATATTATTTA 0.870223 -94 AACAACATCAAGAAATAAAATTTAATTTATGACT 10 107 0 AAAATATTTA 0.874105 -137 AGTTGATTGAAAAATTTTATTTTATCAATATATA 14 106 0 AAATTATTTA 0.963677 -187 ATCAATTCGGAAAATTATAATTTATGTACGCGTT 14 141 1 AAATTATTTA 0.928085 -152 AGATTTATTGACAATTTCATTTTACTCCTCCCTC 14 191 0 AAATTATTTA 0.97354 -102 * **** * **** Masking position 9 Map Score: 5.19258 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 17 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 AAATAAAGCGTTTACAATATATGTAGAAAC 1 30 0 TTTACAATAT 0.544502 -130 GTCCCACCTTTTATCAGGATGAATTGAAAT 4 41 0 TTATCAGGAT 0.883656 -29 ATGCTGATATCTTTCAAGATTAGCTGGATG 7 43 1 CTTTCAAGAT 0.853203 -133 TGAAAAATCTTTTTCAAGCTCCATTATTCA 8 25 0 TTTTCAAGCT 0.914503 -88 TGTGGTGAAATTATCAAGATCGCATCGTAT 9 104 0 TTATCAAGAT 0.973272 -197 GGAGGTGACGTTTACAAGATAATTAGT 11 8 0 TTTACAAGAT 0.873658 -108 AAATTTTATTTTATCAATATATATTTCTTG 14 99 0 TTATCAATAT 0.862868 -194 TGTAAGCACTTTATTAAGATTTATTGACAA 14 211 0 TTATTAAGAT 0.760775 -82 TTAAACCCAGATATCAAGATTTGTCTATGC 15 89 0 ATATCAAGAT 0.85155 -161 TTTATTTGCATTATCAAGCTCGTTTCGTTT 17 71 0 TTATCAAGCT 0.939975 -164 ********** Masking position 6 Map Score: 5.44298 Number of sites scoring better than the average of aligned sites = 361 Number in coding regions = 315 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 6 TCACTAACTATTTATTGGAGAAAGGAAGTT 2 44 1 TTTATTGGAG 0.953662 -27 TGCCTATTCTTTTATTGCAGAAAAAATGCT 7 18 1 TTTATTGCAG 0.77305 -158 GATGTTACTGAATAATGGAGCTTGAAAAAG 8 17 1 AATAATGGAG 0.74539 -96 ATTCAAATTTAATATGGGAGCTATCGATTA 9 198 0 AATATGGGAG 0.881648 -103 TTGACGCCCTTTTGAGGGAGGAGTAAAATG 14 178 1 TTTGAGGGAG 0.920146 -115 CAGATAGACGTTTGTTGGAGGTACAATT 15 232 1 TTTGTTGGAG 0.920975 -18 TTTTGGCGGATTTATGGGAGT 16 2 0 TTTATGGGAG 0.970277 -158 CCCAGAAAACTATAAGGGAGTTAGAGATAA 16 137 1 TATAAGGGAG 0.926924 -23 ********** Masking position 9 Map Score: 4.74041 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 85 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 7 TGAAAAAGATTTTTCATATGGAAAAAAATC 8 39 1 TTTTCATATG 0.955294 -74 ACATACGTAGTTATCATATTCATGATTTTT 8 62 0 TTATCATATT 0.886885 -51 ATATGACTTTATATCATCTGAATCAAACGA 9 245 0 ATATCATCTG 0.769221 -56 CATTCTTTTTTTATCATATGACTTTATATC 9 260 0 TTATCATATG 0.971655 -41 TATAGTCGAGATATCATATGTAAGAAGGGC 11 41 0 ATATCATATG 0.926195 -75 CTTGCTTAATTTTTCATAAGAATTACAGGA 14 73 0 TTTTCATAAG 0.792931 -220 GCTTAGCGGCTTTTCACATGATTCGTTTTT 16 31 0 TTTTCACATG 0.850199 -129 CCCATTATCATTATCATATTTTATTTGCAT 17 90 0 TTATCATATT 0.886885 -145 ********** Masking position 6 Map Score: 4.51354 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 143 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 8 GATCTCTTGCCCCACTTTCTCTC 3 113 0 TCTCTTCCCC 0.99124 -13 CACTCAAGGATCTCTTACGCACAAAAGCGTT 10 211 0 TCTCTTCGCA 0.976588 -33 GTAAACGTCACCTCCTGCGCCCTTCTTACAT 11 23 1 CCTCCTCGCC 0.946916 -93 TAAGAAAAAACCTCTTCCGCATGGGAGAGGT 12 13 1 CCTCTTCGCA 0.965599 -50 ATCTGTCTCCCCTCTCTCCTGC 14 2 1 TCTGTCCCCC 0.936275 -291 ATGTGCTAAATCTCTTCCCCCACTTCTTTCA 14 243 0 TCTCTTCCCC 0.99124 -50 CAAACGTCTATCTGTTCCCCAGTATATGACG 15 215 0 TCTGTTCCCA 0.958539 -35 ****** **** Masking position 3 Map Score: 5.28303 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 75 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 9 CATATAAAATACGCCGCTAAGGGAGGCTTT 15 155 1 ACGCCGCTAA 0.986708 -95 ACTCCCATAAATCCGCCAAAAAAAACGAA 16 10 1 AATCCGCCAA 0.949197 -150 ATCATGTGAAAAGCCGCTAAGCCCTTGTTT 16 39 1 AAGCCGCTAA 0.99216 -121 AGCAGAAACCAAGCCGCTAAACAAGGGCTT 16 57 0 AAGCCGCTAA 0.99216 -103 ********** Masking position 9 Map Score: 2.59819 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 41 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 10 ACCACTTCGCTCCACAACTTCATTTTACACT 3 64 0 TCACAACTTC 0.963142 -62 CTCACCACTATTCACCACTTCGCTCCACAAC 3 77 0 TCACCACTTC 0.981808 -49 GATCTCTTGCCCCACTTTCTCTCCTTAA 3 108 0 TCCCCACTTT 0.89422 -18 CTAAATCTCTTCCCCCACTTCTTTCAATTGT 14 238 0 TCCCCACTTC 0.984888 -55 GATTTGTCTATGCACAGCTGCTGTAAAGCGG 15 71 0 TCACAGCTGC 0.906626 -179 CGGTTTTTAGTATACCACTGCTGGTCGGCCC 16 105 0 TTACCACTGC 0.89422 -55 ATTTGGATCATACCAAACTGCTTGAGGCAAA 17 160 0 TCCAAACTGC 0.831728 -75 * ********* Masking position 9 Map Score: 1.33201 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 171 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 11 GATGTCACACCCAATTTAGCATTT 1 146 0 TCACACCCAA 0.923753 -14 ATCATTGAAGTCACATCAAATGATGTGGTA 7 119 0 TCACATCAAA 0.835894 -57 CCTGTTTCTTTCAAACGACATACGTAGTTA 8 79 0 TCAAACGACA 0.942145 -34 ATCATCTGAATCAAACGAAAAAGAACCATT 9 233 0 TCAAACGAAA 0.966395 -68 AGGACTTTAGTCAAACAACATCAAGAAATA 10 124 0 TCAAACAACA 0.803872 -120 GGGTTCATTTTCACACCAAACATGGTATGA 15 14 1 TCACACCAAA 0.978547 -236 GTACACGATGTTAAACGAAACGAGCTTGAT 17 59 1 TTAAACGAAA 0.762545 -176 TCCATTTGGATCATACCAAACTGCTTGAGG 17 164 0 TCATACCAAA 0.919876 -71 ********** Masking position 5 Map Score: 1.74943 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 147 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 12 GTTAGTGATCCGAAATGAGTATAGCATGTT 2 22 0 CGAAATGAGT 0.932539 -49 AGGCATAAAATGAAACAAGCCTAAATAAGG 6 84 1 TGAAACAAGC 0.868818 -33 TTGATAAGTGCGAAATGTGCTAAATCTCTT 14 258 0 CGAAATGTGC 0.956381 -35 GGTCGCAAATTGAAATGAGCGTCATATACT 15 196 1 TGAAATGAGC 0.969713 -54 CGATGTTAAACGAAACGAGCTTGATAATGC 17 64 1 CGAAACGAGC 0.987322 -171 ********** Masking position 5 Map Score: 0.626768 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 80 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 13 CCCATAAAAAGAAACCCTGAACTAGTCAGG 3 29 0 GAAACCCTGA 0.80467 -97 AAAGAAAGCCGTCGTTATGCAGG 6 4 1 GAAAGCCGTC 0.730531 -113 CATAAAAAAAGAAAGCCTGCATAACGACGG 6 19 0 GAAAGCCTGC 0.960977 -98 GAGACCGTTCACTCCTTATT 6 107 0 GAGACCGTTC 0.623497 -10 GAATGAGACAGAAAGCGTGAGAAGTG 9 285 1 GAAAGCGTGA 0.638602 -16 TCTTACGCACAAAAGCGTTCCGTGTCTATT 10 200 0 AAAAGCGTTC 0.785297 -44 GTATTGTAACCCTCCTTGCTAAGGT 11 101 0 GTAACCCTCC 0.95339 -15 GGATCATTCTGTAATCCTCCCCCCTGTTTG 14 46 0 GTAATCCTCC 0.726267 -247 GCGGCGGCTGAAAAGCCTCCCTTAGCGGCG 15 166 0 AAAAGCCTCC 0.956201 -84 TGGTATACTAAAAACCGTCCCAGAAAACTA 16 119 1 AAAACCGTCC 0.930183 -41 AATAAAAATCCCTCCTTATGTATAT 17 6 1 AAATCCCTCC 0.853691 -229 TTCATATCCCTCCAGTTGTTTAT 17 222 0 ATATCCCTCC 0.674741 -13 ********** Masking position 6 Map Score: 2.46107 Number of sites scoring better than the average of aligned sites = 1048 Number in coding regions = 838 Number in noncoding regions = 210 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 14 GCTGCTGTAAAGCGGCATAGCTGTTAAATG 15 56 0 AGCGGCATAG 0.981545 -194 AGCCTCCCTTAGCGGCGTATTTTATATGTT 15 153 0 AGCGGCGTAT 0.976419 -97 AATTGAAATGAGCGTCATATACTGGGGAAC 15 203 1 AGCGTCATAT 0.904224 -47 ACAAGGGCTTAGCGGCTTTTCACATGATTC 16 37 0 AGCGGCTTTT 0.951216 -123 GCCCTTGTTTAGCGGCTTGGTTTCTGCTGA 16 59 1 AGCGGCTTGG 0.968942 -101 ********** Masking position 8 Map Score: 0.25757 Number of sites scoring better than the average of aligned sites = 171 Number in coding regions = 160 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 15 ********** No masking Map Score: -6.939e-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